Contacts of the helix formed by residues 1064 - 1084 (chain A) in PDB entry 3QCF
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 VAL1064 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883A ILE* 3.7 11.0 - - + -
1060A CYS* 3.8 1.6 - - - -
1062A ALA* 3.7 23.3 - - + +
1063A GLY* 1.3 85.3 - - - +
1065A GLY* 1.3 75.7 + - - +
1068A GLY 3.2 8.2 + - - -
1099A ARG* 3.9 3.6 - - - +
1100A ASN* 3.2 39.5 - - - +
1101A TYR* 3.7 19.7 - - + +
1102A LEU* 3.1 10.6 - - - +
1103A VAL 2.8 23.9 + - - -
1104A GLN* 3.9 23.6 - - - +
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Residues in contact with GLY1065 (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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1060A CYS* 4.3 3.0 - - - -
1064A VAL* 1.3 84.8 - - - +
1066A ARG* 1.3 60.8 + - - +
1068A GLY* 3.7 0.2 - - - -
1069A THR* 3.0 28.8 + - - -
1103A VAL* 3.8 2.3 - - - -
1104A GLN* 3.7 16.2 - - - -
1108A GLN* 3.4 27.1 - - - +
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Residues in contact with ARG1066 (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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950A ILE* 3.1 43.0 + - + +
951A THR* 3.6 7.4 - - - +
955A GLU* 3.0 39.2 + - - -
960A LYS* 5.5 2.2 - - - +
1026A TRP* 3.3 59.8 - - + +
1027A PRO 3.5 10.3 + - - -
1028A ASP 4.5 5.7 + - - -
1030A GLY 5.2 1.0 + - - -
1060A CYS* 3.9 15.3 - - + -
1065A GLY* 1.3 70.6 - - - +
1067A THR* 1.3 61.0 + - - +
1069A THR* 3.1 10.2 + - - -
1070A TYR* 2.9 31.2 + - - +
1108A GLN* 4.1 10.4 - - - +
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Residues in contact with THR1067 (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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923A ALA* 3.6 24.0 - - + -
950A ILE* 4.4 1.3 - - - -
1058A VAL* 3.6 35.2 - - + +
1059A HIS* 3.3 5.4 - - - -
1060A CYS* 3.1 32.5 + - - +
1063A GLY* 3.3 21.8 - - - +
1066A ARG* 1.3 79.4 - - - +
1068A GLY* 1.3 63.6 + - - +
1070A TYR* 3.2 3.6 + - - +
1071A ILE* 3.1 26.5 + - + +
1102A LEU* 4.5 1.8 - - + -
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Residues in contact with GLY1068 (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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1064A VAL 3.2 19.0 + - - -
1065A GLY 3.7 0.4 - - - -
1067A THR* 1.3 80.3 - - - +
1069A THR* 1.3 61.1 + - - +
1071A ILE* 3.2 6.1 + - - +
1072A VAL* 2.9 29.9 + - - +
1095A ILE* 5.2 0.9 - - - -
1102A LEU* 3.8 15.2 - - - +
1103A VAL* 3.5 16.2 - - - -
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Residues in contact with THR1069 (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 TRP* 4.7 9.4 - - + -
1038A VAL* 6.3 0.2 - - + -
1065A GLY 3.0 15.1 + - - -
1066A ARG* 3.1 11.8 + - - -
1068A GLY* 1.3 76.0 - - - +
1070A TYR* 1.3 62.1 + - - +
1072A VAL* 3.9 1.0 - - - +
1073A ILE* 3.1 49.7 + - + +
1103A VAL* 3.7 11.7 - - - +
1108A GLN* 3.5 25.8 + - + +
1111A PHE* 3.9 19.5 - - + -
1112A ILE* 3.8 14.1 - - + -
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Residues in contact with TYR1070 (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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921A TYR* 4.2 13.9 - + - -
948A VAL* 3.8 17.6 - - + +
950A ILE* 3.2 32.8 - - + -
1041A PHE* 4.1 8.1 - + - -
1042A VAL* 3.9 32.1 + - + +
1045A SER* 2.8 34.2 + - - -
1046A SER* 3.9 11.6 + - - -
1056A VAL* 5.3 2.2 - - + +
1058A VAL* 4.0 30.1 - - + -
1066A ARG 2.9 5.4 + - - +
1067A THR 3.5 4.3 - - - +
