Contacts of the helix formed by residues 1108 - 1129 (chain H) in PDB entry 3F5P
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 SER1108 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106H PRO 3.6 1.3 + - - -
1107H PRO* 1.3 72.2 - - - +
1109H LEU* 1.3 57.5 + - - +
1110H SER* 3.9 8.6 + - - -
1111H LYS* 2.6 51.8 + - - +
1112H MET 3.0 9.2 + - - -
1001R MET* 4.0 21.2 - - - +
1014R TYR* 2.8 19.2 + - - -
1034R THR* 4.6 14.1 + - - -
1036R ASN* 6.4 2.0 - - - -
1074R PRO* 6.0 5.8 - - - -
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Residues in contact with LEU1109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107H PRO 3.4 4.1 + - - -
1108H SER* 1.3 69.7 - - - +
1110H SER* 1.3 56.9 + - - +
1112H MET* 3.2 9.9 + - + -
1113H ILE* 2.8 53.5 + - + +
1238H PRO* 4.0 29.5 - - + +
1240H MET* 4.0 24.7 - - + -
1241H LEU* 4.6 13.9 - - + -
1036R ASN* 6.0 3.7 - - + +
1073R GLN* 5.9 7.4 - - + -
1074R PRO* 6.0 5.4 - - + -
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Residues in contact with SER1110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108H SER* 2.9 9.7 + - - -
1109H LEU* 1.3 82.0 - - - +
1111H LYS* 1.3 62.7 + - - +
1113H ILE* 3.5 6.3 + - - +
1114H GLN* 3.2 22.5 + - - +
1269H GLU* 4.6 14.0 + - - +
1271H GLU* 5.9 2.9 - - - +
1001R MET* 6.3 0.9 - - - -
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Residues in contact with LYS1111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107H PRO* 3.8 13.9 - - + -
1108H SER* 2.6 34.8 + - - +
1110H SER* 1.3 74.0 - - - +
1112H MET* 1.3 60.3 - - - +
1114H GLN* 3.2 8.5 + - + +
1115H MET* 3.2 29.4 + - + +
1271H GLU* 6.0 0.2 + - - -
1001R MET* 4.0 14.3 + - - +
1002R SER 2.7 29.1 + - - -
1004R GLU* 3.9 9.9 - - - +
1014R TYR* 3.4 32.5 - - - +
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Residues in contact with MET1112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106H PRO* 3.4 21.5 - - + -
1107H PRO* 3.7 27.1 - - + +
1108H SER 3.0 6.6 + - - +
1109H LEU* 3.6 12.8 - - + +
1111H LYS* 1.3 75.3 - - - +
1113H ILE* 1.3 54.6 + - - +
1114H GLN 3.2 0.2 + - - -
1115H MET* 3.2 6.2 + - - +
1116H ALA* 2.7 37.0 + - - +
1202H LEU* 5.2 0.6 - - + +
1205H ILE* 3.1 34.3 - - + +
1206H ALA* 2.8 44.2 - - + +
1238H PRO* 5.1 5.8 - - - -
1241H LEU* 3.5 24.9 - - + -
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Residues in contact with ILE1113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109H LEU* 2.8 36.4 + - + +
1110H SER* 3.9 6.3 - - - +
1112H MET* 1.3 71.2 - - - +
1114H GLN* 1.3 56.3 + - - +
1116H ALA* 3.5 7.5 - - + +
1117H GLY* 2.7 24.8 + - - -
1240H MET* 3.9 22.7 - - + -
1241H LEU* 3.7 28.0 - - + -
1244H LEU* 5.3 1.1 - - + -
1266H ILE* 3.9 34.5 - - + +
1269H GLU* 4.2 26.0 - - + +
1270H MET* 3.5 5.9 - - - +
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Residues in contact with GLN1114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110H SER 3.2 13.8 + - - +
1111H LYS* 3.3 12.6 - - + +
1112H MET 3.1 0.6 - - - -
1113H ILE* 1.3 75.1 - - - +
1115H MET* 1.3 66.7 + - - +
1117H GLY 3.3 0.5 + - - -
1118H GLU* 2.9 56.2 + - - +
1147H PHE 6.1 0.7 - - - +
1269H GLU 4.2 2.6 - - - +
1270H MET* 3.5 25.9 - - - +
1271H GLU* 3.0 56.1 + - + +
1274H PHE* 5.2 4.0 - - - +
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Residues in contact with MET1115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087H LEU* 3.7 22.2 - - + -
1090H TYR* 3.4 35.2 - - + +
