Contacts of the helix formed by residues 1012 - 1032 (chain A) in PDB entry 4M76
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 GLU1012 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A ALA* 3.1 1.0 - - + +
1011A GLY* 1.3 80.8 - - - +
1013A GLN* 1.3 65.5 + - - +
1014A ASN 3.2 2.2 + - - -
1015A MET* 3.4 4.7 + - - +
1016A ILE* 3.2 28.3 + - - +
1068A ALA* 3.3 32.5 + - + +
1072A ARG* 4.6 2.6 + - - -
1075A SER* 5.5 0.9 - - - -
1078A LEU* 3.8 23.1 - - + +
1124A VAL* 3.3 25.1 - - + +
1125A ILE* 3.1 29.2 + - - +
1126A HIS* 3.1 28.7 + - + +
1129A MET* 3.9 10.1 - - - +
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Residues in contact with GLN1013 (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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1008A SER 3.3 20.9 + - - +
1009A GLY* 3.7 4.7 - - - -
1010A ALA* 3.4 21.3 + - + +
1012A GLU* 1.3 78.2 - - - +
1014A ASN* 1.3 60.6 + - - +
1016A ILE* 3.5 14.3 + - - +
1017A GLY* 3.5 15.2 + - - -
1126A HIS* 3.0 34.7 + - + -
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Residues in contact with ASN1014 (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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1007A PRO* 3.3 15.1 - - - +
1008A SER 3.7 8.3 + - - +
1009A GLY 4.2 9.2 - - - +
1010A ALA 3.0 18.7 + - - +
1013A GLN* 1.3 76.6 - - - +
1015A MET* 1.3 58.9 - - - +
1017A GLY* 3.3 2.9 + - - -
1018A MET* 2.8 33.4 + - - +
1052A GLY* 2.9 29.5 + - - -
1055A GLN* 2.9 34.7 + - + -
1056A GLN* 3.2 22.0 + - - +
1059A PHE* 5.2 1.6 - - + -
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Residues in contact with MET1015 (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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1011A GLY 3.7 5.8 - - - +
1012A GLU* 3.4 7.9 + - - +
1014A ASN* 1.3 76.3 - - - +
1016A ILE* 1.3 60.5 + - - +
1018A MET* 3.8 20.0 - - + +
1019A THR* 2.8 36.4 + - - -
1056A GLN* 3.4 43.7 - - - +
1078A LEU* 4.5 4.5 - - + -
1081A TYR* 4.4 9.2 - - + -
1082A VAL* 4.3 22.2 - - + -
1085A VAL* 3.8 42.0 - - + -
1086A PHE* 4.5 4.7 - - + -
1129A MET* 4.4 12.6 - - + -
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Residues in contact with ILE1016 (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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1012A GLU 3.2 15.2 + - - +
1013A GLN* 3.6 16.6 - - - +
1014A ASN 3.2 0.6 - - - -
1015A MET* 1.3 78.4 - - - +
1017A GLY* 1.3 57.5 + - - +
1019A THR* 4.1 1.9 - - - -
1020A PRO* 3.1 20.4 - - - +
1126A HIS* 4.1 29.6 - - + -
1128A GLU* 4.3 6.5 - - + +
1129A MET* 3.7 28.5 - - + -
1265A GLY 6.0 2.2 - - - +
1269A THR* 3.8 24.9 + - - +
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Residues in contact with GLY1017 (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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1005A VAL* 3.5 37.2 - - - +
1006A THR 5.0 0.2 - - - -
1007A PRO* 4.4 12.1 - - - -
1008A SER 5.5 0.7 - - - -
1013A GLN 3.5 6.0 + - - -
1014A ASN 3.3 6.1 + - - -
1015A MET 3.3 0.2 - - - -
1016A ILE* 1.3 80.2 - - - +
1018A MET* 1.3 62.1 + - - +
1020A PRO* 3.4 12.7 - - - +
1021A THR* 3.6 1.7 + - - -
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Residues in contact with MET1018 (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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1007A PRO* 4.4 11.2 - - + -
1014A ASN* 2.8 17.8 + - - +
1015A MET* 3.3 29.8 + - + +
1017A GLY* 1.3 77.8 - - - +
1019A THR* 1.3 64.6 + - - +
1021A THR* 3.3 7.4 + - - -
1022A VAL* 3.1 47.0 + - + +
1049A ILE* 3.8 28.0 - - + +
1052A GLY* 3.8 22.0 - - - +
1053A TYR* 3.9 8.1 - - + +
1085A VAL* 4.4 4.5 - - + -
