Contacts of the helix formed by residues 1181 - 1203 (chain M) in PDB entry 2X4Y
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 LYS1181 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180M ARG* 1.3 101.8 - - + +
1182M SER* 1.3 68.7 + - - +
1183M ASN* 3.2 20.1 + - - +
1184M ILE* 3.2 24.6 + - + +
1185M ARG* 3.1 26.2 + - - +
40N ARG* 6.4 0.4 - - - +
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Residues in contact with SER1182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185K ARG* 5.3 7.0 + - - -
1181M LYS* 1.3 73.3 - - - +
1183M ASN* 1.3 58.0 + - - +
1185M ARG* 3.3 27.5 + - - +
1186M LYS* 2.9 28.3 + - - +
1189M GLN* 5.6 0.2 + - - -
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Residues in contact with ASN1183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181M LYS* 3.5 22.2 - - - +
1182M SER* 1.3 75.2 - - - +
1184M ILE* 1.3 76.5 + - - +
1186M LYS* 3.4 12.2 + - - +
1187M SER* 3.2 22.5 + - - -
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Residues in contact with ILE1184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097M PRO* 3.5 36.6 - - + -
1179M GLY* 3.9 8.1 - - - -
1180M ARG* 4.1 32.8 - - + +
1181M LYS* 3.5 29.4 - - + +
1183M ASN* 1.3 90.3 - - - +
1185M ARG* 1.3 66.7 + - - +
1187M SER* 3.3 7.8 + - - -
1188M VAL* 3.1 23.2 + - + +
39N HIS* 5.8 1.3 - - - +
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Residues in contact with ARG1185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182E SER* 3.6 24.0 + - - -
1186E LYS* 3.5 28.5 - - - +
1176M MET 4.1 6.9 - - - +
1177M LEU* 3.8 19.7 - - - +
1179M GLY* 3.0 43.4 + - - +
1180M ARG 3.1 22.6 + - - -
1181M LYS 3.1 7.1 + - - +
1182M SER* 3.5 35.7 + - - +
1184M ILE* 1.3 81.2 - - - +
1186M LYS* 1.3 57.4 + - - +
1188M VAL* 3.2 9.0 + - - +
1189M GLN* 2.9 45.3 + - - +
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Residues in contact with LYS1186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177K LEU* 2.9 46.8 + - + +
1178K GLU 3.9 6.9 + - - -
1179K GLY 3.5 15.7 + - - -
1180K ARG* 4.9 8.5 - - - +
1185K ARG* 3.7 28.9 - - - +
1182M SER 2.9 17.4 + - - +
1183M ASN* 3.8 10.1 - - - +
1184M ILE 3.1 0.4 - - - -
1185M ARG* 1.3 78.5 - - - +
1187M SER* 1.3 56.3 + - - +
1189M GLN* 3.2 11.2 + - - +
1190M ILE* 2.9 39.9 + - + +
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Residues in contact with SER1187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099M TYR* 2.9 26.8 + - - -
1183M ASN 3.2 12.4 + - - -
1184M ILE* 3.3 10.5 + - - -
1186M LYS* 1.3 77.1 - - - +
1188M VAL* 1.3 62.7 + - - +
1190M ILE* 3.6 9.2 + - - +
1191M ALA* 3.0 24.4 + - - +
1194M ARG* 5.4 0.7 + - - -
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Residues in contact with VAL1188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M TRP* 3.7 31.2 - - + -
1097M PRO* 4.0 17.5 - - + -
1098M SER 4.0 11.7 - - - +
1099M TYR* 3.8 26.7 - - + -
1100M PRO* 3.9 2.6 - - + +
1175M LYS 4.7 2.0 - - - +
1176M MET* 4.2 18.2 - - + +
1179M GLY 5.9 1.6 - - - +
1184M ILE* 3.1 15.5 + - + +
1185M ARG* 3.5 11.0 - - - +
1186M LYS 3.2 0.2 - - - -
1187M SER* 1.3 77.2 - - - +
1189M GLN* 1.3 57.4 + - - +
1191M ALA* 3.2 4.4 + - - +
1192M TYR* 2.9 26.0 + - - +
