Contacts of the helix formed by residues 1414 - 1440 (chain A) in PDB entry 6AGF
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 VAL1414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410A TYR* 3.5 45.1 + - + +
1411A TYR 4.4 1.0 + - - -
1413A THR* 1.3 77.5 - - + +
1415A GLY* 1.3 62.3 + - - +
1416A TRP* 3.8 24.9 - - + +
1417A ASN* 3.0 28.1 + - + +
1418A ILE* 3.0 15.1 + - - +
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Residues in contact with GLY1415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413A THR 3.6 2.2 + - - -
1414A VAL* 1.3 72.5 - - - +
1416A TRP* 1.3 65.2 + - - +
1417A ASN 3.3 0.2 - - - -
1418A ILE* 3.6 16.0 + - - +
1419A PHE* 3.4 18.2 + - - +
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Residues in contact with TRP1416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1414A VAL* 3.2 14.9 - - + +
1415A GLY* 1.3 77.2 - - - +
1417A ASN* 1.3 57.5 + - - +
1419A PHE* 3.1 25.4 + + + +
1420A ASP* 3.0 24.1 + - - +
1459A LEU* 4.9 9.2 - - + -
1460A ARG* 5.3 8.5 - - + +
1462A ILE* 4.8 14.1 - - + -
1463A ARG* 3.5 54.5 - - + +
1469A ARG* 3.9 31.9 - - + +
1472A LEU* 6.5 0.4 - - + -
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Residues in contact with ASN1417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1403A LYS* 4.0 15.6 - - - +
1410A TYR 4.5 2.4 + - - -
1411A TYR* 3.1 65.0 + - - +
1412A PHE* 5.8 0.2 - - - -
1414A VAL* 3.0 17.1 + - + +
1416A TRP* 1.3 76.6 - - - +
1418A ILE* 1.3 64.6 + - - +
1420A ASP* 3.3 16.3 - - - +
1421A PHE* 3.2 21.0 + - - +
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Residues in contact with ILE1418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1411A TYR 5.3 0.2 - - - -
1412A PHE* 3.3 31.2 - - + +
1413A THR 4.0 8.3 - - - +
1414A VAL 3.0 15.1 + - - +
1415A GLY* 3.8 15.0 - - - +
1416A TRP 3.2 0.2 - - - -
1417A ASN* 1.3 77.9 - - - +
1419A PHE* 1.3 62.6 + - - +
1421A PHE* 3.4 10.5 + - - +
1422A VAL* 3.3 24.2 + - + +
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Residues in contact with PHE1419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415A GLY 3.4 10.0 + - - +
1416A TRP* 3.1 25.4 + + + +
1418A ILE* 1.3 81.0 - - - +
1420A ASP* 1.3 64.6 + - - +
1422A VAL* 3.6 7.1 + - + +
1423A VAL* 3.3 32.8 + - + +
1456A GLY* 3.6 27.8 - - - -
1459A LEU* 3.8 35.4 - - + -
1460A ARG* 4.3 17.5 - - + -
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Residues in contact with ASP1420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1399A GLU* 3.5 12.4 - - - +
1400A CYS* 4.7 1.2 - - - +
1403A LYS* 5.2 4.5 + - - +
1411A TYR* 3.7 10.3 + - - -
1416A TRP 3.0 12.7 + - - +
1417A ASN* 3.3 24.5 - - - +
1418A ILE 3.3 0.2 - - - -
1419A PHE* 1.3 81.4 - - - +
1421A PHE* 1.3 63.1 + - - +
1423A VAL* 3.2 7.0 + - - +
1424A VAL* 3.1 28.4 + - - +
1460A ARG* 2.5 44.7 + - + +
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Residues in contact with PHE1421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400A CYS* 3.9 9.4 - - - -
1404A MET* 4.1 20.6 - - - -
1411A TYR* 3.1 35.0 - + + +
1412A PHE* 3.7 28.3 - + + -
1417A ASN 3.2 15.1 + - - +
1418A ILE* 3.4 6.0 + - - +
1419A PHE 3.3 0.2 - - - -
1420A ASP* 1.3 78.2 - - - +
1422A VAL* 1.3 67.4 + - + +
1424A VAL* 3.7 3.5 + - + +
1425A ILE* 3.3 52.9 + - + +
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Residues in contact with VAL1422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1418A ILE* 3.3 22.6 + - + +
1419A PHE* 4.0 8.3 - - + +
1420A ASP 3.3 0.6 - - - -
