Contacts of the helix formed by residues 1081 - 1108 (chain A) in PDB entry 1VDV
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 VAL1081 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A ILE* 3.3 32.3 - - + -
1008A SER* 3.8 16.8 - - - +
1009A PHE* 3.6 28.0 - - + -
1015A ASN* 4.4 4.0 - - - +
1078A ALA 3.4 14.8 + - - +
1079A ALA* 2.8 12.9 + - + +
1080A SER* 1.3 74.0 - - - +
1082A SER* 1.3 64.9 + - - +
1083A THR 3.3 3.4 - - - -
1084A ASP* 3.0 16.1 + - + +
1085A ILE* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1082 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A LEU* 3.8 21.8 - - - -
1077A THR* 3.2 26.2 - - - +
1078A ALA 3.9 4.2 + - - -
1081A VAL* 1.3 77.1 - - - +
1083A THR* 1.3 61.8 + - - +
1085A ILE* 4.2 2.0 - - - -
1086A TYR* 2.9 46.4 + - - +
3003A MTE 2.7 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1083 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A LEU* 3.8 14.5 - - - +
1045A LYS* 3.6 30.6 + - + +
1046A MET* 4.0 9.6 - - + -
1080A SER 4.8 3.1 + - - -
1081A VAL 3.3 0.8 - - - -
1082A SER* 1.3 77.0 - - - +
1084A ASP* 1.3 63.4 + - - +
1087A GLY* 2.9 29.1 + - - -
1186A LEU* 3.3 34.3 - - + -
1253A ILE* 3.8 6.3 - - + +
1256A SER* 4.9 2.7 - - - +
1257A LYS 6.5 0.2 - - - -
1258A ALA* 6.1 2.7 - - - -
3003A MTE 4.1 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A ILE* 4.1 6.8 - - - +
1080A SER 4.9 0.3 - - - +
1081A VAL* 3.0 21.7 + - + +
1083A THR* 1.3 83.7 - - - +
1085A ILE* 1.3 65.0 + - + +
1087A GLY* 4.2 0.2 - - - -
1088A GLN* 3.4 20.4 + - - +
1133A TYR* 4.5 5.0 - - + -
1151A HIS* 5.6 1.0 - - - -
1152A TYR* 2.5 42.0 + - - -
1252A ALA* 3.9 16.4 - - + +
1253A ILE* 4.2 12.8 + - - +
1256A SER* 4.7 4.5 + - - -
1257A LYS 4.3 2.8 - - - -
1258A ALA* 3.9 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A PHE* 4.7 4.7 - - + -
1014A LEU 4.7 5.2 - - - +
1015A ASN* 4.9 8.3 - - - +
1016A GLN 3.6 26.0 - - - +
1017A ALA* 3.5 21.5 - - + +
1075A SER* 5.6 1.1 - - - -
1081A VAL* 2.9 40.8 + - + +
1082A SER* 3.8 3.6 - - - +
1084A ASP* 1.3 74.5 - - + +
1086A TYR* 1.3 79.6 + - + +
1087A GLY 3.2 1.6 - - - -
1088A GLN* 3.2 4.7 + - - +
1089A ALA* 3.0 21.8 + - - +
1133A TYR* 3.8 19.5 - - + +
1135A THR* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1086 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A GLN 4.8 1.6 + - - -
1017A ALA* 3.4 28.9 - - + -
1018A GLY 3.9 8.3 - - - -
1033A HIS* 3.8 14.6 - - + +
1034A GLY* 3.4 37.3 + - - -
1035A GLY* 3.2 26.0 - - - -
1042A LEU* 4.4 2.0 - - + -
1046A MET* 3.5 13.2 - - - -
1074A SER* 4.2 1.8 - - - -
1075A SER* 3.4 27.9 + - - -
1076A PRO 4.8 2.4 + - - -
1077A THR* 5.0 3.4 - - - -
1082A SER* 2.9 47.3 + - - +
1085A ILE* 1.3 81.6 - - + +
1087A GLY* 1.3 60.3 + - - +
1089A ALA* 3.7 2.2 - - - +
1090A VAL* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1087 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A MET* 3.4 19.6 - - - -
1049A VAL* 3.8 10.7 - - - +
1083A THR 2.9 21.4 + - - -
1084A ASP 4.2 0.2 - - - -
1086A TYR* 1.3 77.9 - - - +
1088A GLN* 1.3 57.7 + - - +
1090A VAL* 3.8 0.6 - - - +
1091A TYR* 2.9 28.4 + - - +
1253A ILE* 3.9 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A ASP 3.4 11.5 + - - +
1085A ILE 3.2 4.4 + - - +
1086A TYR 3.2 0.4 - - - -
1087A GLY* 1.3 75.1 - - - +
