Contacts of the helix formed by residues 1105 - 1126 (chain B) in PDB entry 1M7N
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 SER1105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103B PRO 3.5 1.6 + - - -
1104B PRO* 1.3 73.6 - - - +
1106B LEU* 1.3 66.4 + - - +
1107B SER* 3.4 11.4 + - - -
1108B LYS* 2.8 40.7 + - - +
1109B MET* 3.0 14.6 + - - +
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Residues in contact with LEU1106 (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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1104B PRO 4.1 0.2 + - - -
1105B SER* 1.3 72.5 - - - +
1107B SER* 1.3 58.6 + - - +
1109B MET* 3.3 11.9 + - + +
1110B ILE* 2.9 55.9 + - + +
1235B PRO* 3.3 39.4 - - + +
1237B MET* 4.2 27.4 - - + -
1238B LEU* 4.7 10.1 - - + -
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Residues in contact with SER1107 (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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1105B SER* 3.0 10.8 + - - -
1106B LEU* 1.3 80.8 - - - +
1108B LYS* 1.3 61.6 + - - +
1110B ILE* 3.5 9.3 + - - +
1111B GLN* 3.3 22.7 + - - +
1266B GLU* 4.7 11.3 + - - +
1268B GLU* 4.9 8.7 + - - -
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Residues in contact with LYS1108 (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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1104B PRO* 4.2 13.0 - - + +
1105B SER* 2.8 36.4 + - - +
1107B SER* 1.3 73.6 - - - +
1109B MET* 1.3 62.0 + - - +
1111B GLN* 3.2 21.3 + - + +
1112B MET* 3.2 17.0 + - - +
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Residues in contact with MET1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104B PRO* 3.7 33.7 - - + +
1105B SER 3.0 11.8 + - - +
1106B LEU* 3.7 9.6 - - - +
1108B LYS* 1.3 75.0 - - - +
1110B ILE* 1.3 58.9 + - - +
1112B MET* 3.5 7.3 + - - +
1113B ALA* 2.9 28.1 + - - +
1199B LEU* 5.4 0.2 - - - +
1202B ILE* 3.7 43.3 - - + +
1203B ALA* 4.3 6.5 - - + -
1235B PRO* 3.8 34.5 - - + -
1238B LEU* 4.0 24.3 - - + +
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Residues in contact with ILE1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B LEU* 2.9 37.5 + - + +
1107B SER* 3.8 7.2 - - - +
1109B MET* 1.3 74.5 - - - +
1111B GLN* 1.3 57.0 + - - +
1113B ALA* 3.3 6.8 - - - +
1114B GLY* 2.8 29.3 + - - -
1237B MET* 3.6 35.2 - - + -
1238B LEU* 5.1 5.4 - - + -
1263B ILE* 3.9 14.7 - - + +
1266B GLU* 3.5 47.6 - - + +
1267B MET* 3.3 13.2 - - - +
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Residues in contact with GLN1111 (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 SER 3.3 10.1 + - - +
1108B LYS* 3.2 13.7 + - + +
1110B ILE* 1.3 77.4 - - - +
1112B MET* 1.3 56.7 + - + +
1114B GLY 3.3 0.3 + - - -
1115B GLU* 2.7 65.2 + - - +
1266B GLU 4.1 3.1 - - - +
1267B MET* 3.6 28.3 - - - +
1268B GLU* 2.8 58.5 + - + +
1271B PHE* 4.4 7.1 - - - +
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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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1084B LEU* 3.5 32.3 - - + -
1087B TYR* 4.0 20.4 - - + +
1088B LEU* 5.4 3.6 - - + -
1104B PRO* 5.9 6.3 - - - -
1108B LYS* 3.2 18.4 + - - +
1109B MET* 3.8 7.4 - - - +
1110B ILE 3.4 0.2 - - - -
1111B GLN* 1.3 77.1 - - + +
1113B ALA* 1.3 55.0 + - - +
1115B GLU* 3.6 9.5 - - - +
1116B ILE* 2.8 44.2 + - + +
1140B VAL* 5.2 1.8 - - + -
1144B PHE 5.1 4.7 - - - +
1146B VAL* 3.8 22.9 - - + -
1202B ILE* 4.0 30.1 - - + -