1421A PHE* 1.3 82.8 - - + +
1423A VAL* 1.3 59.8 + - + +
1425A ILE* 3.3 10.4 + - + +
1426A LEU* 2.9 42.4 + - + +
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Residues in contact with VAL1423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419A PHE* 3.3 32.3 - - + +
1420A ASP* 3.2 10.6 + - - +
1422A VAL* 1.3 77.3 - - + +
1424A VAL* 1.3 58.8 + - + +
1426A LEU* 4.1 6.4 - - + +
1427A SER* 2.7 40.1 + - - +
1453A ALA 4.9 6.5 - - - +
1456A GLY* 3.9 18.6 - - - +
1457A ARG* 3.7 39.7 - - + +
1460A ARG* 6.0 2.9 - - - +
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Residues in contact with VAL1424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1396A PHE* 3.4 21.3 - - + +
1397A THR* 3.8 28.9 + - + +
1399A GLU* 4.2 0.4 - - - +
1400A CYS* 3.8 32.5 - - + -
1420A ASP* 3.1 31.2 + - - +
1421A PHE* 4.0 5.4 - - + +
1422A VAL 3.3 0.2 - - - -
1423A VAL* 1.3 77.4 - - + +
1425A ILE* 1.3 65.6 + - + +
1427A SER* 3.8 6.9 + - - -
1428A ILE* 3.5 21.4 + - + +
1460A ARG* 4.4 2.9 - - - +
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Residues in contact with ILE1425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421A PHE* 3.3 52.9 + - + +
1422A VAL* 3.3 10.2 + - + +
1423A VAL 3.3 0.2 - - - -
1424A VAL* 1.3 80.0 - - + +
1426A LEU* 1.3 63.1 + - + +
1428A ILE* 3.3 12.0 + - - +
1429A VAL* 3.3 26.8 + - + +
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Residues in contact with LEU1426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1422A VAL* 2.9 31.9 + - + +
1423A VAL* 4.1 5.4 - - - +
1425A ILE* 1.3 75.8 - - + +
1427A SER* 1.3 60.6 + - - +
1429A VAL* 3.2 18.8 + - + +
1430A GLY* 2.9 25.1 + - - +
1450A ILE* 4.9 10.1 - - + +
1453A ALA* 3.7 37.2 - - + +
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Residues in contact with SER1427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393A ILE* 3.6 24.1 - - - +
1423A VAL* 2.7 33.2 + - - +
1424A VAL* 4.1 6.2 - - - -
1425A ILE 3.3 0.2 - - - -
1426A LEU* 1.3 78.0 - - - +
1428A ILE* 1.3 60.9 + - - +
1430A GLY* 3.3 10.6 + - - +
1431A LEU 3.5 7.1 + - - -
1453A ALA 4.9 5.2 + - - -
1454A ARG* 5.0 4.1 - - - +
1457A ARG* 3.1 33.2 + - - +
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Residues in contact with ILE1428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393A ILE* 3.7 24.7 - - + -
1397A THR* 3.8 24.0 - - + +
1424A VAL* 3.5 19.3 - - + +
1425A ILE* 3.3 9.1 + - - +
1426A LEU 3.3 0.2 - - - -
1427A SER* 1.3 72.8 - - - +
1429A VAL* 1.3 65.5 + - + +
1431A LEU* 3.1 17.6 + - + +
1432A ALA* 3.2 17.7 + - + +
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Residues in contact with VAL1429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425A ILE* 3.3 23.8 - - + +
1426A LEU* 3.2 22.9 + - + +
1428A ILE* 1.3 78.1 - - + +
1430A GLY* 1.3 57.3 + - - +
1431A LEU 3.1 5.2 + - - -
1432A ALA* 4.1 3.1 - - - +
1433A LEU* 3.2 45.8 + - + +
1450A ILE* 5.5 4.3 - - + -
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Residues in contact with GLY1430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426A LEU* 2.9 14.7 + - - -
1427A SER* 3.3 7.4 + - - -
1428A ILE 3.2 0.6 - - - -
1429A VAL* 1.3 74.5 - - - +
1431A LEU* 1.3 57.6 + - - +
1433A LEU* 4.5 3.0 - - - +
1434A SER* 3.6 13.3 + - - -
1450A ILE* 4.3 22.1 - - - +
1451A ARG* 5.0 15.7 + - - +
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Residues in contact with LEU1431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386A TYR* 3.6 40.4 + - + +
1390A MET* 4.2 31.0 - - + -