1089A ALA* 1.3 58.7 + - - +
1091A TYR* 3.3 29.2 + - - +
1092A GLU* 2.9 45.0 + - + +
1133A TYR* 3.0 50.6 - - + -
1252A ALA* 4.7 1.2 - - - -
1253A ILE* 3.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ALA 3.6 26.0 - - - +
1018A GLY 3.9 5.2 - - - -
1019A ALA* 3.8 16.4 - - + -
1085A ILE 3.0 13.9 + - - +
1086A TYR* 3.7 7.4 - - - +
1088A GLN* 1.3 76.0 - - - +
1090A VAL* 1.3 62.3 + - - +
1092A GLU* 3.4 0.6 + - - +
1093A ALA* 3.1 18.7 + - - +
1131A GLY* 3.3 18.3 - - - +
1132A PHE* 4.0 12.1 - - - +
1133A TYR* 4.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A ALA* 4.0 17.5 - - + -
1021A ILE* 4.2 7.6 - - + -
1031A VAL* 4.2 18.6 - - + -
1033A HIS* 4.4 7.6 - - + -
1046A MET* 4.0 24.9 - - + +
1049A VAL* 4.3 2.5 - - + -
1050A ALA* 3.8 32.1 - - + +
1086A TYR 2.9 22.2 + - - +
1087A GLY* 3.8 5.2 - - - +
1089A ALA* 1.3 73.0 - - - +
1091A TYR* 1.3 66.6 + - - +
1093A ALA* 3.2 5.8 + - - +
1094A CYS* 2.9 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A VAL* 4.6 6.1 - - + -
1053A ALA* 4.0 4.9 - - + -
1087A GLY 2.9 19.0 + - - +
1088A GLN* 3.4 20.6 - - - +
1090A VAL* 1.3 76.9 - - - +
1092A GLU* 1.3 82.9 + - - +
1094A CYS* 3.1 9.5 + - - +
1095A GLN* 3.0 64.2 + - + +
1253A ILE* 4.1 9.6 - - + -
1254A TYR* 3.6 37.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A GLN* 2.9 32.1 + - + +
1089A ALA 3.7 5.2 - - - +
1091A TYR* 1.3 99.3 - - - +
1093A ALA* 1.3 63.1 + - - +
1095A GLN* 3.0 20.8 + - - +
1096A THR* 3.1 15.8 + - - -
1130A THR 5.1 0.2 - - - -
1131A GLY* 4.4 1.6 - - - -
1132A PHE 3.9 25.1 - - - +
1133A TYR* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A ALA* 4.7 2.0 - - + -
1021A ILE* 3.4 30.5 - - + -
1089A ALA 3.1 14.9 + - - +
1090A VAL* 3.5 4.0 - - - +
1092A GLU* 1.3 75.0 - - - +
1094A CYS* 1.3 62.7 + - - +
1096A THR* 3.4 2.9 + - - -
1097A ILE* 3.2 26.4 + - - +
1129A THR* 3.4 11.6 - - + +
1130A THR 3.8 23.8 - - - +
1131A GLY* 3.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A ILE* 3.8 15.9 - - - -
1050A ALA* 3.8 27.1 - - - -
1053A ALA* 3.8 17.5 - - + -
1054A LEU* 3.7 33.1 - - + +
1090A VAL* 2.9 21.5 + - - -
1091A TYR 3.1 8.5 + - - +
1093A ALA* 1.3 75.4 - - - +
1095A GLN* 1.3 58.5 + - - +
1097A ILE* 3.1 7.6 + - - +
1098A LEU* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1095 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053A ALA* 3.9 15.0 + - - +
1091A TYR* 3.0 67.7 + - + +
1092A GLU* 3.0 15.2 + - - +
1094A CYS* 1.3 75.2 - - - +
1096A THR* 1.3 58.1 + - - +
1098A LEU* 3.2 22.4 + - - +
1099A LYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1096 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092A GLU 3.1 12.3 + - - -
1093A ALA* 3.6 9.9 - - - -
1095A GLN* 1.3 76.8 - - - +
1097A ILE* 1.3 62.4 + - - +
1099A LYS* 3.3 8.7 + - + +
1100A ARG* 3.1 47.9 + - + +
1129A THR* 3.6 25.1 + - + +
1130A THR 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1097 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A ILE* 4.7 12.1 - - + +
1023A VAL* 4.1 23.1 - - + -
1054A LEU* 4.3 14.6 - - + -
1093A ALA 3.2 16.6 - - - +
1094A CYS* 3.1 11.2 + - - +
1096A THR* 1.3 75.4 - - - +
1098A LEU* 1.3 65.2 + - - +
1100A ARG* 3.2 11.9 + - + +
1101A LEU* 3.0 40.3 + - + +
1113A TRP* 4.4 1.3 - - + -
1127A LEU* 4.1 32.7 - - + +
