Contacts of the helix formed by residues 1061 - 1085 (chain A) in PDB entry 3MPX
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 SER1061 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057A LEU* 5.4 1.8 - - - -
1058A CYS* 3.1 27.4 + - - -
1059A PRO 3.6 1.2 + - - -
1060A ASP* 1.3 78.5 - - - +
1062A ALA* 1.3 63.9 + - - +
1063A GLU* 3.0 14.4 - - - -
1064A TYR* 3.0 16.5 + - - +
1065A ASP* 3.2 16.9 + - - +
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Residues in contact with ALA1062 (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 ASP 4.5 0.4 + - - -
1061A SER* 1.3 71.8 - - - +
1063A GLU* 1.4 55.7 + - - +
1065A ASP* 3.7 7.8 - - - +
1066A ASN* 3.0 40.3 + - - +
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Residues in contact with GLU1063 (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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3A UNX 4.1 6.7 - - - -
974A GLN 4.2 2.5 - - - +
975A LYS* 3.5 25.0 - - + +
976A VAL 2.7 18.8 + - - -
977A ALA* 3.0 21.8 + - - +
978A ASP* 4.3 1.7 - - - +
1053A TYR* 2.6 30.9 + - - +
1057A LEU* 3.6 15.7 - - + -
1061A SER* 3.0 7.9 - - - -
1062A ALA* 1.4 76.5 - - - +
1064A TYR* 1.4 55.1 + - - +
1065A ASP 3.2 1.3 - - - -
1066A ASN* 3.8 11.1 + - - +
1067A THR* 2.7 37.6 + - - -
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Residues in contact with TYR1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A LEU* 3.3 57.3 - - + +
1057A LEU* 3.6 14.6 - - + +
1058A CYS 3.3 20.2 - - - +
1059A PRO* 3.6 43.9 - - + +
1061A SER* 3.0 10.3 + - - +
1063A GLU* 1.4 77.0 - - - +
1065A ASP* 1.3 65.4 + - - +
1068A GLN* 3.2 52.1 + - - +
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Residues in contact with ASP1065 (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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1059A PRO 5.0 3.6 - - - +
1060A ASP* 6.0 0.2 - - - -
1061A SER 3.2 14.3 + - - +
1062A ALA* 3.7 12.3 - - - +
1064A TYR* 1.3 79.6 - - - +
1066A ASN* 1.3 62.2 + - - +
1068A GLN* 3.2 20.4 + - - +
1069A GLY* 3.0 23.4 + - - -
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Residues in contact with ASN1066 (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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977A ALA* 3.7 14.4 - - + +
978A ASP* 3.8 20.4 + - - +
981A LEU* 3.7 26.1 - - + +
1062A ALA* 3.0 25.5 + - - +
1063A GLU* 3.4 13.7 + - - +
1065A ASP* 1.3 73.9 - - - +
1067A THR* 1.4 54.0 + - - +
1069A GLY* 3.3 3.0 + - - +
1070A ALA* 2.8 34.5 + - - +
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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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977A ALA* 3.3 10.8 - - - +
1050A LEU* 3.3 36.3 - - + +
1053A TYR* 3.3 31.7 - - + -
1054A LEU* 3.7 19.5 - - + -
1057A LEU* 3.4 2.8 - - - +
1063A GLU 2.7 27.3 + - - -
1064A TYR 3.8 4.9 - - - -
1065A ASP 3.3 0.4 - - - -
1066A ASN* 1.4 67.9 - - - +
1068A GLN* 1.4 55.4 + - - +
1070A ALA* 3.3 4.4 + - - +
1071A LEU* 2.8 37.2 + - + +
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Residues in contact with GLN1068 (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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1054A LEU* 3.8 17.3 - - + +
1064A TYR* 3.2 50.2 + - - +
1065A ASP* 3.2 20.0 + - - +
1067A THR* 1.4 75.9 - - - +
1069A GLY* 1.3 56.0 + - - +
1071A LEU* 3.2 10.5 + - + +
1072A SER* 2.9 28.6 + - - -
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Residues in contact with GLY1069 (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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981A LEU* 3.5 17.4 - - - +
1065A ASP 3.0 13.0 + - - -
