| Chain sequence(s) |
A: SLCYRNYYADNQTCDGELLFNMTKKMCCCSYNIGRAWNKPCEQCPIPSTDEFATLCGSQRPGFVIDIYTGLPVDIDECREIPGVCENGVCINMVGSFRCECPVGFFYNDKLLVCEDIDECQNGPVCQRNAECINTAGSYRCDCKPGYRFTSTGQCNDRNECQEIPNICSHGQCIDTVGSFYCLCHTGFKTNDDQTMCLDINECERDACGNGTCRNTIGSFNCRCNHGFILSHNNDCIDVDECASGNGNLCRNGQCINTVGSFQCQCNEGYEVAPDGRTCVDINECLLEPRKCAPGTCQNLDGSYRCICPPGYSLQNEKCEDIDECVEEPEICALGTCSNTEGSFKCLCPEGFSLSSSGRRCQDLRMSYCYAKFEGGKCSSPKSRNHSKQECCCALKGEGWGDPCELCPTEPDEAFRQIC
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/2f27cf7badb4e78/tmp/folded.pdb (00:03:57)
[INFO] Main: Simulation completed successfully. (00:05:42)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1693 | S | A | -0.7390 | |
| 1694 | L | A | -0.6403 | |
| 1695 | C | A | 0.0000 | |
| 1696 | Y | A | 0.0000 | |
| 1697 | R | A | -2.2319 | |
| 1698 | N | A | -1.5672 | |
| 1699 | Y | A | -1.3334 | |
| 1700 | Y | A | -0.9112 | |
| 1701 | A | A | -1.3629 | |
| 1702 | D | A | -2.4809 | |
| 1703 | N | A | -2.4773 | |
| 1704 | Q | A | -2.3369 | |
| 1705 | T | A | -1.4587 | |
| 1706 | C | A | -1.6127 | |
| 1707 | D | A | -1.7360 | |
| 1708 | G | A | -1.7431 | |
| 1709 | E | A | -1.6444 | |
| 1710 | L | A | 0.0000 | |
| 1711 | L | A | 0.8958 | |
| 1712 | F | A | 0.0000 | |
| 1713 | N | A | -1.1367 | |
| 1714 | M | A | 0.0000 | |
| 1715 | T | A | -1.1375 | |
| 1716 | K | A | -1.1096 | |
| 1717 | K | A | -1.2397 | |
| 1718 | M | A | -0.9684 | |
| 1719 | C | A | 0.0000 | |
| 1720 | C | A | 0.0000 | |
| 1721 | C | A | 0.0000 | |
| 1722 | S | A | 0.0000 | |
| 1723 | Y | A | -0.0796 | |
| 1724 | N | A | -1.4621 | |
| 1725 | I | A | 0.0000 | |
| 1726 | G | A | -1.5890 | |
| 1727 | R | A | -2.1873 | |
| 1728 | A | A | 0.0000 | |
| 1729 | W | A | -1.7425 | |
| 1730 | N | A | -1.7388 | |
| 1731 | K | A | -2.1044 | |
| 1732 | P | A | -1.6286 | |
| 1733 | C | A | -1.8592 | |
| 1734 | E | A | -2.2809 | |
| 1735 | Q | A | -1.5361 | |
| 1736 | C | A | 0.0000 | |
| 1737 | P | A | -0.5245 | |
| 1738 | I | A | 0.5774 | |
| 1739 | P | A | -0.5973 | |
| 1740 | S | A | -1.3080 | |
| 1741 | T | A | -1.4934 | |
| 1742 | D | A | -2.6696 | |
| 1743 | E | A | -2.4975 | |
| 1744 | F | A | 0.0000 | |
| 1745 | A | A | -1.5506 | |
| 1746 | T | A | -1.3145 | |
| 1747 | L | A | -0.9375 | |
| 1748 | C | A | 0.0000 | |
| 1749 | G | A | -0.2073 | |
| 1750 | S | A | 0.0000 | |
| 1751 | Q | A | -2.3460 | |
| 1752 | R | A | -1.9793 | |
| 1753 | P | A | -0.9553 | |
| 1754 | G | A | 0.0000 | |
| 1755 | F | A | 0.0000 | |
| 1756 | V | A | 0.7561 | |
| 1757 | I | A | 2.1969 | |
| 1758 | D | A | 2.0311 | |
| 1759 | I | A | 2.9538 | |
| 1760 | Y | A | 2.4058 | |
| 1761 | T | A | 1.5573 | |
| 1762 | G | A | 1.5245 | |