1086A PHE* 3.5 28.9 - - + -
1089A ALA* 5.6 2.2 - - + -
1093A ILE* 5.2 1.3 - - + -
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Residues in contact with THR1019 (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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1015A MET* 2.8 22.8 + - - +
1018A MET* 1.3 76.9 - - - +
1020A PRO* 1.3 69.8 - - + +
1022A VAL* 3.4 5.5 + - - +
1023A ILE* 3.2 22.3 + - - +
1081A TYR* 2.5 36.6 + - - +
1085A VAL* 4.2 7.3 - - - +
1269A THR* 3.6 29.2 - - + +
1272A THR* 5.1 1.3 - - - -
1273A PHE* 3.6 23.3 - - + +
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Residues in contact with PRO1020 (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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1003A LEU* 3.4 32.4 - - + +
1005A VAL* 3.7 20.4 - - + -
1016A ILE 3.1 19.7 - - - +
1017A GLY 3.4 14.1 - - - +
1019A THR* 1.3 91.7 - - + +
1021A THR* 1.3 57.1 + - - +
1023A ILE* 3.4 11.0 - - + +
1024A ALA* 2.9 30.3 + - - +
1264A GLY* 5.8 2.2 - - - +
1269A THR* 6.0 0.4 - - + -
1272A THR* 4.2 10.5 - - + -
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Residues in contact with THR1021 (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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1003A LEU 3.3 6.3 + - - +
1004A ILE* 4.9 4.3 - - + -
1005A VAL 2.8 38.7 + - - +
1007A PRO* 6.0 0.7 - - - -
1017A GLY 3.6 3.7 + - - -
1018A MET* 3.3 8.5 + - - -
1019A THR 3.3 0.4 - - - -
1020A PRO* 1.3 77.2 - - - +
1022A VAL* 1.3 65.5 + - - +
1024A ALA* 3.2 12.6 + - - +
1025A VAL* 3.3 15.9 + - - +
1045A ALA* 3.8 22.7 - - + +
1048A LEU* 4.4 12.3 - - + -
1049A ILE* 3.7 23.3 - - + +
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Residues in contact with VAL1022 (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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1018A MET* 3.1 36.4 + - + +
1019A THR 3.9 3.4 - - - +
1021A THR* 1.3 77.4 - - - +
1023A ILE* 1.3 61.3 + - - +
1025A VAL* 3.5 5.0 - - - +
1026A HIS* 3.3 21.5 + - - +
1049A ILE* 3.7 33.4 - - + -
1085A VAL* 4.2 17.3 - - + +
1088A LEU* 3.9 20.4 - - + -
1089A ALA* 3.9 21.1 - - + -
1092A LEU* 3.9 4.3 - - + +
1273A PHE* 5.2 2.7 - - + -
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Residues in contact with ILE1023 (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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1003A LEU* 5.1 0.7 - - + -
1019A THR 3.2 14.2 + - - +
1020A PRO* 3.4 15.9 - - + +
1022A VAL* 1.3 77.0 - - - +
1024A ALA* 1.3 65.7 + - - +
1026A HIS* 3.9 13.0 - - + -
1027A TYR* 3.3 21.8 + - - +
1088A LEU* 3.8 34.5 - - + -
1272A THR* 3.8 21.3 - - + +
1273A PHE* 3.6 37.7 - - + +
1276A PHE* 3.7 19.9 - - + +
1277A GLN* 4.0 8.1 - - + +
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Residues in contact with ALA1024 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A LEU* 5.1 5.6 - - + +
1003A LEU* 3.9 25.1 - - + -
1004A ILE* 4.4 15.5 - - + -
1020A PRO 2.9 19.6 + - - +
1021A THR* 3.5 8.5 - - - +
1022A VAL 3.2 0.2 - - - -
1023A ILE* 1.3 79.3 - - - +
1025A VAL* 1.3 57.8 - - - +
1027A TYR* 3.3 3.7 + - - +
1028A LEU* 3.1 38.1 + - + +
1276A PHE* 6.2 0.4 - - - -
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Residues in contact with VAL1025 (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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1004A ILE* 5.1 3.1 - - + -
1021A THR 3.3 9.2 + - - +
1022A VAL 3.5 11.7 - - - +
1024A ALA* 1.3 75.6 - - + +
1026A HIS* 1.3 61.8 + - - +
1027A TYR 3.3 0.2 - - - -
1028A LEU 3.7 0.4 - - - -
1029A ASP* 2.8 38.2 + - - +
1034A TRP* 3.8 33.4 - - + -
1042A ARG* 5.2 3.8 - - + +
