Contacts of the helix formed by residues 1413 - 1446 (chain E) in PDB entry 6JLE
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 ASP1413 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410E ASP* 3.1 25.8 + - + +
1411E ASN 4.6 1.1 - - - -
1412E LYS* 1.3 74.6 - - - +
1414E SER* 1.3 62.7 + - - +
1415E LYS* 3.3 12.8 + - - +
1416E ALA* 3.1 31.9 + - + +
1417E THR* 3.2 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1414 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 5.2 7.6 - - - +
1411E ASN 5.4 1.1 - - - -
1412E LYS 3.1 11.0 + - - -
1413E ASP* 1.3 71.9 + - - +
1415E LYS* 1.3 62.4 + - - +
1417E THR* 3.4 6.3 + - - -
1418E SER* 3.1 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1415 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413E ASP* 3.2 7.9 + - - +
1414E SER* 1.3 80.0 - - - +
1416E ALA* 1.3 63.5 + - - +
1417E THR 3.3 0.2 + - - -
1418E SER* 3.3 3.7 + - - -
1419E GLU* 2.6 61.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1416 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410E ASP 5.6 1.1 - - - +
1413E ASP* 3.1 31.5 + - + +
1415E LYS* 1.3 76.4 - - - +
1417E THR* 1.3 57.7 + - - +
1419E GLU* 3.3 14.7 + - - +
1420E ARG* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1417 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 4.1 21.8 - - + +
1410E ASP 4.6 6.2 + - - -
1411E ASN* 4.7 9.4 + - - -
1413E ASP 3.2 16.5 + - - -
1414E SER* 3.7 6.5 - - - -
1415E LYS 3.2 0.2 - - - -
1416E ALA* 1.3 79.2 - - - +
1418E SER* 1.3 63.5 + - - +
1420E ARG* 3.3 29.8 + - - +
1421E GLU* 2.9 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1418 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE 3.4 19.3 + - - -
110A PRO* 3.9 11.1 - - - +
1414E SER* 3.1 18.2 + - - -
1415E LYS* 3.9 4.5 - - - -
1417E THR* 1.3 76.7 - - - +
1419E GLU* 1.3 58.1 + - - +
1421E GLU* 3.4 4.4 + - - +
1422E ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1419 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415E LYS* 2.6 57.6 + - + +
1416E ALA* 3.6 12.7 - - - +
1418E SER* 1.3 74.8 - - - +
1420E ARG* 1.3 65.0 + - - +
1422E ALA* 3.4 5.7 + - - +
1423E CYS* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1420 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409E SER* 3.9 27.4 - - - -
1410E ASP 5.8 0.6 + - - -
1411E ASN* 6.2 0.6 - - - +
1416E ALA* 2.9 25.1 + - - +
1417E THR* 3.3 42.8 + - - +
1419E GLU* 1.3 74.5 - - - +
1421E GLU* 1.3 66.2 + - + +
1423E CYS* 3.3 6.7 + - - +
1424E GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1421 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 3.6 34.1 - - + -
106A SER* 5.5 1.0 + - - -
108A GLY* 3.4 20.7 - - - -
109A ILE* 3.0 32.2 + - - +
112A ASN* 4.4 10.7 + - - +
1417E THR* 2.9 35.4 + - + +
1418E SER* 3.9 3.9 - - - +
1420E ARG* 1.3 87.4 + - + +
1422E ALA* 1.3 56.4 + - - +
1424E GLY* 3.2 1.3 + - - -
1425E LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1422 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 5.8 1.3 - - - +
119A ASN 4.8 1.0 - - - +
1418E SER 3.0 18.6 + - - +
1419E GLU* 3.8 6.1 - - - +
1421E GLU* 1.3 74.8 - - - +
1423E CYS* 1.3 63.0 + - - +
1425E LEU* 3.4 10.5 + - - +
1426E ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1423 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419E GLU 3.0 17.6 + - - +
1420E ARG* 3.6 6.7 - - - +
1422E ALA* 1.3 76.6 - - - +
1424E GLY* 1.3 62.0 + - - +
1426E ALA* 3.2 7.3 + - - +
1427E ILE* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1424 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.8 1.2 + - - -
83A MET* 4.3 16.7 - - - +
102A PHE* 5.3 2.2 - - - -
1420E ARG 2.9 15.5 + - - -
1421E GLU* 3.2 4.0 + - - -
1423E CYS* 1.3 77.8 - - - +
1425E LEU* 1.3 61.3 + - - +
1427E ILE* 3.5 7.9 + - - +
