Contacts of the helix formed by residues 1068 - 1093 (chain A) in PDB entry 4TU4
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 ASP1068 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A ASP* 3.3 23.6 - - + +
1067A ARG* 1.3 97.2 - - + +
1069A PRO* 1.3 76.8 - - + +
1070A GLY* 3.3 15.2 + - - -
1071A ASP* 3.2 23.8 + - - +
1072A ARG* 3.0 18.7 + - - +
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Residues in contact with PRO1069 (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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1067A ARG* 3.7 16.3 - - - +
1068A ASP* 1.3 89.8 - - + +
1070A GLY* 1.3 57.7 + - - +
1072A ARG* 3.9 8.0 - - + +
1073A LEU* 2.9 32.1 + - - +
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Residues in contact with GLY1070 (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 ASP* 3.3 9.9 + - - -
1069A PRO* 1.3 79.5 - - - +
1071A ASP* 1.3 63.1 - - - +
1073A LEU* 3.8 7.1 - - - +
1074A ILE* 3.2 23.2 + - - +
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Residues in contact with ASP1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A TYR 4.8 0.3 - - - +
1064A ASN* 3.1 32.5 - - - +
1065A PRO* 3.3 2.6 - - - +
1066A ASP* 2.9 46.1 + - - +
1068A ASP* 3.2 21.6 + - - +
1070A GLY* 1.3 74.3 - - - +
1072A ARG* 1.3 67.0 + - - +
1074A ILE* 3.3 7.7 - - - +
1075A ARG* 2.9 29.3 + - - +
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Residues in contact with ARG1072 (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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1066A ASP 4.1 0.9 - - - +
1067A ARG* 3.2 56.3 + - - +
1068A ASP 3.0 10.3 + - - +
1069A PRO* 3.9 7.4 - - + +
1071A ASP* 1.3 77.6 - - - +
1073A LEU* 1.3 58.2 + - - +
1075A ARG* 3.3 28.5 + - - +
1076A HIS* 2.9 29.5 + - - +
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Residues in contact with LEU1073 (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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1069A PRO 2.9 18.1 + - - +
1070A GLY* 3.8 7.0 - - - +
1072A ARG* 1.3 74.3 - - - +
1074A ILE* 1.3 65.9 + - - +
1076A HIS* 3.2 10.0 + - + +
1077A ARG* 3.0 72.7 + - + +
1205A CL 4.5 7.4 - - + -
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Residues in contact with ILE1074 (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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1008A VAL* 4.0 10.8 - - + -
1009A PHE* 4.0 16.2 - - + -
1060A ALA* 4.6 4.0 - - + +
1064A ASN* 3.5 31.6 - - + +
1070A GLY 3.2 12.6 + - - +
1071A ASP 3.3 13.2 - - - +
1073A LEU* 1.3 79.0 - - - +
1075A ARG* 1.3 56.8 + - - +
1077A ARG* 3.3 8.2 + - - +
1078A ALA* 2.8 29.2 + - - +
1204A 37N 3.4 65.3 - - + +
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Residues in contact with ARG1075 (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 ALA* 4.5 3.1 - - - +
1061A LEU* 3.8 42.2 - - + +
1064A ASN* 2.8 37.8 + - + +
1065A PRO* 3.3 12.4 + - - -
1066A ASP 2.7 25.9 + - - +
1067A ARG* 4.9 0.2 - - - +
1071A ASP* 2.9 26.9 + - - +
1072A ARG* 3.3 35.8 - - - +
1074A ILE* 1.3 77.3 - - - +
1076A HIS* 1.3 62.4 + - - +
1078A ALA* 3.3 2.0 + - - +
1079A CYS* 3.0 30.0 + - - -
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Residues in contact with HIS1076 (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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1005A ARG* 6.2 2.0 - - - -
1072A ARG 2.9 17.9 + - - +
1073A LEU* 3.6 11.9 - - + +
1075A ARG* 1.3 76.3 - - - +
1077A ARG* 1.3 63.0 + - + +
1079A CYS* 3.4 7.0 + - + +
1080A ALA* 2.9 36.3 + - + +
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Residues in contact with ARG1077 (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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1004A LYS 5.4 2.1 + - - -
1005A ARG* 3.3 45.4 + - + +
1006A PHE* 3.4 9.0 - - - -
