Contacts of the helix formed by residues 1108 - 1129 (chain B) in PDB entry 2ZM3
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 SER1108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107B PRO* 1.3 78.5 - - - +
1109B LEU* 1.3 64.2 + - - +
1110B SER* 3.7 8.7 + - - -
1111B LYS* 3.1 29.4 + - - +
1112B MET* 3.1 18.9 + - - +
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Residues in contact with LEU1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107B PRO 3.7 1.4 + - - -
1108B SER* 1.3 72.0 - - - +
1110B SER* 1.3 53.2 + - - +
1112B MET* 3.3 6.8 + - + -
1113B ILE* 2.8 60.8 + - + +
1238B PRO* 3.7 42.1 - - + +
1240B MET* 4.4 21.3 - - + -
1241B LEU* 4.4 15.9 - - + -
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Residues in contact with SER1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108B SER* 3.1 9.0 + - - -
1109B LEU* 1.3 76.6 - - - +
1111B LYS* 1.3 68.7 + - - +
1113B ILE* 3.4 8.1 + - - +
1114B GLN* 2.9 24.1 + - - +
1269B GLU* 5.2 8.3 - - - +
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Residues in contact with LYS1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107B PRO* 4.2 15.0 - - + -
1108B SER* 3.1 25.8 + - - +
1110B SER* 1.3 77.1 - - - +
1112B MET* 1.3 58.2 + - - +
1114B GLN* 3.1 9.1 + - + +
1115B MET* 2.9 41.3 + - + +
1271B GLU* 5.8 4.9 - - - +
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Residues in contact with MET1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B PRO* 3.9 7.4 - - - -
1107B PRO* 3.5 33.2 - - + +
1108B SER 3.1 12.6 + - - +
1109B LEU* 3.7 10.1 - - + +
1111B LYS* 1.3 72.8 - - - +
1113B ILE* 1.3 65.7 + - - +
1115B MET* 3.3 8.7 + - - +
1116B ALA* 2.9 25.6 + - - +
1202B LEU* 5.3 0.5 - - - +
1205B ILE* 3.5 25.4 - - + +
1206B ALA* 3.2 41.5 - - + +
1238B PRO* 4.9 8.3 - - + -
1241B LEU* 3.4 37.9 - - + -
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Residues in contact with ILE1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109B LEU* 2.8 39.3 + - + +
1110B SER* 3.6 7.4 - - - +
1112B MET* 1.3 71.6 - - - +
1114B GLN* 1.3 58.2 + - - +
1116B ALA* 3.6 5.4 - - + +
1117B GLY* 2.9 25.6 + - - -
1240B MET* 3.7 39.3 - - + -
1241B LEU* 4.1 12.8 - - + -
1244B LEU* 5.9 1.1 - - + -
1266B ILE* 3.9 21.0 - - + +
1269B GLU* 3.8 31.6 - - + +
1270B MET* 3.1 15.7 - - + +
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Residues in contact with GLN1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110B SER 2.9 13.7 + - - +
1111B LYS* 3.1 14.3 + - + +
1113B ILE* 1.3 76.0 - - - +
1115B MET* 1.3 64.2 + - + +
1117B GLY 3.2 1.7 + - - -
1118B GLU* 2.9 58.7 + - - +
1147B PHE 6.1 0.2 - - - +
1269B GLU 4.4 2.3 - - - +
1270B MET* 3.2 23.5 - - - +
1271B GLU* 2.9 60.3 + - - +
1274B PHE* 5.0 6.3 - - - +
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Residues in contact with MET1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B LEU* 4.3 17.7 - - + -
1090B TYR* 3.8 33.4 - - + +
1091B LEU* 4.6 7.0 - - + -
1094B LEU* 5.4 0.9 - - + -
1107B PRO* 5.3 6.3 - - + -
1111B LYS* 2.9 26.4 + - + +
1112B MET* 3.3 7.2 + - - +
1114B GLN* 1.3 77.5 - - + +
1116B ALA* 1.3 62.8 + - - +
1118B GLU* 3.3 11.2 + - - +
1119B ILE* 3.0 31.8 + - + +
1143B VAL* 6.1 1.1 - - + -