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Residues in contact with GLN1189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177K LEU* 3.6 31.0 - - + +
1176M MET* 4.2 30.6 + - + +
1177M LEU* 6.0 3.4 - - - +
1185M ARG* 2.9 38.3 + - - +
1186M LYS* 3.2 7.2 + - - +
1188M VAL* 1.3 75.3 - - - +
1190M ILE* 1.3 65.8 + - - +
1192M TYR* 3.2 7.4 + - - +
1193M HIS* 3.1 33.4 + - + +
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Residues in contact with ILE1190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174K GLU* 4.0 20.5 - - + +
1177K LEU* 3.6 46.0 - - + +
1178K GLU* 4.7 4.5 - - - +
1186M LYS* 2.9 32.9 + - + +
1187M SER* 3.8 7.9 - - - +
1189M GLN* 1.3 76.3 - - - +
1191M ALA* 1.3 55.8 + - - +
1193M HIS* 3.2 5.0 + - - +
1194M ARG* 2.9 69.8 + - - +
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Residues in contact with ALA1191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099M TYR* 3.5 30.1 - - + +
1100M PRO* 3.7 8.0 - - + +
1148M PHE* 3.6 26.2 - - + +
1187M SER 3.0 18.8 + - - +
1188M VAL 3.4 5.4 - - - +
1189M GLN 3.2 0.2 - - - -
1190M ILE* 1.3 77.9 - - - +
1192M TYR* 1.3 57.4 + - - +
1194M ARG* 3.3 3.3 + - - +
1195M ALA* 2.9 28.6 + - - +
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Residues in contact with TYR1192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M TRP* 3.6 18.4 - + - -
1100M PRO* 3.6 10.7 - - + +
1165M LEU* 3.9 19.7 - - + -
1166M GLY* 4.6 1.4 - - - -
1169M GLN* 5.6 3.1 - - - +
1172M ASP* 2.8 46.3 + - + +
1176M MET* 3.7 31.3 - - + +
1188M VAL 2.9 13.6 + - - +
1189M GLN 3.4 8.5 - - - +
1191M ALA* 1.3 78.0 - - - +
1193M HIS* 1.3 79.3 + + - +
1195M ALA* 3.2 4.6 + - - +
1196M LEU* 3.0 54.3 + - + +
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Residues in contact with HIS1193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170K ASP* 3.0 43.0 + - + +
1173K LYS* 3.4 50.3 - - + +
1174K GLU* 4.1 7.6 - - + -
1177K LEU* 4.5 8.3 - - + +
1176M MET* 5.0 6.2 - - + -
1189M GLN* 3.1 28.7 + - + +
1190M ILE* 3.9 5.2 - - - +
1192M TYR* 1.3 94.5 - + - +
1194M ARG* 1.3 65.6 + - - +
1196M LEU 3.4 0.6 + - - +
1197M GLN* 3.0 32.0 + - - +
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Residues in contact with ARG1194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174K GLU* 3.3 30.7 + - - +
1099M TYR* 4.9 1.6 + - - -
1148M PHE* 2.9 39.4 + - + -
1149M ASP* 3.6 11.8 - - - +
1150M ASN* 2.5 33.1 + - - +
1187M SER 5.4 0.4 + - - -
1190M ILE* 2.9 40.6 + - - +
1191M ALA* 3.6 7.5 - - - +
1193M HIS* 1.3 77.7 - - - +
1195M ALA* 1.3 61.7 + - - +
1197M GLN* 3.3 9.6 + - - +
1198M HIS* 3.0 23.0 + - - +
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Residues in contact with ALA1195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 3.6 17.8 - - + +
1100M PRO* 4.2 9.2 - - + -
1148M PHE* 3.5 34.5 - - + -
1165M LEU* 4.3 13.0 - - + -
1191M ALA 2.9 13.6 + - - +
1192M TYR 3.4 10.3 - - - +
1194M ARG* 1.3 76.8 - - - +
1196M LEU* 1.3 57.7 + - - +
1198M HIS* 3.3 5.2 - - - +
1199M ARG 3.0 21.5 + - - -
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Residues in contact with LEU1196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170K ASP* 3.5 34.4 - - - +
1088M LEU* 4.4 3.4 - - + -