1045A ALA* 4.1 23.6 - - + -
1046A LEU* 5.1 4.3 - - + +
1049A ILE* 3.6 25.1 - - + -
1092A LEU* 3.7 19.1 - - + -
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Residues in contact with HIS1026 (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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1022A VAL 3.3 15.8 + - - +
1023A ILE* 3.9 22.2 - - + +
1024A ALA 3.2 0.4 - - - -
1025A VAL* 1.3 84.0 - - - +
1027A TYR* 1.3 61.7 + - - +
1029A ASP* 3.6 8.1 + - - +
1030A GLU* 3.4 22.7 + - + +
1088A LEU* 3.5 41.2 + - + +
1091A ASN* 5.3 9.6 + - - -
1092A LEU* 4.8 6.8 - - + +
1276A PHE 4.6 0.9 - - - -
1277A GLN* 4.8 6.6 + - - +
1280A ALA* 4.1 20.8 - - + +
1281A GLN 5.7 0.2 + - - -
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Residues in contact with TYR1027 (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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994A ALA* 3.7 7.1 - - - +
995A VAL* 2.8 45.7 + - + +
1000A LEU* 3.9 11.7 - - + -
1023A ILE 3.3 15.4 + - - +
1024A ALA* 3.7 4.5 - - - +
1025A VAL 3.3 0.4 - - - -
1026A HIS* 1.3 79.2 - - - +
1028A LEU* 1.3 72.6 + - + +
1030A GLU* 3.3 2.8 + - - +
1031A THR* 2.9 52.0 + - + +
1033A GLN* 3.8 13.0 - - - -
1276A PHE* 3.8 25.8 - + + +
1279A LEU* 4.0 16.2 - - + +
1280A ALA* 3.7 36.1 - - + -
1283A GLN* 4.3 4.0 + - + -
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Residues in contact with LEU1028 (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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997A ALA* 4.0 28.9 - - + +
1000A LEU* 3.9 18.8 - - + -
1004A ILE* 6.6 0.2 - - + -
1024A ALA* 3.1 24.0 + - + +
1027A TYR* 1.3 93.2 - - + +
1029A ASP* 1.3 59.5 + - - +
1031A THR* 3.5 5.4 - - - +
1032A GLU* 2.9 26.8 + - - -
1033A GLN* 3.3 14.7 + - + +
1034A TRP* 3.4 45.0 + - + -
1037A PHE* 4.2 17.0 - - + -
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Residues in contact with ASP1029 (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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1025A VAL* 2.8 26.6 + - - +
1026A HIS* 3.6 8.1 - - - +
1027A TYR 3.2 0.4 - - - -
1028A LEU* 1.3 78.8 - - - +
1030A GLU* 1.3 61.6 + - - +
1032A GLU* 3.4 19.1 - - - +
1034A TRP* 2.9 24.6 + - - +
1042A ARG* 3.3 27.0 + - - -
1091A ASN* 5.5 2.8 + - - +
1092A LEU* 3.6 15.7 - - - +
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Residues in contact with GLU1030 (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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1026A HIS* 3.4 12.8 + - + +
1027A TYR 3.3 7.6 + - - +
1029A ASP* 1.3 82.5 - - - +
1031A THR* 1.3 63.8 + - + +
1032A GLU* 3.1 11.3 + - - +
1280A ALA* 3.6 29.2 - - + +
1283A GLN* 4.4 6.4 - - + -
1284A LYS* 3.3 44.0 - - + +
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Residues in contact with THR1031 (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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994A ALA* 3.7 17.5 - - + -
1027A TYR* 2.9 55.2 + - + +
1028A LEU* 3.5 8.0 - - - -
1030A GLU* 1.3 73.3 - - + +
1032A GLU* 1.3 73.0 + - - +
1033A GLN* 3.0 29.4 + - - +
1280A ALA* 5.4 0.2 - - - -
1283A GLN* 3.8 17.7 - - + -
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Residues in contact with GLU1032 (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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1028A LEU 2.9 15.0 + - - -
1029A ASP 3.4 15.5 - - - +
1030A GLU 3.1 9.5 - - - +
1031A THR* 1.3 81.9 - - - +
1033A GLN* 1.3 58.5 + - - +
1034A TRP* 3.5 7.9 + - + +
1035A GLU* 4.0 10.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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