Contacts of the helix formed by residues 1108 - 1129 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106S PRO 3.6 2.0 + - - -
1107S PRO* 1.3 73.4 - - - +
1109S LEU* 1.3 55.6 + - - +
1110S SER* 3.5 11.4 + - - -
1111S LYS* 2.6 51.1 + - - +
1112S MET* 3.0 11.3 + - - +
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Residues in contact with LEU1109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107S PRO 4.0 1.4 + - - -
1108S SER* 1.3 71.3 - - - +
1110S SER* 1.3 63.3 + - - +
1112S MET* 3.4 6.4 + - - -
1113S ILE* 3.0 49.6 + - + +
1238S PRO* 3.7 35.7 - - + +
1240S MET* 4.2 20.4 - - + -
1241S LEU* 4.7 9.4 - - + -
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Residues in contact with SER1110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108S SER* 2.9 11.3 + - - -
1109S LEU* 1.3 79.6 - - - +
1111S LYS* 1.3 62.6 + - - +
1113S ILE* 3.9 6.0 + - - +
1114S GLN* 3.3 21.7 + - - +
1269S GLU 4.9 10.3 + - - +
1271S GLU* 5.0 13.9 + - - +
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Residues in contact with LYS1111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107S PRO* 4.3 9.9 - - + -
1108S SER* 2.6 37.6 + - - +
1110S SER* 1.3 73.7 - - - +
1112S MET* 1.3 63.4 + - - +
1114S GLN* 3.1 20.4 - - + +
1115S MET* 3.2 20.5 + - + +
1147S PHE* 5.7 10.7 - - - +
1271S GLU* 5.0 13.1 + - - +
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Residues in contact with MET1112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107S PRO* 3.7 33.9 - - + +
1108S SER 3.0 10.7 + - - +
1109S LEU* 3.9 11.0 - - + +
1111S LYS* 1.3 71.2 - - - +
1113S ILE* 1.3 55.8 + - - +
1114S GLN 3.0 1.1 - - - -
1115S MET* 2.8 11.6 + - - +
1116S ALA* 2.7 34.8 + - - +
1205S ILE* 3.1 44.7 - - + +
1206S ALA* 3.3 21.5 - - + +
1238S PRO* 4.7 13.2 - - + -
1241S LEU* 3.8 29.6 - - + -
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Residues in contact with ILE1113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109S LEU* 3.0 32.7 + - + +
1110S SER* 4.0 6.1 - - - +
1112S MET* 1.3 75.0 - - - +
1114S GLN* 1.3 58.6 + - - +
1116S ALA* 3.6 4.7 - - + +
1117S GLY 2.8 26.3 + - - -
1240S MET* 3.3 40.6 - - + -
1241S LEU* 3.6 17.3 - - + -
1244S LEU* 5.5 0.4 - - + -
1266S ILE* 4.0 29.2 - - + -
1269S GLU* 4.2 24.7 - - + +
1270S MET* 3.5 12.8 - - - +
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Residues in contact with GLN1114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110S SER 3.3 13.3 + - - +
1111S LYS* 3.1 17.2 + - + +
1112S MET 3.0 0.6 - - - -
1113S ILE* 1.3 80.4 - - - +
1115S MET* 1.3 59.5 + - + +
1118S GLU* 2.9 65.3 + - - +
1269S GLU 4.6 1.1 - - - +
1270S MET* 3.4 19.5 - - - +
1271S GLU* 3.3 50.4 + - + +
1274S PHE* 5.6 3.8 - - - +
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Residues in contact with MET1115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087S LEU* 4.0 20.4 - - + -
1090S TYR* 3.8 31.4 - - + +
1091S LEU* 4.6 4.9 - - + -
1094S LEU* 5.7 1.6 - - + -
1107S PRO* 6.1 5.2 - - + -
1111S LYS* 3.2 17.7 + - + +
1112S MET* 2.8 8.8 + - - +
1114S GLN* 1.3 74.5 - - + +
1116S ALA* 1.3 58.0 + - - +
1118S GLU* 2.7 29.5 + - - +
1119S ILE* 2.8 19.9 + - + +
1143S VAL* 5.7 1.6 - - + -
1147S PHE* 5.1 7.9 - - + +
1149S VAL* 3.7 23.8 - - + -
1205S ILE* 3.8 35.7 - - + -