1147B PHE* 5.4 7.0 - - + +
1149B VAL* 3.8 17.9 - - + +
1205B ILE* 3.9 36.1 - - + -
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Residues in contact with ALA1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112B MET 2.9 18.2 + - - +
1113B ILE* 3.6 8.1 - - + +
1115B MET* 1.3 78.7 - - - +
1117B GLY* 1.3 56.3 + - - +
1119B ILE* 3.5 3.8 + - - -
1120B ALA* 2.9 31.9 + - - +
1198B PHE* 3.5 13.4 - - + -
1202B LEU* 3.5 31.0 - - + -
1205B ILE* 5.1 0.9 - - + +
1241B LEU* 5.4 3.1 - - + -
1244B LEU* 5.6 3.1 - - + -
1266B ILE* 4.4 8.7 - - + -
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Residues in contact with GLY1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B ILE 2.9 12.0 + - - -
1114B GLN 3.9 0.2 - - - -
1116B ALA* 1.3 76.3 - - - +
1118B GLU* 1.3 58.3 + - - +
1120B ALA* 4.0 3.8 - - - +
1121B ASP* 3.0 29.8 + - - +
1263B ILE* 4.4 4.6 - - - +
1266B ILE* 3.8 13.0 - - - +
1270B MET* 3.7 26.7 - - - -
1274B PHE* 4.0 6.2 - - - -
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Residues in contact with GLU1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061B HIS* 3.4 40.4 + - + +
1114B GLN* 2.9 50.7 + - - +
1115B MET* 3.7 8.0 - - - +
1117B GLY* 1.3 76.9 - - - +
1119B ILE* 1.3 63.8 + - - +
1121B ASP* 3.4 1.1 + - - -
1122B GLY* 3.2 17.5 + - - -
1147B PHE 4.3 1.6 - - - +
1148B THR* 3.7 21.4 + - - +
1149B VAL* 3.0 38.6 + - - +
1150B LYS* 6.0 0.2 - - - -
1274B PHE* 4.8 3.4 - - + -
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Residues in contact with ILE1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B LEU* 4.0 10.1 - - + -
1115B MET* 3.0 22.0 + - + +
1116B ALA* 3.9 5.2 - - - +
1118B GLU* 1.3 75.5 - - - +
1120B ALA* 1.3 64.4 + - - +
1122B GLY 3.2 1.7 + - - -
1123B MET* 3.0 23.6 + - + +
1136B LEU* 4.1 23.8 - - + -
1141B CYS* 4.2 8.7 - - - -
1149B VAL* 3.6 28.0 - - + -
1150B LYS* 6.1 0.2 - - - +
1151B ILE* 3.6 12.1 - - + +
1198B PHE* 3.7 22.4 - - + -
1201B VAL* 3.9 26.2 - - + -
1202B LEU* 6.4 0.2 - - + -
1205B ILE* 4.6 5.8 - - + -
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Residues in contact with ALA1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116B ALA 2.9 19.7 + - - +
1117B GLY* 4.0 2.5 - - - +
1119B ILE* 1.3 76.6 - - - +
1121B ASP* 1.3 58.5 + - - +
1123B MET* 3.2 3.3 + - - +
1124B ALA* 2.8 29.5 + - - +
1198B PHE* 3.8 16.6 - - + -
1259B PHE* 3.6 23.6 - - + +
1262B ILE* 4.5 8.7 - - + -
1263B ILE* 3.9 18.4 - - + -
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Residues in contact with ASP1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B CYS* 4.1 2.6 - - - -
1061B HIS* 2.6 27.3 + - - +
1117B GLY 3.0 21.4 + - - +
1118B GLU 3.7 5.4 - - - +
1119B ILE 3.3 0.2 - - - -
1120B ALA* 1.3 77.3 - - - +
1122B GLY* 1.3 57.0 + - - +
1124B ALA* 3.2 4.2 + - - +
1125B TYR* 3.0 26.0 + - - +
1263B ILE* 3.5 11.0 - - + +
1274B PHE* 3.8 6.5 - - + -
1278B SER* 3.4 9.5 - - - -
1279B PHE* 3.0 22.3 + - - +
1280B TYR* 2.9 34.3 + - - +
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Residues in contact with GLY1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B CYS* 4.7 2.5 - - - -
1061B HIS* 4.0 16.8 - - - +
1062B VAL* 4.6 2.5 - - - +
1118B GLU 3.2 11.2 + - - -
1119B ILE 3.2 0.2 + - - -
1121B ASP* 1.3 78.4 + - - +