1393A ILE* 3.8 37.0 - - + -
1427A SER 3.5 1.2 + - - -
1428A ILE* 3.1 12.9 + - + +
1429A VAL 3.1 0.8 - - - -
1430A GLY* 1.3 78.5 - - - +
1432A ALA* 1.3 64.6 + - - +
1433A LEU 3.2 1.6 - - - -
1434A SER* 3.3 21.0 + - - +
1435A ASP 4.6 0.7 + - - -
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Residues in contact with ALA1432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428A ILE* 3.2 15.5 + - + +
1429A VAL* 4.5 3.4 - - - +
1431A LEU* 1.3 77.0 - - - +
1433A LEU* 1.3 68.8 + - + +
1434A SER 3.1 1.6 + - - -
1435A ASP* 3.6 13.0 + - - +
1436A LEU* 3.9 6.6 + - - +
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Residues in contact with LEU1433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429A VAL* 3.2 46.3 + - + +
1430A GLY* 4.9 5.2 - - - +
1431A LEU 3.2 0.2 - - - -
1432A ALA* 1.3 80.9 - - + +
1434A SER* 1.3 58.1 + - - +
1435A ASP 3.2 0.7 - - - -
1436A LEU* 2.9 36.3 + - + +
1437A ILE* 2.9 43.8 + - + +
1446A LEU* 6.5 0.2 - - + -
1447A PHE* 5.8 0.2 - - - -
1450A ILE* 4.9 19.3 - - + -
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Residues in contact with SER1434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386A TYR* 5.4 12.0 - - - -
1430A GLY 3.6 13.9 + - - -
1431A LEU* 3.4 16.3 + - - +
1432A ALA 3.1 1.4 - - - -
1433A LEU* 1.3 78.9 - - - +
1435A ASP* 1.3 58.8 + - - +
1437A ILE* 4.2 3.0 - - - +
1438A GLN* 3.9 14.2 + - - +
1447A PHE* 3.8 28.6 - - - -
1451A ARG* 5.1 3.8 + - - -
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Residues in contact with ASP1435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431A LEU 4.6 0.8 + - - -
1432A ALA 3.6 9.8 + - - +
1433A LEU 3.2 0.2 - - - -
1434A SER* 1.3 77.2 - - - +
1436A LEU* 1.3 61.3 + - - +
1437A ILE 3.3 0.4 - - - -
1438A GLN* 3.2 13.6 + - - +
1439A LYS* 2.9 33.0 + - - +
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Residues in contact with LEU1436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432A ALA 3.9 3.0 + - - +
1433A LEU* 2.9 39.2 + - + +
1435A ASP* 1.3 79.9 - - - +
1437A ILE* 1.3 59.3 + - + +
1439A LYS* 3.1 31.6 + - + +
1440A TYR* 2.7 60.0 + - + +
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Residues in contact with ILE1437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433A LEU* 2.9 29.4 + - + +
1434A SER 4.5 3.1 - - - +
1435A ASP 3.3 0.2 - - - -
1436A LEU* 1.3 83.4 - - + +
1438A GLN* 1.3 59.5 + - - +
1440A TYR* 3.0 39.4 + - + +
1441A PHE 3.6 5.1 - - - +
1443A SER* 3.7 30.1 - - - +
1446A LEU* 3.8 30.5 - - + +
1447A PHE* 3.7 33.9 - - + +
1450A ILE* 5.5 2.2 - - + -
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Residues in contact with GLN1438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1434A SER 3.9 11.8 + - - +
1435A ASP* 3.2 20.9 + - - +
1437A ILE* 1.3 79.2 - - - +
1439A LYS* 1.3 60.2 + - - +
1440A TYR 3.3 7.4 - - - +
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Residues in contact with LYS1439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435A ASP* 2.9 23.3 + - - +
1436A LEU* 3.1 32.3 + - + +
1438A GLN* 1.3 76.1 - - - +
1440A TYR* 1.3 65.5 + - + +
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Residues in contact with TYR1440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436A LEU* 2.7 48.3 + - + +
1437A ILE* 3.0 25.8 + - + +
1438A GLN* 3.3 6.9 - - - +
1439A LYS* 1.3 86.5 - - + +
1441A PHE* 1.3 86.3 + + + +
1446A LEU* 5.3 5.4 - - + -
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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