1428E PHE* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1425 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 5.6 0.2 - - - -
85A PHE* 5.9 0.9 - - + -
94A VAL* 5.8 3.8 - - + -
100A LEU* 4.0 31.4 - - + -
102A PHE* 5.0 1.6 - - - -
112A ASN* 4.4 7.6 - - - +
116A PHE* 3.8 29.6 - - + -
119A ASN 3.8 7.2 - - - +
120A LYS* 3.9 5.6 - - - -
121A LEU* 3.6 33.0 - - + +
1421E GLU 2.9 16.9 + - - +
1422E ALA* 3.7 7.4 - - - +
1424E GLY* 1.3 75.5 - - - +
1426E ALA* 1.3 59.5 + - - +
1428E PHE* 3.6 9.1 - - + +
1429E SER* 2.8 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1426 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.5 24.6 - - + +
120A LYS* 6.2 0.7 - - + -
1422E ALA 3.0 17.4 + - - +
1423E CYS* 3.6 8.1 - - - +
1425E LEU* 1.3 75.7 - - - +
1427E ILE* 1.3 64.4 + - + +
1429E SER* 3.5 1.0 + - - -
1430E LYS* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.5 4.7 - - - +
1423E CYS* 3.1 35.1 + - - +
1424E GLY* 3.9 6.1 - - - +
1426E ALA* 1.3 78.6 - - + +
1428E PHE* 1.3 63.3 + - - +
1430E LYS* 3.3 7.5 + - + +
1431E GLN* 2.9 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1428 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.8 23.1 - + - -
79A ARG* 3.8 23.5 - - + +
83A MET* 3.5 48.0 - - + -
84A THR* 3.9 0.2 - - - -
85A PHE* 3.8 26.2 - - + -
94A VAL* 5.6 1.3 - - + -
100A LEU* 3.8 27.8 - - + -
1424E GLY 3.0 18.8 + - - +
1425E LEU* 3.6 10.5 - - + +
1427E ILE* 1.3 77.5 - - - +
1429E SER* 1.3 63.4 + - - +
1431E GLN* 3.2 15.1 + - - +
1432E ILE* 3.1 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 6.0 0.2 - - - +
94A VAL* 4.3 22.7 + - - +
119A ASN* 2.6 41.0 + - - -
1425E LEU* 2.8 28.2 + - - -
1426E ALA 3.9 0.4 - - - -
1428E PHE* 1.3 74.1 - - - +
1430E LYS* 1.3 62.7 + - - +
1432E ILE* 3.2 12.1 + - - +
1433E SER* 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1430 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.6 31.9 - - - +
1426E ALA* 3.0 28.9 + - + +
1427E ILE* 3.8 7.0 - - + +
1429E SER* 1.3 75.3 - - - +
1431E GLN* 1.3 58.1 + - - +
1433E SER* 3.4 5.9 + - - +
1434E LYS* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1431 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 6.3 0.9 - - + -
79A ARG* 2.8 41.1 + - - +
80A TYR* 4.0 16.5 + - - -
1427E ILE* 2.9 34.5 + - + +
1428E PHE* 3.2 11.2 + - - +
1430E LYS* 1.3 77.9 - - - +
1432E ILE* 1.3 63.2 + - + +
1434E LYS* 3.3 7.5 + - - +
1435E LEU* 3.0 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1432 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.9 20.5 - - + -
77A PHE* 3.7 39.5 - - + -
85A PHE* 5.1 0.4 - - + -
89A PHE* 4.2 9.4 - - + -
92A GLY 3.8 14.6 - - - +
94A VAL* 3.7 29.2 - - + +
1428E PHE* 3.1 38.6 + - + +
1429E SER* 3.6 6.5 - - - +
1431E GLN* 1.3 76.2 - - + +
1433E SER* 1.3 63.1 + - - +
1435E LEU* 3.2 9.7 + - - +
1436E SER* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY 3.9 9.0 - - - -
93A ARG* 3.3 37.0 - - - +
119A ASN* 4.6 5.2 + - - -
1429E SER* 3.1 18.2 + - - -
1430E LYS* 3.8 6.5 - - - -
1431E GLN 3.3 0.2 - - - -
1432E ILE* 1.3 76.6 - - - +
1434E LYS* 1.3 62.0 + - - +
1436E SER* 3.3 2.8 + - - -
1437E GLU* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430E LYS* 3.0 24.1 + - + +
1431E GLN* 3.6 7.2 - - - +
1432E ILE 3.2 0.2 - - - -
1433E SER* 1.3 78.0 - - - +
1435E LEU* 1.3 62.0 + - + +
1437E GLU* 3.5 4.5 + - + +
1438E GLU* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.0 39.3 - - + -
58A ASP* 5.3 9.4 - - - +
60A SER* 5.2 3.4 - - - -
71A PHE* 5.7 0.9 - - + -
77A PHE* 3.7 32.5 - - + -
1431E GLN* 3.0 25.2 + - + +
1432E ILE* 3.2 4.2 + - - +
1434E LYS* 1.3 74.4 - - + +
1436E SER* 1.3 66.8 + - - +
1438E GLU* 3.2 18.8 + - - +
1439E TYR* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 5.0 1.2 - - - +
70A LYS* 4.3 13.8 - - - +