1066A ASN* 3.3 4.0 + - - -
1068A GLN* 1.3 76.0 - - - +
1070A ALA* 1.4 55.9 + - - +
1072A SER* 3.1 9.7 + - - -
1073A LEU* 3.0 28.9 + - - +
1076A LYS* 5.0 0.3 + - - -
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Residues in contact with ALA1070 (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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977A ALA* 4.0 10.5 - - + +
980A PHE* 3.8 31.0 - - + -
981A LEU* 3.5 7.7 - - + +
1050A LEU* 4.5 7.6 - - + -
1066A ASN 2.8 19.3 + - - +
1067A THR* 3.6 9.2 - - - +
1069A GLY* 1.4 70.5 - - - +
1071A LEU* 1.3 62.1 + - - +
1073A LEU* 3.7 5.6 - - - +
1074A ILE* 3.1 32.8 + - - +
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Residues in contact with LEU1071 (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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1047A GLN* 3.7 42.4 - - + +
1050A LEU* 3.8 28.7 - - + +
1051A THR* 3.7 18.4 - - - +
1054A LEU* 4.6 13.5 - - + -
1067A THR* 2.8 26.0 + - + +
1068A GLN* 3.2 9.1 + - + +
1070A ALA* 1.3 79.9 - - - +
1072A SER* 1.3 56.2 + - - +
1074A ILE* 3.7 2.7 + - + +
1075A SER* 3.0 27.5 + - - -
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Residues in contact with SER1072 (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 GLN 2.9 13.4 + - - -
1069A GLY* 3.1 16.3 + - - -
1070A ALA 3.4 0.2 - - - -
1071A LEU* 1.3 75.2 - - - +
1073A LEU* 1.4 59.3 + - - +
1075A SER* 2.9 22.1 + - - -
1076A LYS* 2.9 37.3 + - - +
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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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980A PHE* 3.9 20.6 - - + +
981A LEU* 3.9 21.1 - - + +
983A ARG 4.4 0.9 - - - +
984A GLU* 4.0 37.2 - - + +
987A PHE* 3.7 39.7 - - + -
1069A GLY 3.0 16.1 + - - +
1070A ALA* 3.7 6.3 - - - +
1072A SER* 1.4 77.2 + - - +
1074A ILE* 1.3 64.1 + - + +
1076A LYS* 3.4 30.3 - - - +
1077A VAL* 3.4 13.0 - - + +
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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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980A PHE* 4.0 11.4 - - + -
987A PHE* 4.4 19.1 - - + -
1043A LEU* 3.4 32.3 - - + +
1046A TYR* 3.6 29.4 - - + -
1047A GLN* 3.7 15.5 - - + -
1050A LEU* 3.7 16.6 - - + -
1070A ALA 3.1 21.6 + - - +
1071A LEU* 4.1 4.0 - - + +
1073A LEU* 1.3 79.9 - - + +
1075A SER* 1.4 59.6 - - - +
1077A VAL* 3.0 10.2 + - - +
1078A THR* 2.8 30.9 + - + -
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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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1047A GLN* 3.6 9.2 - - - -
1071A LEU 3.0 16.9 + - - -
1072A SER* 2.9 20.7 + - - -
1074A ILE* 1.4 72.9 - - - +
1076A LYS* 1.4 58.3 + - - +
1078A THR* 3.3 9.4 - - - -
1079A ASP* 2.9 44.0 + - - +
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Residues in contact with LYS1076 (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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984A GLU* 4.7 14.7 + - - -
1069A GLY 5.0 0.4 + - - -
1072A SER* 2.9 32.0 + - - +
1073A LEU* 3.4 30.4 - - - +
1075A SER* 1.4 77.8 + - - +
1077A VAL* 1.4 62.2 + - + +
1079A ASP* 3.6 18.3 - - - +
1080A ARG* 4.1 4.5 + - - +
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Residues in contact with VAL1077 (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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987A PHE* 3.6 42.4 - - + +
988A ASP* 5.6 2.9 - - - +
990A HIS* 3.6 13.0 - - + -
991A ALA* 3.6 26.7 - - + +
994A ILE* 3.8 7.3 - - + +
1043A LEU* 3.8 15.5 - - + -
1073A LEU* 3.4 16.6 - - + +
1074A ILE* 3.0 10.2 + - - +