| 1763 | L | A | 2.2239 | |
| 1764 | P | A | 1.1187 | |
| 1765 | V | A | 1.4410 | |
| 1766 | D | A | 0.5980 | |
| 1767 | I | A | 0.0000 | |
| 1768 | D | A | -0.7818 | |
| 1769 | E | A | 0.0000 | |
| 1770 | C | A | -1.1881 | |
| 1771 | R | A | -2.6143 | |
| 1772 | E | A | -2.5386 | |
| 1773 | I | A | 0.0000 | |
| 1774 | P | A | -1.5206 | |
| 1775 | G | A | -1.4849 | |
| 1776 | V | A | 0.0000 | |
| 1777 | C | A | 0.0000 | |
| 1778 | E | A | -2.1577 | |
| 1779 | N | A | -1.9463 | |
| 1780 | G | A | -0.6082 | |
| 1781 | V | A | 0.5438 | |
| 1782 | C | A | -0.2595 | |
| 1783 | I | A | -0.0899 | |
| 1784 | N | A | -0.1386 | |
| 1785 | M | A | 0.7411 | |
| 1786 | V | A | 1.8536 | |
| 1787 | G | A | 0.0000 | |
| 1788 | S | A | 0.2408 | |
| 1789 | F | A | -0.2294 | |
| 1790 | R | A | -1.5061 | |
| 1791 | C | A | -1.2857 | |
| 1792 | E | A | -0.9316 | |
| 1793 | C | A | -0.1231 | |
| 1794 | P | A | 0.6892 | |
| 1795 | V | A | 1.7870 | |
| 1796 | G | A | 1.0690 | |
| 1797 | F | A | 0.8593 | |
| 1798 | F | A | 1.2231 | |
| 1799 | Y | A | -0.2955 | |
| 1800 | N | A | -1.0509 | |
| 1801 | D | A | -2.4536 | |
| 1802 | K | A | -2.7989 | |
| 1803 | L | A | -1.3538 | |
| 1804 | L | A | 0.0000 | |
| 1805 | V | A | 0.0000 | |
| 1806 | C | A | 0.0000 | |
| 1807 | E | A | -0.6144 | |
| 1808 | D | A | -0.2526 | |
| 1809 | I | A | 0.1925 | |
| 1810 | D | A | -1.0922 | |
| 1811 | E | A | -1.2514 | |
| 1812 | C | A | -1.2741 | |
| 1813 | Q | A | -2.0127 | |
| 1814 | N | A | -2.0107 | |
| 1815 | G | A | -1.2183 | |
| 1816 | P | A | -1.0034 | |
| 1817 | V | A | -0.5170 | |
| 1818 | C | A | -0.9653 | |
| 1819 | Q | A | -1.7955 | |
| 1820 | R | A | -2.8111 | |
| 1821 | N | A | -2.4161 | |
| 1822 | A | A | -2.2876 | |
| 1823 | E | A | -2.3492 | |
| 1824 | C | A | -1.1063 | |
| 1825 | I | A | -0.5061 | |
| 1826 | N | A | -0.8868 | |
| 1827 | T | A | -0.4189 | |
| 1828 | A | A | -0.3357 | |
| 1829 | G | A | 0.2250 | |
| 1830 | S | A | -0.0900 | |
| 1831 | Y | A | -0.3346 | |
| 1832 | R | A | -1.6636 | |
| 1833 | C | A | -1.2845 | |
| 1834 | D | A | -1.4411 | |
| 1835 | C | A | -2.0365 | |
| 1836 | K | A | -2.0174 | |
| 1837 | P | A | -1.3485 | |
| 1838 | G | A | -1.0215 | |
| 1839 | Y | A | -1.5854 | |
| 1840 | R | A | -1.9663 | |
| 1841 | F | A | 0.0002 | |
| 1842 | T | A | -0.4724 | |
| 1843 | S | A | -0.2845 | |
| 1844 | T | A | -0.3223 | |
| 1845 | G | A | -0.7235 | |
| 1846 | Q | A | -1.9347 | |
| 1847 | C | A | 0.0000 | |
| 1848 | N | A | -2.3617 | |
| 1849 | D | A | -1.9162 | |
| 1850 | R | A | -1.8220 | |
| 1851 | N | A | -1.7128 | |
| 1852 | E | A | 0.0000 | |
| 1853 | C | A | -1.2599 | |
| 1854 | Q | A | -1.9500 | |
