Contacts of the helix formed by residues 1452 - 1481 (chain H) in PDB entry 2NQB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1452 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077G ARG* 3.6 18.4 - - - +
1078G ILE 2.9 15.3 + - - -
1079G ILE* 3.9 13.9 - - - +
1080G PRO* 4.0 4.5 - - - +
1451H ILE* 1.3 76.3 - - - +
1453H SER* 1.3 60.2 + - - +
1454H LYS* 3.7 4.5 + - - +
1455H ALA* 3.2 21.7 + - - +
1456H MET* 2.9 27.1 + - - +
165J A 3.6 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1453 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1452H SER* 1.3 68.9 - - - +
1454H LYS* 1.3 63.4 + - - +
1456H MET* 3.0 8.6 + - - +
1457H SER* 2.9 28.9 + - - -
165J A 2.8 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1454 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 5.0 1.4 - - - -
1080G PRO* 3.9 18.6 - - + -
1104G GLN* 4.8 20.2 - - + -
1452H SER* 3.4 4.6 + - - +
1453H SER* 1.3 79.1 - - - +
1455H ALA* 1.3 63.7 + - - +
1457H SER* 3.0 10.5 + - - -
1458H ILE* 3.0 26.4 + - + +
164J G 5.8 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1455 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078G ILE* 3.5 19.5 - - + +
1079G ILE* 3.9 11.9 - - - -
1080G PRO* 4.0 5.1 - - - +
1083G LEU* 3.6 19.7 - - + +
1451H ILE* 3.5 13.9 - - + -
1452H SER* 3.2 17.6 + - - +
1453H SER 3.2 0.2 - - - -
1454H LYS* 1.3 78.0 - - - +
1456H MET* 1.3 57.4 + - - +
1458H ILE* 3.2 4.7 + - - +
1459H MET* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1456 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435H ALA* 3.4 49.1 - - + +
1438H ILE* 3.8 22.7 - - + -
1439H TYR* 3.9 21.5 - - + +
1451H ILE* 3.8 30.2 - - + +
1452H SER 2.9 13.9 + - - +
1453H SER* 3.0 12.1 + - - +
1455H ALA* 1.3 74.2 - - - +
1457H SER* 1.3 61.9 + - - +
1459H MET* 3.3 1.1 + - - +
1460H ASN* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1457 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 3.5 27.2 + - - -
100B PHE* 4.1 1.2 + - - -
101B GLY* 4.3 6.9 + - - -
1453H SER 2.9 11.5 + - - -
1454H LYS* 3.0 13.7 + - - -
1456H MET* 1.3 78.3 - - - +
1458H ILE* 1.3 56.7 + - - +
1460H ASN* 3.3 8.2 + - - +
1461H SER* 3.0 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1458 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 4.0 9.7 - - + +
99B GLY* 3.8 24.9 - - - +
1080G PRO* 3.7 25.1 - - + -
1083G LEU* 3.6 16.6 - - + -
1102G ILE* 3.6 38.6 - - + -
1103G ALA* 3.5 27.8 - - + +
1454H LYS* 3.0 14.1 + - + +
1455H ALA 3.5 7.2 - - - +
1457H SER* 1.3 76.8 - - - +
1459H MET* 1.3 59.1 + - - +
1461H SER* 3.1 4.0 + - - -
1462H PHE* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1459 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059G ALA* 3.9 27.4 - - + +
1062G VAL* 3.9 12.8 - - + -
1063G LEU* 3.7 30.1 - - + -
1083G LEU* 3.7 26.9 - - + -
1438H ILE* 3.8 18.8 - - + -
1451H ILE* 4.1 17.9 - - + -
1455H ALA 2.9 17.3 + - - +
1456H MET* 3.6 8.5 - - - +
1458H ILE* 1.3 77.2 - - - +
1460H ASN* 1.3 58.3 + - - +