1076A LYS* 1.4 74.3 - - + +
1078A THR* 1.4 63.1 + - - +
1079A ASP 3.2 1.3 - - - -
1080A ARG* 3.3 20.7 + - - +
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Residues in contact with THR1078 (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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994A ILE* 5.1 0.7 - - - -
1043A LEU* 3.6 32.8 - - + -
1044A PHE* 3.7 28.9 - - + -
1047A GLN* 2.7 30.9 + - - +
1074A ILE* 2.8 21.2 + - + +
1075A SER* 3.3 7.6 + - - -
1077A VAL* 1.4 67.1 - - - +
1079A ASP* 1.3 61.0 + - - +
1080A ARG 3.2 0.4 - - - -
1081A ALA* 3.0 17.9 + - + +
1082A ASN* 2.6 27.3 + - - -
1092A GLN* 5.2 0.7 + - - -
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Residues in contact with ASP1079 (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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1075A SER* 2.9 33.9 + - - +
1076A LYS* 3.6 13.0 - - - +
1078A THR* 1.3 79.2 + - - +
1080A ARG* 1.4 59.0 + - - +
1082A ASN* 3.3 11.9 + - - +
1083A ASP* 2.9 33.9 + - - +
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Residues in contact with ARG1080 (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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991A ALA* 4.7 10.5 - - + +
994A ILE* 3.4 16.4 - - + -
995A LEU* 4.7 14.6 - - + -
1076A LYS 4.1 4.9 + - - +
1077A VAL* 3.3 13.5 + - - +
1078A THR 3.2 0.2 - - - -
1079A ASP* 1.4 75.6 - - - +
1081A ALA* 1.3 56.1 + - - +
1083A ASP* 3.7 11.4 - - - +
1084A SER* 2.7 39.0 + - - -
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Residues in contact with ALA1081 (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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994A ILE* 3.4 28.9 - - + +
1040A VAL* 4.2 11.2 - - + -
1044A PHE* 3.8 23.8 - - + -
1077A VAL 3.8 1.0 + - - -
1078A THR* 3.0 13.4 + - - +
1080A ARG* 1.3 77.0 - - - +
1082A ASN* 1.3 56.3 + - - +
1085A MSE 3.0 40.4 + - - +
1088A GLY* 3.6 6.8 - - - -
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Residues in contact with ASN1082 (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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8A UNX 2.9 19.9 - - - -
1044A PHE* 4.1 8.4 - - - -
1078A THR* 2.6 28.9 + - - -
1079A ASP* 3.5 12.5 + - - +
1081A ALA* 1.3 75.4 - - - +
1083A ASP* 1.3 58.6 + - + +
1088A GLY 3.7 5.2 - - - +
1089A GLU* 3.6 25.7 + - + +
1092A GLN* 3.0 32.9 + - - +
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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
----------------------------------------------------------
995A LEU* 5.7 0.2 - - - +
1079A ASP* 2.9 25.8 + - - +
1080A ARG* 3.6 9.2 + - - +
1082A ASN* 1.3 78.9 - - + +
1084A SER* 1.4 70.7 + - - +
1085A MSE 3.8 1.1 - - - -
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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
----------------------------------------------------------
994A ILE* 4.1 14.6 - - - +
995A LEU* 3.7 33.5 - - - +
998A ASP* 3.6 11.6 + - - +
1080A ARG 2.7 20.3 + - - -
1083A ASP* 1.4 85.1 + - - +
1085A MSE 1.4 62.7 + - - +
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Residues in contact with MSE1085 (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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8A UNX 2.1 33.4 - - - -
994A ILE* 3.9 26.2 - - + +
997A PHE* 3.8 34.5 - - + -
998A ASP* 3.4 6.5 - - - +
1037A LEU* 3.7 30.3 - - + -
1040A VAL* 3.7 33.4 - - + -
1081A ALA* 3.0 16.8 + - - +
1083A ASP 3.8 0.4 - - - -
1084A SER* 1.4 81.7 - - - +
1086A GLU* 1.3 57.1 + - - +
1087A GLN* 3.2 3.8 + - + -
1088A GLY* 3.2 16.5 + - - +
1091A LEU* 4.8 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