1069A THR* 1.3 78.0 - - - +
1071A ILE* 1.3 61.6 + - + +
1073A ILE* 3.4 6.8 + - - +
1074A ASP* 2.9 40.9 + - + +
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Residues in contact with ILE1071 (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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912A VAL* 4.0 22.4 - - + -
913A ASP 4.1 11.7 - - - +
921A TYR* 3.7 53.8 - - + -
923A ALA* 4.4 6.3 - - + -
1058A VAL* 4.6 4.9 - - + -
1067A THR* 3.1 27.8 + - + +
1068A GLY* 3.7 10.3 - - - +
1070A TYR* 1.3 81.9 - - + +
1072A VAL* 1.3 63.5 + - - +
1074A ASP* 3.9 0.5 - - - +
1075A SER* 2.8 31.7 + - - -
1091A PHE* 4.1 10.8 - - + -
1095A ILE* 4.4 4.5 - - + -
1102A LEU* 4.9 2.2 - - + -
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Residues in contact with VAL1072 (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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1068A GLY 2.9 16.9 + - - +
1069A THR 3.9 2.7 - - - +
1071A ILE* 1.3 73.9 - - - +
1073A ILE* 1.3 66.8 + - - +
1074A ASP 3.3 0.2 + - - -
1075A SER* 3.8 0.7 - - - -
1076A MET* 3.0 37.8 + - + +
1088A VAL* 4.1 17.9 - - + +
1091A PHE* 4.0 17.5 - - + -
1092A LEU* 4.4 7.4 - - + -
1095A ILE* 4.1 19.7 - - + -
1103A VAL* 3.9 16.2 - - + -
1112A ILE* 3.9 29.6 - - + -
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Residues in contact with ILE1073 (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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1038A VAL* 4.7 10.5 - - + -
1039A LEU* 4.2 15.9 - - + -
1042A VAL* 4.2 13.2 - - + -
1069A THR* 3.1 35.6 + - + +
1070A TYR* 3.9 4.5 - - - +
1072A VAL* 1.3 77.3 - - - +
1074A ASP* 1.3 63.4 + - - +
1076A MET* 3.9 4.0 - - - +
1077A LEU* 3.0 48.2 + - + +
1111A PHE* 4.0 12.3 - - + -
1112A ILE* 4.2 23.3 - - + +
1115A ALA* 4.0 20.0 - - + -
1116A LEU* 4.3 8.6 - - + +
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Residues in contact with ASP1074 (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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921A TYR* 2.4 32.9 + - + +
1042A VAL* 4.0 17.9 - - + +
1046A SER* 2.6 37.6 + - - -
1049A ARG* 4.9 3.6 + - - -
1070A TYR* 2.9 27.9 + - + +
1071A ILE 3.9 0.7 - - - +
1073A ILE* 1.3 78.1 - - - +
1075A SER* 1.3 62.7 + - - +
1077A LEU* 3.3 4.7 + - - +
1078A GLN* 3.1 30.8 + - - +
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Residues in contact with SER1075 (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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914A GLY* 3.5 13.9 - - - -
915A TYR* 3.5 22.7 - - - +
921A TYR* 3.7 5.4 + - - -
1071A ILE 2.8 22.6 + - - -
1072A VAL 3.8 0.9 - - - -
1074A ASP* 1.3 76.1 - - - +
1076A MET* 1.3 63.9 + - - +
1078A GLN* 3.3 8.9 + - - +
1079A GLN* 2.9 24.1 + - - +
1091A PHE* 3.1 34.7 - - - -
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Residues in contact with MET1076 (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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915A TYR* 5.4 1.3 - - + -
1072A VAL* 3.0 24.8 + - + +
1075A SER* 1.3 81.9 - - - +
1077A LEU* 1.3 62.5 + - - +
1079A GLN* 3.3 25.3 + - - +
1080A ILE* 2.8 36.8 + - - +
1085A THR 4.5 0.2 - - - +
1086A VAL* 3.8 7.6 - - + -
1087A ASN 3.6 38.1 - - - +
1088A VAL* 4.0 8.5 - - + -
1091A PHE* 3.9 31.4 - - + -
1116A LEU* 3.8 32.1 - - + -
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Residues in contact with LEU1077 (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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1039A LEU* 4.4 8.3 - - + -