1091H LEU* 4.5 4.9 - - + -
1107H PRO* 5.5 6.5 - - + -
1111H LYS* 3.2 17.5 + - + +
1112H MET* 3.6 7.9 - - - +
1114H GLN* 1.3 79.7 - - + +
1116H ALA* 1.3 63.1 + - - +
1118H GLU* 3.8 8.8 - - - +
1119H ILE* 2.9 32.6 + - + +
1143H VAL* 5.5 1.1 - - + -
1147H PHE* 5.1 7.6 - - + +
1149H VAL* 3.4 24.2 - - + -
1205H ILE* 4.0 31.6 - - + -
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Residues in contact with ALA1116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112H MET 2.7 21.7 + - - +
1113H ILE* 3.5 17.9 - - + +
1115H MET* 1.3 73.0 - - - +
1117H GLY* 1.3 57.3 + - - +
1119H ILE* 4.7 1.1 - - - -
1120H ALA* 3.0 31.2 + - - +
1198H PHE* 3.6 12.3 - - + -
1202H LEU* 3.5 32.1 - - + -
1205H ILE* 4.7 2.4 - - - +
1241H LEU* 5.0 0.7 - - + -
1244H LEU* 5.5 2.9 - - + -
1266H ILE* 4.4 6.5 - - + -
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Residues in contact with GLY1117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113H ILE 2.7 20.6 + - - -
1116H ALA* 1.3 73.0 - - - +
1118H GLU* 1.3 57.5 + - - +
1120H ALA* 3.3 7.0 + - - +
1121H ASP* 2.8 29.7 + - - +
1263H ILE* 4.2 6.9 - - - +
1266H ILE* 3.7 17.0 - - - +
1270H MET* 3.8 14.4 - - - -
1274H PHE* 4.4 3.5 - - - -
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Residues in contact with GLU1118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061H HIS* 3.4 31.9 + - + +
1114H GLN* 2.9 49.5 + - - +
1115H MET* 3.8 4.0 - - - +
1117H GLY* 1.3 75.6 - - - +
1119H ILE* 1.3 61.6 + - - +
1121H ASP* 3.0 14.2 + - - +
1122H GLY 3.1 10.9 + - - -
1147H PHE 4.3 2.5 - - - +
1148H THR* 3.6 25.0 + - - +
1149H VAL* 2.9 39.4 + - - +
1270H MET* 3.9 11.4 - - + -
1274H PHE* 4.6 0.4 - - + -
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Residues in contact with ILE1119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061H HIS* 5.6 0.2 - - - -
1087H LEU* 3.8 19.3 - - + -
1115H MET* 2.9 21.6 + - + +
1116H ALA* 3.9 4.3 - - - +
1118H GLU* 1.3 74.3 - - - +
1120H ALA* 1.3 64.4 + - - +
1121H ASP 3.0 0.7 + - - -
1122H GLY* 3.2 2.9 + - - -
1123H MET* 3.0 27.2 + - + +
1136H LEU* 4.4 8.7 - - + -
1141H CYS* 4.0 10.8 - - - -
1149H VAL* 3.4 29.8 + - + -
1151H ILE* 3.8 22.9 - - + +
1198H PHE* 3.8 22.2 - - + -
1201H VAL* 4.1 16.4 - - + -
1205H ILE* 4.4 8.3 - - + -
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Residues in contact with ALA1120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116H ALA 3.0 20.2 + - - +
1117H GLY* 3.4 6.7 - - - +
1119H ILE* 1.3 76.9 - - - +
1121H ASP* 1.3 56.9 + - - +
1123H MET* 3.4 1.8 + - - +
1124H ALA* 2.8 30.7 + - - +
1198H PHE* 3.9 17.0 - - + -
1259H PHE* 3.7 20.1 - - + +
1262H ILE* 4.4 8.7 - - + -
1263H ILE* 3.6 19.5 - - + +
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Residues in contact with ASP1121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059H CYS* 4.4 2.5 - - - -
1061H HIS* 2.9 23.2 + - - +
1117H GLY 2.8 13.3 + - - +
1118H GLU 3.0 10.5 + - - +
1120H ALA* 1.3 74.9 - - - +
1122H GLY* 1.3 65.4 + - - +
1124H ALA* 3.2 4.0 + - - +
1125H TYR* 3.1 21.0 + - - +
1263H ILE* 3.5 10.8 - - + +
1274H PHE* 4.0 5.6 - - + -
1278H SER* 3.3 8.5 - - - -
1279H PHE* 2.7 29.3 + - - +
1280H TYR* 2.9 33.3 + - - +
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Residues in contact with GLY1122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059H CYS* 4.2 4.5 - - - -
1061H HIS* 3.8 24.1 - - - +
1062H VAL* 4.2 11.1 - - - +