1462H PHE* 3.2 19.4 + - + +
1463H VAL* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1460 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY* 6.2 1.0 - - - -
102B GLY 5.0 3.2 + - - +
1432H GLU 5.2 1.0 + - - -
1433H SER* 3.9 19.6 - - - +
1434H TYR* 2.8 39.7 + - - +
1435H ALA* 4.0 2.4 + - + +
1438H ILE* 3.7 7.5 - - + +
1456H MET* 2.9 18.6 + - + +
1457H SER* 3.5 8.7 - - - +
1458H ILE 3.2 0.2 - - - -
1459H MET* 1.3 77.6 - - - +
1461H SER* 1.3 61.9 + - - +
1463H VAL* 3.3 3.4 + - - +
1464H ASN* 3.0 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1461 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.6 28.4 - - - -
99B GLY* 3.3 17.5 + - - -
101B GLY 3.6 8.3 + - - -
102B GLY* 3.1 31.1 + - - +
1457H SER 3.0 11.7 + - - -
1458H ILE 3.1 7.6 + - - -
1460H ASN* 1.3 74.9 - - - +
1462H PHE* 1.3 52.7 + - - +
1464H ASN* 3.3 1.7 + - - +
1465H ASP* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1462 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.6 31.8 - + + -
1055G MET 5.6 0.2 - - - -
1058G LEU* 3.8 33.4 - - + -
1059G ALA* 4.2 1.6 - - - -
1062G VAL* 3.7 27.4 - - + -
1087G ILE* 6.2 0.9 - - + -
1093G LEU* 4.9 1.1 - - + -
1096G LEU* 4.6 7.4 - - + -
1097G LEU* 3.8 26.5 - - + -
1458H ILE* 2.9 14.5 + - + +
1459H MET* 3.4 29.4 - - + +
1461H SER* 1.3 75.6 - - - +
1463H VAL* 1.3 63.3 + - + +
1465H ASP* 3.2 2.1 + - - +
1466H ILE* 2.9 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1463 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025G PHE* 3.6 28.3 - - + -
1055G MET* 3.2 35.4 - - + +
1059G ALA* 4.4 12.1 - - + -
1434H TYR* 3.7 18.4 - - + -
1438H ILE* 4.1 16.6 - - + -
1459H MET* 2.9 21.6 + - + +
1460H ASN* 3.8 4.3 - - - +
1462H PHE* 1.3 81.1 - - + +
1464H ASN* 1.3 58.4 + - - +
1466H ILE* 3.4 6.8 + - - +
1467H PHE* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1464 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY* 3.0 31.7 + - - +
1033G LEU* 5.6 2.4 - - - +
1433H SER* 6.1 0.2 - - - +
1434H TYR* 3.4 21.9 + - - -
1460H ASN* 3.0 39.6 + - - +
1461H SER 3.7 0.2 - - - +
1463H VAL* 1.3 73.1 - - - +
1465H ASP* 1.3 66.1 + - - +
1467H PHE* 3.3 9.5 + - - +
1468H GLU* 3.0 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1465 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 5.9 4.0 - - - +
96B THR* 4.1 7.8 + - - +
98B TYR* 2.5 41.0 + - + +
102B GLY 5.8 0.2 - - - -
1100G VAL* 3.9 2.9 - - - +
1461H SER 2.8 18.8 + - - +
1462H PHE 3.2 1.8 + - - +
1464H ASN* 1.3 72.5 - - - +
1466H ILE* 1.3 65.8 + - - +
1468H GLU* 3.3 12.4 + - - +
1469H ARG* 2.8 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1466 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055G MET* 4.2 17.5 - - + -
1058G LEU* 3.7 30.1 - - + -
1096G LEU* 4.2 18.8 - - + -
1097G LEU* 5.1 2.2 - - + -
1462H PHE* 2.9 53.1 + - + +
1463H VAL* 3.6 6.7 - - - +
1465H ASP* 1.3 78.1 - - + +
1467H PHE* 1.3 62.3 + - - +
1469H ARG* 3.4 12.9 + - + +
1470H ILE* 3.1 42.0 + - + +