1128A SER 4.5 0.4 - - - +
1129A THR* 3.7 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053A ALA 3.1 25.6 - - - +
1054A LEU* 4.0 30.7 - - + +
1055A LYS* 4.8 9.4 - - + +
1094A CYS 2.9 16.7 + - - +
1095A GLN* 3.6 26.7 - - - +
1097A ILE* 1.3 75.8 - - - +
1099A LYS* 1.3 63.6 + - - +
1101A LEU* 3.2 6.2 + - + +
1102A GLU* 3.0 28.5 + - + +
1113A TRP* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1099 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A GLN 2.9 13.4 + - - +
1096A THR* 3.5 14.4 - - + +
1098A LEU* 1.3 77.0 - - - +
1100A ARG* 1.3 63.3 - - + +
1102A GLU* 3.3 25.7 - - + +
1103A PRO* 3.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A THR* 3.1 37.9 + - + +
1097A ILE* 3.7 12.6 - - - +
1099A LYS* 1.3 80.1 - - + +
1101A LEU* 1.3 62.1 + - + +
1103A PRO* 3.3 15.1 - - - +
1104A PHE* 3.5 15.6 - - - -
1125A VAL* 3.8 20.5 - - + +
1126A SER* 2.8 48.3 + - - +
1127A LEU* 4.5 2.7 - - + -
1128A SER 2.8 31.9 + - - +
1129A THR* 4.0 7.4 + - - -
1130B THR* 4.8 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A VAL* 6.0 0.2 - - + -
1097A ILE* 3.0 27.9 + - + +
1098A LEU* 3.9 7.4 - - + +
1100A ARG* 1.3 77.2 - - - +
1102A GLU* 1.3 65.3 + - - +
1103A PRO* 3.4 0.7 - - - -
1104A PHE* 3.1 9.7 + - + +
1105A LYS* 3.1 21.7 + - + +
1113A TRP* 3.5 42.8 - - + -
1116A TRP* 3.8 26.9 - - + +
1117A VAL* 4.1 7.4 - - + -
1120A ALA* 3.7 28.3 - - + -
1127A LEU* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098A LEU* 3.0 17.5 + - + +
1099A LYS* 3.3 17.9 - - + +
1101A LEU* 1.3 74.9 - - - +
1103A PRO* 1.3 70.6 - - + +
1105A LYS* 3.0 39.7 + - - +
1106A LYS* 3.0 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A LYS 3.6 5.8 - - - +
1100A ARG* 3.3 17.3 - - - +
1101A LEU 3.4 0.7 - - - -
1102A GLU* 1.3 96.5 - - + +
1104A PHE* 1.3 68.2 + - + +
1106A LYS* 3.6 9.2 + - + +
1107A LYS* 3.1 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100A ARG 3.5 25.4 - - - -
1101A LEU* 3.1 8.5 + - - +
1103A PRO* 1.3 85.7 - - + +
1105A LYS* 1.3 61.3 + - - +
1107A LYS* 3.8 22.0 - - + +
1108A ASN* 3.0 24.3 + - - +
1116A TRP* 3.4 26.7 - - - +
1119A ALA* 3.6 28.5 - - + -
1120A ALA* 3.7 22.2 - - + -
1123A ASP* 3.6 42.8 - - + -
1125A VAL* 3.7 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A LYS* 5.7 6.7 - - - +
1101A LEU* 3.1 12.7 + - + +
1102A GLU* 3.0 29.8 + - - +
1104A PHE* 1.3 77.1 - - - +
1106A LYS* 1.3 59.2 + - + +
1108A ASN 3.1 0.7 - - - -
1109A PRO* 2.9 36.3 - - + +
1116A TRP* 3.7 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A GLU* 3.0 39.3 + - + +
1103A PRO* 3.9 7.1 + - + +
1105A LYS* 1.3 77.6 - - + +
1107A LYS* 1.3 65.7 + - + +
1109A PRO* 3.2 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103A PRO* 3.1 44.1 + - - +
1104A PHE* 3.8 22.4 - - + +
1105A LYS 3.3 0.4 - - - -
1106A LYS* 1.3 77.0 - - + +
1108A ASN* 1.3 60.9 + - + +
1109A PRO* 3.4 5.2 - - - +
1123A ASP* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A PHE 3.0 12.7 + - - +
1105A LYS 3.1 3.6 - - - -
1107A LYS* 1.3 79.4 - - + +
1109A PRO* 1.3 57.7 - - - +
1110A ASP* 4.3 4.3 + - - +
1111A GLY* 3.0 36.9 + - - -
1115A ASP* 4.0 19.4 + - - +
1116A TRP* 2.7 30.5 + - + +
----------------------------------------------------------
Back to top of page
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