1165M LEU* 4.0 22.9 - - + -
1166M GLY* 4.5 4.0 - - - -
1192M TYR* 3.0 49.9 + - + +
1193M HIS 3.4 0.6 + - - +
1194M ARG 3.3 0.2 - - - -
1195M ALA* 1.3 73.9 - - - +
1197M GLN* 1.3 61.6 + - - +
1199M ARG* 3.3 41.9 + - - +
1200M SER* 3.0 27.0 + - - -
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Residues in contact with GLN1197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168K ASN* 4.1 12.0 + - - +
1170K ASP* 3.5 26.8 + - + -
1171K LEU* 3.5 33.1 - - - +
1174K GLU* 2.7 29.8 + - - +
1193M HIS 3.0 27.1 + - - +
1194M ARG* 3.6 7.7 - - - +
1196M LEU* 1.3 76.7 - - - +
1198M HIS* 1.3 65.3 + - - +
1200M SER* 3.2 8.8 + - - -
1201M LYS* 3.0 40.4 + - - +
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Residues in contact with HIS1198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086M LEU* 5.1 2.8 + - - +
1088M LEU* 4.2 19.1 - - + -
1102M LEU* 3.9 30.2 - - + +
1115M HIS* 5.2 3.2 - - - -
1118M VAL* 4.1 20.3 - - + +
1120M ILE* 4.1 10.8 - - + +
1148M PHE* 3.8 19.0 - + + -
1152M ARG* 5.5 2.6 + - - -
1194M ARG 3.0 12.4 + - - +
1195M ALA 3.3 8.5 - - - +
1197M GLN* 1.3 72.7 - - - +
1199M ARG* 1.3 69.7 + - - +
1201M LYS* 3.1 13.7 + - - +
1202M VAL* 3.0 43.9 + - + +
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Residues in contact with ARG1199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170K ASP* 5.8 0.4 + - - -
1088M LEU* 4.0 18.1 - - + +
1165M LEU 4.8 2.2 + - - -
1166M GLY* 2.9 36.4 + - - -
1195M ALA 3.0 13.3 + - - +
1196M LEU* 3.5 36.0 + - - +
1197M GLN 3.2 0.2 - - - -
1198M HIS* 1.3 83.5 - - - +
1200M SER* 1.3 58.5 + - - +
1202M VAL* 3.3 6.3 + - + +
1203M GLN* 2.9 55.7 + - + +
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Residues in contact with SER1200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168K ASN* 4.5 12.0 + - - -
1170K ASP* 5.9 1.3 - - - -
1196M LEU 3.0 16.8 + - - -
1197M GLN* 3.5 9.6 - - - -
1198M HIS 3.2 0.2 - - - -
1199M ARG* 1.3 79.9 - - - +
1201M LYS* 1.3 55.8 + - - +
1203M GLN* 3.3 17.4 + - - +
1204M GLY 3.3 0.2 + - - -
1205M GLU* 2.6 55.4 + - - +
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Residues in contact with LYS1201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116M HIS 4.4 4.9 - - - +
1118M VAL* 3.8 24.1 - - + +
1197M GLN* 3.0 30.8 + - - +
1198M HIS* 3.1 10.5 + - - +
1200M SER* 1.3 77.2 - - - +
1202M VAL* 1.3 62.2 + - - +
1204M GLY* 3.2 12.8 + - - -
1205M GLU* 3.1 31.8 + - - +
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Residues in contact with VAL1202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115M HIS* 3.3 37.5 - - + +
1116M HIS* 3.5 33.3 + - + +
1118M VAL* 3.9 17.9 - - + -
1198M HIS* 3.0 41.5 + - + +
1199M ARG* 3.7 9.0 - - + +
1201M LYS* 1.3 76.3 - - - +
1203M GLN* 1.3 62.3 + - + +
1204M GLY 3.3 1.2 + - - -
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Residues in contact with GLN1203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199M ARG* 2.9 48.7 + - + +
1200M SER* 3.8 12.7 - - - +
1201M LYS 3.2 0.4 - - - -
1202M VAL* 1.3 78.7 - - + +
1204M GLY* 1.3 58.1 + - - +
1205M GLU 3.5 2.7 - - - +
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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