1123B MET* 1.3 57.8 + - - +
1125B TYR* 3.2 10.3 + - - +
1126B LEU* 3.0 29.8 + - - +
1151B ILE* 3.4 19.1 - - - -
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Residues in contact with MET1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B ILE* 3.0 20.5 + - + +
1120B ALA 3.5 2.9 - - - +
1122B GLY* 1.3 72.2 - - - +
1124B ALA* 1.3 59.9 + - - +
1126B LEU* 3.3 13.4 + - + +
1127B ASN* 3.0 38.1 + - - +
1133B HIS* 3.7 15.9 - - + +
1136B LEU* 4.1 26.2 - - + -
1151B ILE* 3.5 18.8 - - + -
1194B ASP* 3.3 41.5 - - + +
1259B PHE* 3.4 36.8 - - + -
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Residues in contact with ALA1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120B ALA 2.8 14.0 + - - +
1121B ASP 3.2 9.8 + - - +
1123B MET* 1.3 72.9 - - - +
1125B TYR* 1.3 65.9 + - - +
1127B ASN* 3.6 3.8 + - - +
1128B ALA* 3.0 25.5 + - - +
1259B PHE* 3.8 18.7 - - + +
1260B LEU* 4.0 20.5 - - + +
1263B ILE* 3.9 15.3 - - + -
1279B PHE* 3.6 8.2 - - + -
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Residues in contact with TYR1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056B GLU 3.6 9.9 + - - -
1057B PHE* 4.1 19.0 - + + -
1058B ASN* 2.9 42.9 + - - +
1059B CYS* 3.7 29.4 - - + -
1062B VAL* 4.2 9.6 - - + -
1121B ASP 3.0 12.3 + - - +
1122B GLY 3.3 7.4 - - - +
1124B ALA* 1.3 74.2 - - - +
1126B LEU* 1.3 72.1 + - + +
1128B ALA* 3.3 3.1 + - - +
1129B ASN* 3.0 52.8 + - - -
1279B PHE* 3.5 35.4 - + + -
1284B GLU* 3.4 18.8 + - - -
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Residues in contact with LEU1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057B PHE* 3.7 33.2 - - + -
1062B VAL* 5.1 2.2 - - + -
1122B GLY 3.0 13.8 + - - +
1123B MET* 3.3 26.4 + - + +
1125B TYR* 1.3 82.1 - - + +
1127B ASN* 1.3 58.0 + - - +
1129B ASN* 3.0 21.4 + - - +
1130B LYS 3.1 7.8 + - - -
1131B PHE* 3.2 25.3 + - + +
1133B HIS* 3.9 25.4 - - + -
1151B ILE* 4.5 3.4 - - + -
1154B PHE* 3.4 38.4 - - + -
1157B THR* 5.4 0.7 - - + -
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Residues in contact with ASN1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123B MET* 3.0 25.8 + - - +
1124B ALA* 4.3 4.3 - - - +
1126B LEU* 1.3 74.3 - - - +
1128B ALA* 1.3 60.5 + - - +
1130B LYS* 3.0 30.1 + - - +
1131B PHE 3.0 21.4 + - - +
1132B VAL* 4.4 1.4 - - - +
1160B ILE* 4.1 9.5 - - - +
1191B THR* 2.9 43.2 + - - +
1194B ASP* 4.1 11.7 + - - -
1259B PHE* 3.7 16.7 - - + -
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Residues in contact with ALA1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124B ALA 3.0 19.7 + - - +
1125B TYR 3.6 3.1 - - - +
1127B ASN* 1.3 77.1 - - - +
1129B ASN* 1.3 59.6 + - - +
1130B LYS* 3.1 10.2 + - - +
1279B PHE* 3.5 27.4 - - + -
1284B GLU* 5.4 1.6 - - - +
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Residues in contact with ASN1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057B PHE* 5.3 4.0 - - + -
1125B TYR* 3.0 61.2 + - + -
1126B LEU* 3.0 11.4 + - - +
1128B ALA* 1.3 76.3 - - - +
1130B LYS* 1.3 70.0 + - - +
1131B PHE* 3.2 25.6 - - + -
1159B ASP* 5.0 0.5 - - - +
1284B GLU* 3.7 13.3 + - - +
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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