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Residues in contact with ALA1116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112S MET 2.7 18.4 + - - +
1113S ILE* 3.6 10.3 - - + +
1115S MET* 1.3 72.6 - - - +
1117S GLY* 1.3 57.8 + - - +
1119S ILE* 4.7 3.6 - - - -
1120S ALA* 3.0 30.0 + - - +
1198S PHE* 3.4 13.9 - - + -
1201S VAL* 6.4 0.2 - - - -
1202S LEU* 3.5 28.7 - - + -
1205S ILE* 4.7 2.4 - - + +
1241S LEU* 4.9 5.8 - - + -
1244S LEU* 5.3 2.9 - - + -
1266S ILE* 4.5 9.8 - - + +
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Residues in contact with GLY1117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113S ILE 2.8 12.1 + - - -
1116S ALA* 1.3 75.2 - - - +
1118S GLU* 1.3 55.1 + - - +
1120S ALA* 3.4 5.0 + - - +
1121S ASP* 2.8 35.4 + - - +
1263S ILE* 4.5 5.3 - - - +
1266S ILE* 3.9 12.3 - - - +
1270S MET* 3.6 24.7 - - - -
1274S PHE* 4.4 5.4 - - - -
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Residues in contact with GLU1118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060S HIS* 5.8 0.2 - - - -
1061S HIS* 3.1 49.2 + - + +
1114S GLN* 2.9 54.2 + - - +
1115S MET* 2.7 5.7 + - - +
1117S GLY* 1.3 73.4 - - - +
1119S ILE* 1.3 65.0 + - - +
1121S ASP* 3.3 1.9 + - - +
1122S GLY* 3.3 16.5 + - - -
1147S PHE 4.2 2.8 - - - +
1148S THR* 3.5 21.6 + - - +
1149S VAL* 3.3 34.5 + - + +
1270S MET* 3.9 5.2 - - + -
1274S PHE* 4.9 1.2 - - + -
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Residues in contact with ILE1119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061S HIS 5.8 0.2 - - - -
1087S LEU* 4.0 26.7 - - + -
1115S MET* 2.8 16.5 + - + +
1116S ALA* 4.0 4.0 - - - +
1118S GLU* 1.3 75.2 - - - +
1120S ALA* 1.3 66.9 + - - +
1121S ASP 3.2 0.3 + - - -
1122S GLY* 3.3 2.9 + - - -
1123S MET* 3.1 26.0 + - + +
1136S LEU* 4.6 7.6 - - + -
1141S CYS* 4.1 15.3 - - - -
1149S VAL* 4.0 19.5 - - + -
1150S LYS 5.9 0.2 - - - -
1151S ILE* 4.0 19.4 - - + +
1198S PHE* 3.4 24.2 - - + -
1201S VAL* 4.3 12.1 - - + -
1205S ILE* 4.2 15.7 - - + -
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Residues in contact with ALA1120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116S ALA 3.0 21.2 + - - +
1117S GLY* 3.7 4.7 - - - +
1119S ILE* 1.3 77.5 - - - +
1121S ASP* 1.3 57.7 + - - +
1123S MET* 4.3 0.7 - - - -
1124S ALA* 2.8 29.5 + - - +
1198S PHE* 3.8 17.3 - - + -
1259S PHE* 3.5 22.8 - - + +
1262S ILE* 4.8 7.4 - - + -
1263S ILE* 3.9 17.0 - - + +
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Residues in contact with ASP1121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059S CYS* 4.0 2.4 - - - -
1061S HIS* 3.1 21.3 + - + -
1117S GLY 2.8 18.3 + - - +
1118S GLU 3.7 5.4 - - - +
1119S ILE 3.1 0.6 - - - -
1120S ALA* 1.3 75.4 - - - +
1122S GLY* 1.3 60.4 + - - +
1124S ALA* 3.2 2.9 + - - +
1125S TYR* 2.9 26.2 + - - +
1263S ILE* 3.4 12.9 - - + +
1274S PHE* 4.0 10.3 - - + -
1278S SER* 3.5 7.9 - - - -
1279S PHE* 3.0 26.3 + - - +
1280S TYR* 2.9 32.7 + - - +
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Residues in contact with GLY1122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059S CYS* 4.2 1.6 - - - -
1061S HIS* 3.8 27.3 - - - +
1062S VAL* 4.1 15.6 - - - +
1118S GLU 3.3 8.3 + - - -
1119S ILE 3.3 2.2 + - - -
1121S ASP* 1.3 78.4 - - - +
1123S MET* 1.3 57.6 + - - +
1125S TYR* 3.1 9.2 + - - +
1126S LEU* 2.9 25.7 + - - +