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Residues in contact with ALA1113 (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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1109B MET 2.9 19.1 + - - +
1110B ILE* 3.3 10.1 - - - +
1112B MET* 1.3 76.5 - - - +
1114B GLY* 1.3 59.0 + - - +
1116B ILE* 3.3 1.5 + - - -
1117B ALA* 2.9 30.2 + - - +
1195B PHE* 3.5 11.3 - - + -
1199B LEU* 3.8 29.6 - - + -
1202B ILE* 4.7 0.8 - - - +
1238B LEU* 5.1 6.1 - - + -
1241B LEU* 5.3 5.2 - - + -
1263B ILE* 4.3 9.6 - - + -
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Residues in contact with GLY1114 (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 ILE 2.8 14.9 + - - -
1113B ALA* 1.3 73.3 - - - +
1115B GLU* 1.3 56.9 + - - +
1117B ALA* 3.9 5.5 - - - +
1118B ASP* 3.1 28.8 + - - +
1260B ILE* 4.3 4.6 - - - +
1263B ILE* 3.8 15.0 - - - +
1267B MET* 3.4 24.0 - - - -
1271B PHE* 3.7 6.4 - - - -
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Residues in contact with GLU1115 (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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1058B HIS* 3.3 53.2 + - + +
1111B GLN* 2.7 52.9 + - - +
1112B MET* 3.7 7.5 + - - +
1114B GLY* 1.3 70.5 - - - +
1116B ILE* 1.3 64.1 + - - +
1118B ASP 3.7 0.2 + - - -
1119B GLY 3.6 4.2 + - - -
1144B PHE 4.3 1.6 - - - +
1145B THR* 3.5 23.4 + - - +
1146B VAL* 2.9 41.9 + - + +
1267B MET* 4.5 2.2 - - + -
1271B PHE* 4.4 1.6 - - + -
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Residues in contact with ILE1116 (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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1084B LEU* 4.0 18.6 - - + -
1112B MET* 2.8 27.2 + - + +
1113B ALA* 3.8 3.1 - - - +
1115B GLU* 1.3 75.1 - - - +
1117B ALA* 1.3 62.1 + - - +
1118B ASP 3.1 0.2 - - - -
1119B GLY 3.1 2.9 + - - -
1120B MET* 3.0 26.9 + - + +
1133B LEU* 4.5 8.5 - - + -
1138B CYS* 4.1 12.3 - - - -
1146B VAL* 4.0 18.4 - - + -
1147B LYS* 6.0 0.2 - - - +
1148B ILE* 3.5 24.4 - - + +
1195B PHE* 4.0 20.0 - - + -
1198B VAL* 3.7 28.0 - - + -
1202B ILE* 4.1 10.3 - - + -
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Residues in contact with ALA1117 (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 ALA 2.9 18.4 + - - +
1114B GLY* 3.9 3.4 - - - +
1116B ILE* 1.3 77.0 - - - +
1118B ASP* 1.3 57.4 + - - +
1120B MET* 3.8 0.7 - - - -
1121B ALA* 2.9 28.9 + - - +
1195B PHE* 3.9 16.7 - - + -
1256B PHE* 3.5 25.8 - - + +
1259B ILE* 4.4 7.2 - - + -
1260B ILE* 3.6 22.3 - - + +
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Residues in contact with ASP1118 (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 CYS* 4.2 2.9 - - - -
1058B HIS* 3.1 22.7 + - - +
1114B GLY 3.1 18.2 + - - +
1115B GLU 3.8 6.7 - - - +
1116B ILE 3.1 0.4 - - - -
1117B ALA* 1.3 75.4 - - - +
1119B GLY* 1.3 65.4 + - - +
1121B ALA* 3.4 1.3 + - - +
1122B TYR* 2.9 22.9 + - - +
1260B ILE* 3.6 8.6 - - + +
1271B PHE* 3.9 8.7 - - + -
1275B SER* 3.3 8.0 - - - -
1276B PHE* 2.8 26.4 + - - +
1277B TYR* 2.9 34.1 + - - +
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Residues in contact with GLY1119 (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 CYS* 4.2 3.1 - - - -
1058B HIS* 3.7 14.0 - - - +
1059B VAL* 3.7 21.3 - - - +
1115B GLU 3.6 4.6 + - - -
1116B ILE 3.1 6.2 + - - -
1118B ASP* 1.3 78.8 - - - +
1120B MET* 1.3 64.0 + - - +
1122B TYR* 3.1 4.3 + - - +
1123B LEU* 3.0 26.2 + - - +
1148B ILE* 3.8 8.7 - - - -