1007A ARG* 6.0 0.6 - - - +
1008A VAL* 4.6 22.0 - - - +
1009A PHE* 3.8 10.3 - - + -
1073A LEU* 3.0 53.9 + - + +
1074A ILE* 3.6 7.3 - - - +
1075A ARG 3.2 0.2 - - - -
1076A HIS* 1.3 77.4 - - + +
1078A ALA* 1.3 61.0 + - - +
1080A ALA* 3.2 6.2 + - - -
1081A LEU* 2.8 27.5 + - - +
1204A 37N 5.0 4.9 + - - -
1205A CL 3.3 31.7 - - - +
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Residues in contact with ALA1078 (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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1009A PHE* 3.6 13.1 - - + -
1057A CYS* 3.6 22.8 - - - +
1060A ALA* 3.6 27.1 - - + -
1061A LEU* 4.1 10.8 - - + -
1074A ILE 2.8 17.0 + - - +
1075A ARG 3.6 4.7 - - - +
1077A ARG* 1.3 76.3 - - - +
1079A CYS* 1.3 62.1 + - - +
1081A LEU* 3.3 6.0 + - - +
1082A ARG* 3.1 18.4 + - - +
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Residues in contact with CYS1079 (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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1057A CYS* 4.0 17.9 - - - -
1061A LEU* 4.2 15.7 - - - -
1075A ARG* 3.0 22.2 + - - +
1076A HIS* 3.7 6.7 - - + +
1078A ALA* 1.3 75.0 - - - +
1080A ALA* 1.3 58.8 + - - +
1082A ARG* 3.4 2.7 + - - +
1083A ASP* 2.9 42.4 + - - +
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Residues in contact with ALA1080 (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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1005A ARG* 4.0 20.2 - - - +
1006A PHE* 3.7 12.8 - - + -
1076A HIS* 2.9 27.3 + - + +
1077A ARG* 3.5 7.6 - - - +
1079A CYS* 1.3 74.1 - - - +
1081A LEU* 1.3 58.2 + - - +
1083A ASP* 3.9 7.5 - - - +
1084A THR* 2.8 37.3 + - - +
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Residues in contact with LEU1081 (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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1000A LEU* 4.0 25.5 - - + +
1006A PHE* 3.3 39.1 - - + -
1009A PHE* 3.9 18.2 - - + -
1031A LEU* 4.4 9.0 - - + -
1053A ILE* 4.7 9.4 - - + +
1056A ILE* 3.5 42.0 - - + -
1057A CYS* 5.3 1.1 - - + +
1077A ARG 2.8 14.1 + - - +
1078A ALA* 3.3 10.5 + - - +
1080A ALA* 1.3 76.1 - - - +
1082A ARG* 1.3 56.8 + - - +
1084A THR* 3.3 2.3 + - - -
1085A ALA* 2.9 30.7 + - - +
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Residues in contact with ARG1082 (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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1053A ILE* 4.0 14.4 - - + -
1054A ASP* 2.5 35.2 + - - +
1057A CYS* 3.9 29.4 - - + -
1078A ALA 3.1 9.8 + - - +
1079A CYS* 3.7 7.2 - - - +
1080A ALA 3.3 0.2 - - - -
1081A LEU* 1.3 79.6 - - - +
1083A ASP* 1.3 65.5 + - - +
1084A THR 3.3 0.2 + - - -
1085A ALA* 3.3 1.9 + - - +
1086A TYR* 3.0 43.4 + - + -
1203A GOL 3.2 44.8 - - - -
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Residues in contact with ASP1083 (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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1079A CYS* 2.9 29.1 + - - +
1080A ALA* 3.9 7.6 - - - +
1082A ARG* 1.3 80.0 + - - +
1084A THR* 1.3 56.7 + - - +
1086A TYR* 3.5 1.6 + - - +
1087A ALA* 2.9 30.0 + - - +
1203A GOL 2.8 33.7 + - - +
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Residues in contact with THR1084 (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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1000A LEU* 3.5 22.2 - - + -
1003A ASP* 5.6 1.1 - - - +
1005A ARG* 3.9 19.8 + - - +
1006A PHE* 3.9 6.4 - - + -
1080A ALA* 2.8 24.5 + - - -
1081A LEU 3.7 3.4 - - - -
1083A ASP* 1.3 72.9 - - - +
1085A ALA* 1.3 62.1 + - - +
1087A ALA* 3.2 6.2 + - + +
1088A ILE* 2.9 42.6 + - + +
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Residues in contact with ALA1085 (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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996A VAL* 4.9 5.8 - - + +