1151S ILE* 4.5 4.0 - - - -
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Residues in contact with MET1123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119S ILE* 3.1 22.6 + - + +
1120S ALA 3.7 3.1 - - - +
1122S GLY* 1.3 74.0 - - - +
1124S ALA* 1.3 63.9 + - - +
1126S LEU* 2.9 13.4 + - - -
1127S ASN* 2.7 29.7 + - - +
1133S HIS* 3.9 27.4 - - + -
1136S LEU* 3.7 30.1 - - + -
1151S ILE* 4.3 11.9 - - + +
1194S ASP* 3.5 41.5 - - + +
1259S PHE* 3.4 29.6 - - + -
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Residues in contact with ALA1124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120S ALA 2.8 17.7 + - - +
1121S ASP 3.3 6.7 - - - +
1123S MET* 1.3 74.6 - - - +
1125S TYR* 1.3 63.6 + - - +
1127S ASN* 3.3 3.4 + - - +
1128S ALA* 3.0 25.1 + - - +
1259S PHE* 3.6 21.4 - - + +
1260S LEU* 3.9 28.7 - - + +
1263S ILE* 4.1 6.1 - - + -
1279S PHE* 4.0 7.0 - - + -
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Residues in contact with TYR1125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056S GLU 3.5 10.6 + - - -
1057S PHE* 3.7 27.8 - + + -
1058S ASN* 2.8 38.4 + - - +
1059S CYS* 3.5 28.9 - - + -
1062S VAL* 4.4 6.7 - - + -
1121S ASP 2.9 12.3 + - - +
1122S GLY 3.1 9.8 + - - +
1124S ALA* 1.3 77.8 - - - +
1126S LEU* 1.3 63.7 + - + +
1128S ALA* 3.5 1.0 - - - +
1129S ASN* 2.8 51.2 + - - -
1279S PHE* 3.4 39.0 - + + -
1284S GLU* 4.3 18.4 + - - -
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Residues in contact with LEU1126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057S PHE* 3.7 40.4 - - + -
1062S VAL* 4.8 3.1 - - + -
1122S GLY 2.9 13.1 + - - +
1123S MET* 2.9 20.3 + - - +
1125S TYR* 1.3 82.2 - - + +
1127S ASN* 1.3 61.8 + - - +
1129S ASN* 3.0 20.0 + - - +
1130S LYS 3.3 0.2 + - - -
1131S PHE* 3.2 50.3 + - + +
1132S VAL 4.5 0.4 - - - -
1133S HIS* 4.2 22.9 - - + +
1151S ILE* 5.8 1.1 - - + -
1154S PHE* 4.2 22.2 - - + -
1157S THR* 4.7 3.6 - - - -
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Residues in contact with ASN1127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123S MET* 2.7 25.7 + - - +
1124S ALA* 4.1 3.1 - - - +
1126S LEU* 1.3 79.0 - - - +
1128S ALA* 1.3 64.3 + - - +
1130S LYS* 3.3 20.6 + - - +
1131S PHE 3.6 17.4 + - - +
1160S ILE* 5.8 0.6 - - - +
1191S THR* 2.9 43.6 - - + +
1194S ASP* 4.1 10.8 + - - +
1259S PHE* 3.4 25.4 - - + -
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Residues in contact with ALA1128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124S ALA 3.0 17.8 + - - +
1125S TYR 3.5 6.7 - - - +
1127S ASN* 1.3 74.3 - - - +
1129S ASN* 1.3 61.9 + - - +
1130S LYS* 3.0 17.1 + - - +
1260S LEU* 6.4 1.6 - - + -
1279S PHE* 3.6 24.7 - - + -
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Residues in contact with ASN1129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056S GLU* 4.1 22.8 - - - +
1057S PHE* 5.0 3.6 - - + -
1125S TYR* 2.8 50.4 + - - +
1126S LEU* 3.0 9.8 + - - +
1128S ALA* 1.3 78.1 - - - +
1130S LYS* 1.3 70.9 + - - +
1131S PHE* 3.4 26.1 - - + -
1159S ASP* 5.2 0.9 - - - +
1279S PHE* 5.4 1.2 - - - -
1284S GLU* 5.4 3.4 + - - +
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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
------------------------------------------------------------
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