1499H LEU* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1467 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030G ILE* 4.0 13.2 - - + -
1033G LEU* 3.5 39.7 - - + -
1034G LEU* 3.8 23.3 - - + -
1039G TYR* 3.7 21.5 - + - -
1051G LEU* 3.5 34.8 - - + +
1055G MET* 3.9 26.2 - - + +
1434H TYR* 4.6 3.6 - - - +
1463H VAL 3.0 17.4 + - - +
1464H ASN* 3.6 10.1 - - - +
1466H ILE* 1.3 77.2 - - - +
1468H GLU* 1.3 70.6 + - + +
1470H ILE* 3.9 0.9 - - - +
1471H ALA* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1468 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 3.3 26.4 + - - -
102B GLY 5.6 1.8 - - - +
1279D HIS* 5.7 4.3 - - - -
1280D TYR* 5.8 4.3 - - - -
1039G TYR* 4.6 10.0 + - - +
1464H ASN* 3.0 28.4 + - + +
1465H ASP* 3.7 11.8 - - - +
1467H PHE* 1.3 85.9 - - + +
1469H ARG* 1.3 66.2 + - + +
1471H ALA* 4.0 3.2 - - - +
1472H ALA* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1469 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 5.8 0.6 + - - -
1096G LEU* 2.8 44.5 + - - +
1097G LEU* 3.7 14.1 - - - +
1099G GLY* 5.9 1.0 - - - +
1100G VAL* 3.8 9.9 - - - +
1465H ASP* 2.8 54.0 + - - +
1466H ILE* 3.9 11.9 - - + +
1468H GLU* 1.3 75.5 - - + +
1470H ILE* 1.3 64.5 + - + +
1472H ALA* 3.9 3.8 - - - +
1473H GLU* 3.0 18.7 + - - +
1476H ARG* 4.9 0.9 + - - -
1498H LEU* 3.5 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1470 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051G LEU* 3.7 27.8 - - + -
1054G VAL* 3.8 30.1 - - + -
1058G LEU* 5.5 0.9 - - + -
1466H ILE* 3.1 25.8 + - + +
1467H PHE 3.9 2.0 - - - +
1469H ARG* 1.3 76.4 - - + +
1471H ALA* 1.3 65.2 + - - +
1473H GLU* 3.3 2.8 + - - +
1474H ALA* 3.0 22.2 + - - +
1491H ILE* 4.0 26.9 - - + +
1494H ALA* 3.8 9.2 - - + +
1495H VAL* 3.9 14.4 - - + -
1498H LEU* 3.7 20.2 - - + -
1499H LEU* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1471 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034G LEU* 3.8 25.4 - - + -
1039G TYR* 3.6 34.7 - - + +
1051G LEU* 5.1 1.3 - - + +
1467H PHE* 2.9 21.7 + - + +
1468H GLU 4.0 1.8 - - - +
1470H ILE* 1.3 78.4 - - - +
1472H ALA* 1.3 57.8 + - - +
1474H ALA* 3.4 5.7 + - - +
1475H SER* 2.9 28.6 + - - -
1486H ILE* 4.6 1.0 - - - +
1491H ILE* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1472 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039G TYR* 4.1 9.1 - - + -
1468H GLU 2.9 18.3 + - - +
1469H ARG* 3.9 4.7 - - - +
1471H ALA* 1.3 77.9 - - - +
1473H GLU* 1.3 61.4 + - - +
1475H SER* 3.2 9.2 - - - -
1476H ARG* 3.0 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1473 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 2.9 28.9 + - - -
292F ARG* 3.2 23.6 + - - +
1469H ARG 3.0 16.8 + - - +
1470H ILE 3.3 0.2 + - - -
1472H ALA* 1.3 77.4 - - - +
1474H ALA* 1.3 56.3 + - - +
1476H ARG* 3.1 31.6 + - - +
1477H LEU* 2.8 28.6 + - + +
1494H ALA* 3.6 31.0 - - + +
1497H LEU* 3.6 16.7 - - + +
1498H LEU* 3.8 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1474 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1470H ILE 3.0 16.8 + - - +