1000A LEU* 3.9 24.8 - - + +
1049A TYR* 5.1 0.7 - - + -
1050A LEU* 4.4 6.5 - - + -
1053A ILE* 3.9 23.8 - - + -
1081A LEU 2.9 16.7 + - - +
1082A ARG 3.8 3.8 - - - +
1084A THR* 1.3 78.9 - - - +
1086A TYR* 1.3 62.1 + - - +
1088A ILE* 3.3 5.6 + - - +
1089A ILE* 3.0 30.1 + - + +
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Residues in contact with TYR1086 (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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1050A LEU* 3.8 43.8 - - + +
1053A ILE* 5.2 2.0 - - + -
1054A ASP* 3.0 39.1 + - - -
1082A ARG* 3.0 48.4 + - + +
1083A ASP 3.9 3.1 - - - +
1085A ALA* 1.3 76.9 - - + +
1087A ALA* 1.3 57.6 + - - +
1089A ILE* 3.4 6.2 + - - +
1090A LYS* 2.8 30.5 + - - +
1203A GOL 3.9 36.1 - - - +
1206A DMS 4.9 12.8 - - + -
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Residues in contact with ALA1087 (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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1083A ASP 2.9 19.0 + - - +
1084A THR* 3.2 6.9 + - + +
1086A TYR* 1.3 71.7 - - - +
1088A ILE* 1.3 67.0 + - + +
1090A LYS* 3.7 7.0 - - - +
1091A GLU* 3.0 41.7 + - - +
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Residues in contact with ILE1088 (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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992A PHE* 5.1 0.2 - - + -
996A VAL* 3.9 34.1 - - + -
999A ARG* 3.9 33.4 - - + +
1000A LEU* 4.4 11.7 - - + -
1084A THR* 2.9 37.7 + - + +
1085A ALA 3.7 3.8 - - - +
1087A ALA* 1.3 76.1 - - - +
1089A ILE* 1.3 59.3 + - - +
1091A GLU* 3.3 3.9 + - - -
1092A GLU* 2.9 57.0 + - + +
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Residues in contact with ILE1089 (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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992A PHE* 4.1 21.8 - - + -
993A LEU* 5.3 0.4 - - + -
996A VAL* 4.9 7.9 - - + -
1046A VAL* 3.7 22.9 - - + -
1049A TYR* 4.1 15.9 - - + -
1050A LEU* 3.5 32.3 - - + -
1085A ALA 3.0 17.5 + - - +
1086A TYR* 3.8 5.4 - - + +
1088A ILE* 1.3 75.6 - - - +
1090A LYS* 1.3 66.9 + - - +
1093A LEU* 2.9 52.4 + - + +
1206A DMS 4.4 21.1 - - + -
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Residues in contact with LYS1090 (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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1086A TYR 2.8 18.9 + - - +
1087A ALA* 3.7 8.3 - - - +
1088A ILE 3.3 0.2 - - - -
1089A ILE* 1.3 81.1 - - - +
1091A GLU* 1.3 63.2 + - + +
1093A LEU 4.6 5.2 - - - +
1206A DMS 6.4 0.7 - - - -
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Residues in contact with GLU1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A ALA* 3.0 32.6 + - - +
1088A ILE* 3.9 5.2 - - - +
1090A LYS* 1.3 79.9 - - + +
1092A GLU* 1.3 71.1 + - + +
1093A LEU 5.4 0.2 - - - -
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Residues in contact with GLU1092 (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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992A PHE* 4.2 16.8 - - + -
995A ASN* 4.7 0.3 - - - +
999A ARG* 2.5 47.6 + - - -
1088A ILE* 2.9 26.5 + - - +
1091A GLU* 1.3 93.8 - - + +
1093A LEU* 1.3 59.6 + - - +
1094A ASP 3.7 0.2 + - - -
1202A GOL 3.2 19.6 + - - -
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Residues in contact with LEU1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992A PHE* 4.1 21.3 - - + -
1046A VAL* 3.6 36.1 - - + -
1089A ILE* 2.9 34.9 + - + +
1090A LYS 4.6 5.4 - - - +
1091A GLU 5.4 0.2 - - - -
1092A GLU* 1.3 77.9 - - - +
1094A ASP* 1.3 72.7 + - - +
1095A GLU* 3.4 4.2 + - - +
1097A PHE* 3.9 25.1 - - + -
1098A GLU* 3.8 17.3 - - + +
1202A GOL 3.5 7.6 - - - -
1206A DMS 4.0 11.0 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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