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Residues in contact with MET1120 (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 ILE* 3.0 19.8 + - + +
1117B ALA 3.8 0.2 - - - +
1119B GLY* 1.3 77.0 - - - +
1121B ALA* 1.3 57.9 + - - +
1123B LEU* 3.3 18.8 + - + +
1124B ASN* 2.8 41.3 + - - +
1129B VAL 5.1 0.2 - - - -
1130B HIS* 3.8 18.8 - - + +
1133B LEU* 3.8 22.9 - - + -
1148B ILE* 3.9 14.3 - - + +
1191B ASP* 3.6 40.6 - - + +
1256B PHE* 3.3 35.7 - - + -
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Residues in contact with ALA1121 (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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1117B ALA 2.9 19.8 + - - +
1118B ASP 3.8 4.0 - - - +
1119B GLY 3.3 0.2 - - - -
1120B MET* 1.3 73.5 - - - +
1122B TYR* 1.3 57.4 + - - +
1124B ASN* 3.6 5.1 - - - +
1125B ALA* 2.7 36.9 + - - +
1256B PHE* 3.7 17.2 - - + +
1257B LEU* 4.0 26.5 - - + +
1260B ILE* 4.3 4.7 - - + -
1276B PHE* 3.9 10.8 - - + -
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Residues in contact with TYR1122 (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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1053B GLU 3.5 14.0 + - - -
1054B PHE* 3.8 24.7 - + + -
1055B ASN* 3.4 30.3 + - - +
1056B CYS* 3.5 35.0 - - + -
1059B VAL* 4.6 2.7 - - + -
1118B ASP 2.9 15.5 + - - +
1119B GLY 3.2 7.9 - - - +
1121B ALA* 1.3 79.0 - - - +
1123B LEU* 1.3 75.5 + - + +
1125B ALA* 3.0 10.6 + - - +
1126B ASN* 3.0 34.5 + - - -
1276B PHE* 3.7 35.1 - + + -
1281B GLU* 6.0 5.4 - - - -
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Residues in contact with LEU1123 (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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1054B PHE* 3.7 37.7 - - + -
1059B VAL* 4.4 10.8 - - + -
1119B GLY 3.0 15.2 + - - +
1120B MET* 3.6 28.0 - - + +
1122B TYR* 1.3 88.1 - - + +
1124B ASN* 1.3 65.5 + - - +
1126B ASN* 3.0 14.3 + - - +
1127B LYS 3.1 0.2 + - - -
1128B PHE* 2.9 37.4 + - + +
1129B VAL 5.8 3.1 - - - +
1130B HIS* 5.1 5.4 - - + -
1148B ILE* 4.1 21.5 - - + -
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Residues in contact with ASN1124 (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 MET* 2.8 31.6 + - - +
1121B ALA* 3.8 5.8 - - - +
1123B LEU* 1.3 70.4 - - - +
1125B ALA* 1.3 64.2 + - - +
1127B LYS* 3.0 13.5 + - - +
1128B PHE 2.9 22.1 + - - +
1188B THR* 3.1 37.6 - - + +
1191B ASP* 3.4 16.2 + - - -
1256B PHE* 3.0 27.6 - - + -
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Residues in contact with ALA1125 (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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1121B ALA 2.7 17.2 + - - +
1122B TYR 3.0 10.5 + - - +
1124B ASN* 1.3 75.6 - - - +
1126B ASN* 1.3 63.8 + - - +
1127B LYS* 3.0 13.3 + - - +
1257B LEU* 6.3 1.6 - - + -
1276B PHE* 3.7 25.6 - - + -
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Residues in contact with ASN1126 (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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1053B GLU* 4.3 11.4 - - - +
1054B PHE* 4.8 5.5 - - + -
1122B TYR* 3.0 40.6 + - - +
1123B LEU* 3.0 10.5 + - - +
1125B ALA* 1.3 79.2 - - - +
1127B LYS* 1.3 75.7 + - - +
1128B PHE* 3.5 24.2 - - + -
1276B PHE* 5.8 1.2 - - - -
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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) + - + + + + + -
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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