1471H ALA* 3.8 4.9 - - - +
1473H GLU* 1.3 72.7 - - - +
1475H SER* 1.3 66.6 + - - +
1477H LEU* 3.2 8.4 + - - +
1478H ALA* 2.9 26.7 + - - +
1486H ILE* 4.1 11.2 - - + +
1490H GLU* 3.8 29.6 - - + +
1491H ILE* 4.0 20.4 - - + -
1494H ALA* 4.0 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1475 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838C ASN* 5.2 2.8 - - - +
1038G ASN 4.6 2.3 + - - -
1039G TYR* 2.8 40.9 + - - +
1471H ALA 2.9 15.4 + - - -
1472H ALA* 3.2 13.9 - - - -
1473H GLU 3.2 0.2 - - - -
1474H ALA* 1.3 77.6 - - - +
1476H ARG* 1.3 64.0 + - - +
1478H ALA* 3.4 2.3 + - - +
1479H HIS* 3.0 24.4 + - - +
1486H ILE* 4.0 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1476 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 5.6 0.7 - - - -
292F ARG* 6.5 0.4 - - - -
1469H ARG 4.9 0.6 + - - -
1472H ALA* 3.0 33.6 + - - +
1473H GLU* 3.1 50.1 + - - +
1475H SER* 1.3 76.7 - - - +
1477H LEU* 1.3 57.9 + - - +
1479H HIS* 3.0 6.9 + - - +
1480H TYR* 2.8 65.7 + - + +
1498H LEU* 6.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1477 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 3.5 34.1 - - + -
275F HIS* 4.0 25.0 + - + +
1473H GLU* 2.8 27.1 + - + +
1474H ALA* 3.5 7.9 - - - +
1476H ARG* 1.3 73.8 - - - +
1478H ALA* 1.3 61.7 + - - +
1480H TYR* 3.5 4.6 + - - -
1481H ASN* 2.9 31.5 + - - +
1490H GLU* 3.4 31.9 - - + +
1493H THR* 3.5 32.5 - - + -
1494H ALA* 3.7 9.2 - - - +
1497H LEU* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1478 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F HIS* 5.7 0.2 - - - -
1040G ALA* 5.1 4.5 - - + -
1474H ALA 2.9 17.1 + - - +
1475H SER* 3.8 3.8 - - - +
1477H LEU* 1.3 75.9 - - - +
1479H HIS* 1.3 62.1 - - - +
1481H ASN* 3.4 1.3 + - - -
1482H LYS 3.2 3.5 + - - -
1483H ARG* 2.8 49.7 + - + +
1485H THR 4.0 20.0 - - - +
1486H ILE* 4.3 11.4 - - + -
1490H GLU* 4.3 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1479 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C LYS* 4.5 25.1 + - - -
837C GLY* 4.4 27.3 - - - -
838C ASN* 5.0 5.8 - - - -
839C TYR* 5.9 0.6 + - - -
1475H SER* 3.0 17.7 + - - +
1476H ARG* 3.6 6.5 - - - +
1478H ALA* 1.3 74.9 - - - +
1480H TYR* 1.3 72.7 + + + +
1482H LYS* 3.1 18.2 + - + +
1483H ARG 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1480 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 3.7 32.7 + + - -
288F TYR* 3.2 75.4 + + + +
291F LYS* 5.4 6.9 - - - +
1476H ARG* 2.8 56.0 + - + +
1477H LEU* 3.8 5.6 - - + +
1479H HIS* 1.3 79.2 - - + +
1481H ASN* 1.3 66.1 + - - +
1482H LYS* 3.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1481 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 5.2 3.6 + - - -
275F HIS* 3.5 23.6 - - + +
276F ALA* 2.9 36.8 - - - +
278F ARG* 5.0 1.4 + - - -
1477H LEU* 2.9 28.8 + - - +
1479H HIS 3.2 0.6 - - - -
1480H TYR* 1.3 84.9 - - - +
1482H LYS* 1.3 60.3 + - - +
1483H ARG* 2.7 49.7 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il