| 1855 | E | A | -1.5052 | |
| 1856 | I | A | -0.5074 | |
| 1857 | P | A | -0.9640 | |
| 1858 | N | A | -1.4877 | |
| 1859 | I | A | -0.2953 | |
| 1860 | C | A | 0.0000 | |
| 1861 | S | A | -0.7396 | |
| 1862 | H | A | -1.0625 | |
| 1863 | G | A | -0.8535 | |
| 1864 | Q | A | -1.0798 | |
| 1865 | C | A | -0.3989 | |
| 1866 | I | A | -0.1287 | |
| 1867 | D | A | -1.3163 | |
| 1868 | T | A | 0.0342 | |
| 1869 | V | A | 0.8226 | |
| 1870 | G | A | -0.4782 | |
| 1871 | S | A | -0.0746 | |
| 1872 | F | A | -0.1162 | |
| 1873 | Y | A | 0.3046 | |
| 1874 | C | A | 0.0000 | |
| 1875 | L | A | 0.8466 | |
| 1876 | C | A | -0.3680 | |
| 1877 | H | A | -1.3293 | |
| 1878 | T | A | -0.7546 | |
| 1879 | G | A | -0.3894 | |
| 1880 | F | A | -0.4613 | |
| 1881 | K | A | -1.6028 | |
| 1882 | T | A | -1.1146 | |
| 1883 | N | A | -1.8103 | |
| 1884 | D | A | -2.9844 | |
| 1885 | D | A | -2.6749 | |
| 1886 | Q | A | -1.3270 | |
| 1887 | T | A | -0.1267 | |
| 1888 | M | A | 0.2655 | |
| 1889 | C | A | 0.0000 | |
| 1890 | L | A | 0.1226 | |
| 1891 | D | A | -0.0026 | |
| 1892 | I | A | -0.2960 | |
| 1893 | N | A | -1.5858 | |
| 1894 | E | A | -2.2525 | |
| 1895 | C | A | -2.7868 | |
| 1896 | E | A | -3.3499 | |
| 1897 | R | A | -3.7099 | |
| 1898 | D | A | -3.5475 | |
| 1899 | A | A | -2.6728 | |
| 1900 | C | A | 0.0000 | |
| 1901 | G | A | -1.5573 | |
| 1902 | N | A | -1.2385 | |
| 1903 | G | A | -1.8128 | |
| 1904 | T | A | -1.9268 | |
| 1905 | C | A | -2.5563 | |
| 1906 | R | A | -2.6100 | |
| 1907 | N | A | -1.2705 | |
| 1908 | T | A | 0.0636 | |
| 1909 | I | A | 1.7991 | |
| 1910 | G | A | 0.3272 | |
| 1911 | S | A | -0.1302 | |
| 1912 | F | A | -0.8179 | |
| 1913 | N | A | -2.2124 | |
| 1914 | C | A | -1.8562 | |
| 1915 | R | A | -2.4798 | |
| 1916 | C | A | -1.1622 | |
| 1917 | N | A | -1.8546 | |
| 1918 | H | A | -1.5880 | |
| 1919 | G | A | -0.1263 | |
| 1920 | F | A | 0.6478 | |
| 1921 | I | A | 1.8749 | |
| 1922 | L | A | 0.9911 | |
| 1923 | S | A | 0.0833 | |
| 1924 | H | A | -1.2669 | |
| 1925 | N | A | -1.7527 | |
| 1926 | N | A | -1.1862 | |
| 1927 | D | A | -1.0128 | |
| 1928 | C | A | 0.0000 | |
| 1929 | I | A | 1.3829 | |
| 1930 | D | A | 0.8268 | |
| 1931 | V | A | 0.7361 | |
| 1932 | D | A | -0.3870 | |
| 1933 | E | A | -0.8828 | |
| 1934 | C | A | -0.8184 | |
| 1935 | A | A | -0.6229 | |
| 1936 | S | A | -0.9479 | |
| 1937 | G | A | -1.3981 | |
| 1938 | N | A | -1.8134 | |
| 1939 | G | A | -1.7873 | |
| 1940 | N | A | -2.2605 | |
| 1941 | L | A | -1.9922 | |
| 1942 | C | A | 0.0000 | |
| 1943 | R | A | -3.2142 | |
| 1944 | N | A | -3.1488 | |
| 1945 | G | A | -2.8578 | |
| 1946 | Q | A | -2.4412 | |
| 1947 | C | A | -1.5967 | |