1042A VAL* 3.7 26.0 - - + -
1043A ARG* 4.2 27.4 - - + +
1073A ILE* 3.0 33.7 + - + +
1074A ASP* 3.5 5.8 - - - +
1076A MET* 1.3 75.9 - - - +
1078A GLN* 1.3 60.7 + - + +
1080A ILE* 3.0 13.1 + - + +
1081A LYS* 2.9 28.7 + - - +
1116A LEU* 4.1 12.1 - - + -
1119A ALA* 3.8 29.6 - - + -
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Residues in contact with GLN1078 (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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915A TYR* 3.7 30.6 + - + +
921A TYR* 4.6 3.4 + - - -
1046A SER* 4.6 7.3 + - - +
1049A ARG* 5.9 3.6 - - - +
1074A ASP* 3.1 31.6 + - - +
1075A SER* 3.4 10.2 - - - +
1077A LEU* 1.3 76.6 - - + +
1079A GLN* 1.3 63.2 + - - +
1081A LYS* 3.9 6.4 - - - +
1082A ASP* 3.0 26.0 + - - +
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Residues in contact with GLN1079 (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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827A ALA* 3.8 9.5 - - - +
915A TYR* 3.5 37.7 - - + +
1075A SER 2.9 15.2 + - - +
1076A MET* 3.3 29.6 + - - +
1078A GLN* 1.3 74.9 - - - +
1080A ILE* 1.3 54.2 + - - +
1083A LYS* 2.7 32.6 + - + -
1084A SER 3.3 2.9 + - - -
1085A THR* 2.8 40.0 + - - +
1086A VAL* 3.6 12.2 + - - -
1087A ASN* 3.8 5.6 + - - +
1091A PHE* 5.9 1.0 - - - -
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Residues in contact with ILE1080 (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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830A VAL* 4.3 15.5 - - + -
1076A MET 2.8 23.3 + - - +
1077A LEU* 3.2 15.9 - - + +
1079A GLN* 1.3 77.8 - - - +
1081A LYS* 1.3 61.1 + - - +
1084A SER* 2.9 32.5 + - - +
1085A THR 3.7 14.4 - - - +
1086A VAL* 3.8 18.6 - - + -
1116A LEU* 3.9 24.5 - - + +
1119A ALA* 5.8 0.2 - - + -
1120A ILE* 4.0 27.1 - - + -
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Residues in contact with LYS1081 (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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1077A LEU 2.9 14.9 + - - +
1078A GLN* 3.9 7.4 - - - +
1080A ILE* 1.3 79.5 - - - +
1082A ASP* 1.3 61.8 + - - +
1084A SER* 4.9 1.4 + - - -
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Residues in contact with ASP1082 (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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915A TYR* 2.4 34.3 + - + +
916A ASN* 4.0 7.1 + - - -
1078A GLN 3.0 19.3 + - - +
1079A GLN 3.8 0.4 - - - +
1081A LYS* 1.3 81.3 - - - +
1083A LYS* 1.3 61.3 + - - +
1084A SER* 5.5 0.2 - - - -
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Residues in contact with LYS1083 (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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915A TYR* 4.4 11.9 - - - +
1079A GLN* 2.7 10.4 + - + +
1082A ASP* 1.3 75.7 - - - +
1084A SER* 1.3 72.0 + - - +
1085A THR* 3.2 29.9 + - + +
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Residues in contact with SER1084 (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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829A PRO* 3.5 6.8 - - - +
830A VAL* 3.1 37.6 + - - -
1079A GLN 3.3 0.2 + - - -
1080A ILE* 2.9 23.1 + - - +
1081A LYS 5.1 1.4 + - - -
1082A ASP 3.7 0.4 - - - -
1083A LYS* 1.3 81.2 - - - +
1085A THR* 1.3 58.5 + - - +
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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