71A PHE* 3.2 23.8 - - - -
91A ASN 5.0 0.2 - - - -
92A GLY* 2.7 41.4 + - - -
93A ARG* 5.9 0.2 - - - -
1432E ILE 2.9 10.6 + - - -
1433E SER 3.7 4.5 - - - -
1434E LYS 3.3 0.2 - - - -
1435E LEU* 1.3 77.1 - - - +
1437E GLU* 1.3 58.0 + - - +
1439E TYR* 3.8 3.3 - - - +
1440E PHE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.1 27.1 + - - +
1433E SER 3.1 13.2 + - - +
1434E LYS* 4.0 5.4 - - + +
1436E SER* 1.3 79.6 - - - +
1438E GLU* 1.3 63.8 + - - +
1440E PHE* 3.3 9.7 + - - -
1441E ILE* 3.0 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1438 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GOL 4.1 17.8 + - - -
1434E LYS 3.0 18.0 + - - +
1435E LEU* 3.2 17.8 + - - +
1437E GLU* 1.3 78.5 - - - +
1439E TYR* 1.3 79.1 + - + +
1441E ILE* 3.5 9.7 + - - +
1442E LEU* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.5 51.3 - + - -
35A ASP* 4.0 7.6 + - - -
37A GLY* 5.7 0.2 - - - -
48A PHE* 4.8 2.9 - + + -
54A LEU* 4.4 14.1 - - + -
56A PHE* 3.5 42.0 - + - +
57A SER 5.1 0.7 + - - -
69A GLY 5.7 0.7 - - - +
202A GOL 3.1 23.3 + - - -
1435E LEU* 2.9 25.5 + - + +
1436E SER* 4.2 3.1 - - - +
1438E GLU* 1.3 99.1 - - + +
1440E PHE* 1.3 60.3 + - - +
1442E LEU* 3.7 13.8 - - + +
1443E GLN* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1440 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.2 14.6 - - + -
68A GLN* 3.4 27.6 - - + -
69A GLY* 4.4 5.8 + - - -
70A LYS* 3.5 33.2 - - + -
1436E SER 2.9 19.6 + - - +
1437E GLU* 3.6 16.8 - - - +
1439E TYR* 1.3 73.1 - - - +
1441E ILE* 1.3 69.7 + - + +
1443E GLN* 3.3 10.8 + - - +
1444E LYS* 3.1 60.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1441 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437E GLU* 3.0 48.6 + - + +
1438E GLU* 3.7 7.9 - - - +
1440E PHE* 1.3 78.5 - - + +
1442E LEU* 1.3 58.6 + - - +
1444E LYS* 3.3 10.1 + - + +
1445E LYS* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1442 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.7 20.2 - - - +
31A LEU* 6.4 0.2 - - + -
33A PHE* 3.6 36.3 - - + -
202A GOL 3.7 30.1 - - - +
1438E GLU* 3.1 19.5 + - + +
1439E TYR* 3.7 14.6 - - + +
1440E PHE 3.1 0.6 - - - -
1441E ILE* 1.3 76.5 - - - +
1443E GLN* 1.3 67.0 + - - +
1445E LYS* 3.1 24.1 + - + +
1446E LEU* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1443 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.1 29.9 + - - +
31A LEU* 5.0 6.5 - - + -
33A PHE* 5.8 1.3 - - + -
46A GLY 4.9 0.2 - - - +
47A LEU* 3.3 19.6 - - + -
48A PHE* 2.8 64.4 + - + -
69A GLY* 2.9 29.4 + - - -
1439E TYR* 3.0 29.4 + - + +
1440E PHE* 3.7 5.9 - - - +
1442E LEU* 1.3 76.7 - - + +
1444E LYS* 1.3 62.5 + - - +
1446E LEU* 3.2 11.0 + - - +
1447E ASN* 3.2 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1444 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.5 11.7 - - + -
1440E PHE* 3.1 57.2 + - + +
1441E ILE* 3.6 10.7 - - - +
1443E GLN* 1.3 73.8 - - - +
1445E LYS* 1.3 67.3 + - - +
1447E ASN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1445 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.4 32.3 + - - -
14A GLU* 4.7 1.6 - - - -
1441E ILE* 2.9 19.6 + - + +
1442E LEU* 3.1 32.5 + - + +
1444E LYS* 1.3 77.4 - - - +
1446E LEU* 1.3 63.4 + - + +
1447E ASN 3.5 0.2 + - - -
1448E GLU* 3.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1446 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 31.2 + - + -
12A SER* 3.8 10.8 - - - +
14A GLU* 3.6 49.4 - - + +
25A ARG* 2.9 26.9 + - - +
31A LEU* 4.6 20.2 - - + -
33A PHE* 5.3 0.2 - - + -
1442E LEU* 3.0 29.2 + - + +
1443E GLN* 3.3 5.6 - - - +
1444E LYS 3.1 0.4 - - - -
1445E LYS* 1.3 87.4 - - - +
1447E ASN* 1.3 54.3 + - - +
1448E GLU* 3.2 11.4 - - - +
----------------------------------------------------------
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