| 1948 | I | A | -0.5446 | |
| 1949 | N | A | -0.3952 | |
| 1950 | T | A | 0.3963 | |
| 1951 | V | A | 1.5349 | |
| 1952 | G | A | 0.3534 | |
| 1953 | S | A | -0.0265 | |
| 1954 | F | A | -0.3290 | |
| 1955 | Q | A | -1.1320 | |
| 1956 | C | A | -1.9806 | |
| 1957 | Q | A | -2.5535 | |
| 1958 | C | A | -2.6418 | |
| 1959 | N | A | -3.3007 | |
| 1960 | E | A | -3.0235 | |
| 1961 | G | A | -1.8770 | |
| 1962 | Y | A | -1.9959 | |
| 1963 | E | A | -1.8063 | |
| 1964 | V | A | -0.9315 | |
| 1965 | A | A | -0.7358 | |
| 1966 | P | A | -1.2628 | |
| 1967 | D | A | -2.3278 | |
| 1968 | G | A | -1.8460 | |
| 1969 | R | A | -2.2252 | |
| 1970 | T | A | -1.9760 | |
| 1971 | C | A | 0.0000 | |
| 1972 | V | A | 0.0171 | |
| 1973 | D | A | -0.9904 | |
| 1974 | I | A | -0.2954 | |
| 1975 | N | A | -0.4576 | |
| 1976 | E | A | -0.3619 | |
| 1977 | C | A | -0.4246 | |
| 1978 | L | A | 1.0932 | |
| 1979 | L | A | 0.9567 | |
| 1980 | E | A | -1.4145 | |
| 1981 | P | A | -1.2225 | |
| 1982 | R | A | -2.4639 | |
| 1983 | K | A | -2.4531 | |
| 1984 | C | A | 0.0000 | |
| 1985 | A | A | -1.2617 | |
| 1986 | P | A | -0.8995 | |
| 1987 | G | A | -0.4518 | |
| 1988 | T | A | -0.5261 | |
| 1989 | C | A | -1.0137 | |
| 1990 | Q | A | -0.9293 | |
| 1991 | N | A | -1.2710 | |
| 1992 | L | A | -1.2494 | |
| 1993 | D | A | -1.6089 | |
| 1994 | G | A | -1.7754 | |
| 1995 | S | A | -1.4257 | |
| 1996 | Y | A | -1.5474 | |
| 1997 | R | A | -1.9738 | |
| 1998 | C | A | 0.0000 | |
| 1999 | I | A | 0.3371 | |
| 2000 | C | A | 0.1260 | |
| 2001 | P | A | 0.0707 | |
| 2002 | P | A | -0.2249 | |
| 2003 | G | A | -0.8910 | |
| 2004 | Y | A | -0.9305 | |
| 2005 | S | A | -0.7590 | |
| 2006 | L | A | -0.9939 | |
| 2007 | Q | A | -2.4715 | |
| 2008 | N | A | -2.8737 | |
| 2009 | E | A | -3.3259 | |
| 2010 | K | A | -2.6985 | |
| 2011 | C | A | 0.0000 | |
| 2012 | E | A | -2.6258 | |
| 2013 | D | A | -2.0479 | |
| 2014 | I | A | -1.1013 | |
| 2015 | D | A | -1.6170 | |
| 2016 | E | A | -1.8063 | |
| 2017 | C | A | -1.2293 | |
| 2018 | V | A | -0.2910 | |
| 2019 | E | A | -2.3502 | |
| 2020 | E | A | -2.9860 | |
| 2021 | P | A | -1.9860 | |
| 2022 | E | A | -2.6026 | |
| 2023 | I | A | 0.0000 | |
| 2024 | C | A | 0.0000 | |
| 2025 | A | A | -1.1288 | |
| 2026 | L | A | -0.0218 | |
| 2027 | G | A | -0.3474 | |
| 2028 | T | A | -0.3037 | |
| 2029 | C | A | -0.7781 | |
| 2030 | S | A | -0.6329 | |
| 2031 | N | A | -1.4074 | |
| 2032 | T | A | -1.7402 | |
| 2033 | E | A | -2.3823 | |
| 2034 | G | A | -1.5964 | |
| 2035 | S | A | -1.3399 | |
| 2036 | F | A | -1.3386 | |
| 2037 | K | A | -1.7577 | |
| 2038 | C | A | 0.0000 | |
| 2039 | L | A | 0.0384 | |