1118H GLU 3.1 7.7 + - - -
1119H ILE 3.2 2.2 + - - -
1121H ASP* 1.3 76.9 - - - +
1123H MET* 1.3 57.3 + - - +
1125H TYR* 2.9 8.0 + - - +
1126H LEU* 2.9 27.9 + - - +
1151H ILE* 4.1 8.7 - - - -
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Residues in contact with MET1123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119H ILE* 3.0 21.5 + - + +
1120H ALA 3.7 4.3 - - - +
1122H GLY* 1.3 75.2 - - - +
1124H ALA* 1.3 62.4 + - - +
1126H LEU* 3.2 9.5 + - + +
1127H ASN* 3.0 29.2 + - - +
1133H HIS* 4.0 22.4 - - + -
1136H LEU* 4.1 34.8 - - + -
1151H ILE* 4.1 11.4 - - + +
1194H ASP* 3.4 37.0 - - + +
1259H PHE* 3.5 38.6 - - + -
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Residues in contact with ALA1124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120H ALA 2.8 18.1 + - - +
1121H ASP 3.4 7.0 - - - +
1122H GLY 3.2 0.2 - - - -
1123H MET* 1.3 77.0 - - - +
1125H TYR* 1.3 56.9 + - - +
1127H ASN* 3.4 3.4 + - - +
1128H ALA* 2.9 30.7 + - - +
1259H PHE* 3.8 19.9 - - + +
1260H LEU* 3.8 29.5 - - + +
1263H ILE* 4.2 4.9 - - + -
1279H PHE* 3.7 7.8 - - + -
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Residues in contact with TYR1125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056H GLU* 3.8 4.7 + - - +
1057H PHE* 3.4 32.2 - + + -
1058H ASN* 2.7 36.9 + - - +
1059H CYS* 3.6 26.0 - - + -
1062H VAL* 4.2 9.0 - - + -
1121H ASP 3.1 12.0 + - - +
1122H GLY 2.9 10.7 + - - +
1124H ALA* 1.3 76.2 - - - +
1126H LEU* 1.3 65.5 + - + +
1128H ALA* 3.5 0.5 + - - +
1129H ASN* 2.7 56.6 + - - -
1279H PHE* 3.6 32.7 - + + -
1284H GLU* 3.8 20.2 + - - -
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Residues in contact with LEU1126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057H PHE* 3.1 49.1 - - + -
1062H VAL* 5.3 3.4 - - + -
1122H GLY 2.9 12.6 + - - +
1123H MET* 3.2 15.9 + - + +
1125H TYR* 1.3 79.9 - - + +
1127H ASN* 1.3 63.3 + - - +
1129H ASN* 3.0 19.5 + - - +
1130H LYS 3.2 8.0 + - - -
1131H PHE* 3.2 21.8 + - + +
1133H HIS* 3.9 35.4 - - + +
1151H ILE* 4.9 1.3 - - + -
1154H PHE* 3.8 24.5 - - + -
1157H THR* 4.8 2.0 - - + +
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Residues in contact with ASN1127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123H MET* 3.0 18.2 + - - +
1124H ALA* 4.0 5.2 - - - +
1126H LEU* 1.3 77.8 - - - +
1128H ALA* 1.3 58.7 + - - +
1130H LYS* 3.0 24.8 + - - +
1131H PHE 2.7 31.1 + - - +
1160H ILE* 5.8 0.6 - - - +
1191H THR* 3.1 39.9 + - + +
1194H ASP* 3.5 16.0 + - - -
1259H PHE* 3.2 26.3 - - + -
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Residues in contact with ALA1128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124H ALA 2.9 18.1 + - - +
1125H TYR 3.8 4.5 - - - +
1126H LEU 3.2 0.4 - - - -
1127H ASN* 1.3 77.9 - - - +
1129H ASN* 1.3 61.0 + - - +
1130H LYS* 3.1 9.8 + - - +
1260H LEU* 6.5 0.9 - - + -
1279H PHE* 3.5 27.4 - - + -
1284H GLU 5.9 0.4 - - - +
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Residues in contact with ASN1129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056H GLU* 4.4 16.2 - - - +
1057H PHE* 5.0 3.1 - - + -
1125H TYR* 2.7 58.0 + - - +
1126H LEU* 3.0 10.0 + - - +
1128H ALA* 1.3 79.8 - - - +
1130H LYS* 1.3 71.5 + - - +
1131H PHE* 3.1 24.2 - - + -
1159H ASP* 4.8 1.0 - - - +
1279H PHE* 5.7 0.6 - - - -
1284H GLU* 5.5 0.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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