| 2040 | C | A | -0.2083 | |
| 2041 | P | A | -0.5387 | |
| 2042 | E | A | -1.7014 | |
| 2043 | G | A | -0.8982 | |
| 2044 | F | A | 0.1073 | |
| 2045 | S | A | 0.1263 | |
| 2046 | L | A | 0.1579 | |
| 2047 | S | A | -0.6917 | |
| 2048 | S | A | -0.7314 | |
| 2049 | S | A | -1.0889 | |
| 2050 | G | A | -1.4599 | |
| 2051 | R | A | -2.5205 | |
| 2052 | R | A | -1.9324 | |
| 2053 | C | A | 0.0000 | |
| 2054 | Q | A | -0.0691 | |
| 2055 | D | A | 0.0000 | |
| 2056 | L | A | 1.0695 | |
| 2057 | R | A | -0.1297 | |
| 2058 | M | A | 0.3437 | |
| 2059 | S | A | -0.1864 | |
| 2060 | Y | A | -0.0902 | |
| 2061 | C | A | 0.0000 | |
| 2062 | Y | A | 0.0000 | |
| 2063 | A | A | -1.1111 | |
| 2064 | K | A | -2.0269 | |
| 2065 | F | A | -1.8634 | |
| 2066 | E | A | -2.8801 | |
| 2067 | G | A | -1.9896 | |
| 2068 | G | A | -1.7536 | |
| 2069 | K | A | -2.6517 | |
| 2070 | C | A | 0.0000 | |
| 2071 | S | A | -1.4803 | |
| 2072 | S | A | -0.6082 | |
| 2073 | P | A | -0.8612 | |
| 2074 | K | A | -1.1698 | |
| 2075 | S | A | -1.4023 | |
| 2076 | R | A | -2.1644 | |
| 2077 | N | A | -1.4375 | |
| 2078 | H | A | -0.7541 | |
| 2079 | S | A | -0.2185 | |
| 2080 | K | A | -0.3253 | |
| 2081 | Q | A | -0.6850 | |
| 2082 | E | A | -1.1110 | |
| 2083 | C | A | 0.0000 | |
| 2084 | C | A | 0.0000 | |
| 2085 | C | A | -0.7356 | |
| 2086 | A | A | -0.5436 | |
| 2087 | L | A | -0.8370 | |
| 2088 | K | A | -2.0104 | |
| 2089 | G | A | 0.0000 | |
| 2090 | E | A | -1.7149 | |
| 2091 | G | A | 0.0000 | |
| 2092 | W | A | 0.0000 | |
| 2093 | G | A | 0.0000 | |
| 2094 | D | A | -1.9792 | |
| 2095 | P | A | -1.5708 | |
| 2096 | C | A | -1.3653 | |
| 2097 | E | A | -1.5922 | |
| 2098 | L | A | 0.1318 | |
| 2099 | C | A | 0.0000 | |
| 2100 | P | A | -1.3462 | |
| 2101 | T | A | -2.0222 | |
| 2102 | E | A | -3.1459 | |
| 2103 | P | A | -2.9130 | |
| 2104 | D | A | -3.9232 | |
| 2105 | E | A | -3.8568 | |
| 2106 | A | A | -2.4306 | |
| 2107 | F | A | -2.4601 | |
| 2108 | R | A | -3.3049 | |
| 2109 | Q | A | -2.1995 | |
| 2110 | I | A | -0.8192 | |
| 2111 | C | A | -0.3490 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -0.457 | 4.4734 | View | CSV | PDB |
| 4.5 | -0.557 | 4.4373 | View | CSV | PDB |
| 5.0 | -0.6811 | 4.4002 | View | CSV | PDB |
| 5.5 | -0.8111 | 4.3627 | View | CSV | PDB |
| 6.0 | -0.9283 | 4.3252 | View | CSV | PDB |
| 6.5 | -1.0181 | 4.288 | View | CSV | PDB |
| 7.0 | -1.076 | 4.2517 | View | CSV | PDB |
| 7.5 | -1.109 | 4.2179 | View | CSV | PDB |
| 8.0 | -1.1258 | 4.1899 | View | CSV | PDB |
| 8.5 | -1.1291 | 4.1715 | View | CSV | PDB |
| 9.0 | -1.1184 | 4.1613 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine