Contacts of the helix formed by residues 1108 - 1129 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105M ALA 4.4 2.8 + - - -
1106M PRO* 4.2 1.4 - - - +
1107M PRO* 1.3 76.2 - - - +
1109M LEU* 1.3 66.3 + - - +
1110M SER* 4.0 8.1 + - - -
1111M LYS* 3.0 35.2 + - - +
1112M MET* 3.1 12.4 + - - +
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Residues in contact with LEU1109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107M PRO 4.1 0.2 + - - -
1108M SER* 1.3 72.5 - - - +
1110M SER* 1.3 60.4 + - - +
1112M MET* 3.3 6.6 + - - +
1113M ILE* 2.9 39.6 + - + +
1238M PRO* 3.7 37.5 - - + +
1240M MET* 4.4 21.8 - - + -
1241M LEU* 4.3 14.1 - - + -
1269M GLU* 6.4 1.1 - - + -
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Residues in contact with SER1110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108M SER* 3.1 8.7 + - - -
1109M LEU* 1.3 76.0 - - - +
1111M LYS* 1.3 68.7 + - - +
1113M ILE* 3.2 8.6 + - - +
1114M GLN* 2.9 24.1 + - - +
1269M GLU* 5.1 15.3 + - - +
1271M GLU* 4.9 13.1 + - - +
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Residues in contact with LYS1111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106M PRO* 6.3 0.9 - - + -
1107M PRO* 3.8 16.2 - - + -
1108M SER* 3.0 25.8 + - - +
1110M SER* 1.3 79.2 - - - +
1112M MET* 1.3 63.1 + - - +
1114M GLN* 3.1 23.1 - - + +
1115M MET* 3.2 17.1 + - + +
1271M GLU* 5.8 5.9 - - - +
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Residues in contact with MET1112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107M PRO* 3.9 31.4 - - + +
1108M SER 3.1 18.9 + - - +
1109M LEU* 3.6 9.0 - - - +
1111M LYS* 1.3 73.1 - - - +
1113M ILE* 1.3 67.8 + - - +
1114M GLN 3.0 1.3 - - - -
1115M MET* 2.8 11.6 + - - +
1116M ALA* 2.8 23.4 + - - +
1205M ILE* 3.3 26.9 - - + +
1206M ALA* 3.2 39.9 - - + +
1237M CYS* 6.1 0.2 - - - -
1238M PRO* 4.7 12.8 - - + -
1241M LEU* 3.7 28.9 - - + -
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Residues in contact with ILE1113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109M LEU* 2.9 36.9 + - + +
1110M SER* 3.6 7.6 - - - +
1112M MET* 1.3 75.1 - - - +
1114M GLN* 1.3 56.7 + - - +
1116M ALA* 3.1 7.1 + - + +
1117M GLY 2.8 26.5 + - - -
1240M MET* 3.2 45.3 - - + -
1241M LEU* 4.9 4.7 - - + +
1266M ILE* 3.7 29.1 - - + +
1269M GLU* 4.0 28.7 - - + +
1270M MET* 3.6 10.1 - - - +
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Residues in contact with GLN1114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110M SER 2.9 12.4 + - - +
1111M LYS* 3.1 19.1 - - + +
1113M ILE* 1.3 77.9 - - - +
1115M MET* 1.3 62.1 + - + +
1118M GLU* 3.0 54.8 + - - +
1269M GLU 4.6 1.2 + - - +
1270M MET* 3.0 32.5 - - - +
1271M GLU* 2.8 56.1 + - + +
1274M PHE* 4.9 3.4 - - - +
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Residues in contact with MET1115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087M LEU* 3.9 23.3 - - + -
1090M TYR* 3.5 32.5 - - + +
1091M LEU* 4.8 5.4 - - + -
1094M LEU* 5.8 1.1 - - + -
1107M PRO* 5.4 6.7 - - + -
1111M LYS* 3.2 14.3 + - + +
1112M MET* 2.8 9.5 + - - +
1114M GLN* 1.3 79.0 - - + +
1116M ALA* 1.3 64.0 + - - +
1118M GLU* 3.2 8.6 + - - +
1119M ILE* 3.0 31.2 + - + +
1143M VAL* 5.1 0.9 - - + -
1147M PHE* 4.9 8.5 - - + +
1149M VAL* 3.5 25.1 - - + +
1205M ILE* 3.8 30.3 - - + -
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Residues in contact with ALA1116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112M MET 2.8 15.9 + - - +
1113M ILE* 3.1 12.1 + - - +
1115M MET* 1.3 73.3 - - - +
1117M GLY* 1.3 57.8 + - - +
1119M ILE* 4.8 2.7 - - - -
1120M ALA* 2.9 30.5 + - - +
1198M PHE* 3.3 13.1 - - + -
1202M LEU* 3.4 34.1 - - + -
1205M ILE* 4.7 0.8 - - - +
1241M LEU* 5.1 4.3 - - + -
1244M LEU* 5.5 4.3 - - + -
1262M ILE* 6.1 0.4 - - + -
1266M ILE* 4.3 8.7 - - + -
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Residues in contact with GLY1117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113M ILE 2.8 12.4 + - - -
1114M GLN 3.9 1.1 - - - -
1116M ALA* 1.3 77.5 - - - +
1118M GLU* 1.3 61.1 + - - +
1120M ALA* 3.7 5.5 - - - +
1121M ASP* 3.0 29.5 + - - +
1263M ILE* 4.3 4.3 - - - +
1266M ILE* 3.6 20.8 - - - +
1270M MET* 3.9 12.1 - - - -
1274M PHE* 3.9 6.5 - - - -
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Residues in contact with GLU1118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061M HIS* 3.2 52.2 + - + +
1114M GLN* 3.0 45.3 + - - +
1115M MET* 3.2 5.1 + - - +
1117M GLY* 1.3 77.1 - - - +
1119M ILE* 1.3 64.8 + - - +
1121M ASP 3.5 0.3 + - - -
1122M GLY* 3.3 6.6 + - - -
1147M PHE 4.3 1.4 - - - +
1148M THR* 3.4 30.6 + - - +
1149M VAL* 3.0 34.9 + - + +
1270M MET* 4.0 9.4 - - + -
1274M PHE* 4.7 1.4 - - + -
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Residues in contact with ILE1119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087M LEU* 3.9 27.1 - - + -
1115M MET* 3.0 23.6 + - + +
1116M ALA* 4.8 1.8 - - - -
1118M GLU* 1.3 72.9 - - - +
1120M ALA* 1.3 68.3 + - - +
1121M ASP 3.1 0.2 + - - -
1122M GLY* 3.2 2.6 + - - -
1123M MET* 2.9 26.9 + - + +
1136M LEU* 4.4 9.2 - - + -
1141M CYS* 4.2 7.9 - - - -
1149M VAL* 3.8 20.0 - - + -
1151M ILE* 3.7 22.5 - - + +
1198M PHE* 3.6 25.4 - - + -
1201M VAL* 4.0 19.1 - - + -
1205M ILE* 4.3 6.7 - - + -
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Residues in contact with ALA1120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116M ALA 2.9 21.3 + - - +
1117M GLY* 3.7 4.3 - - - +
1119M ILE* 1.3 78.7 - - - +
1121M ASP* 1.3 51.1 + - - +
1123M MET* 3.2 2.8 + - - +
1124M ALA* 2.8 35.3 + - - +
1198M PHE* 3.7 17.2 - - + -
1259M PHE* 3.7 18.6 - - + +
1262M ILE* 4.7 8.7 - - + -
1263M ILE* 3.7 21.8 - - + -
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Residues in contact with ASP1121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059M CYS* 4.4 1.9 - - - -
1061M HIS* 2.8 28.8 + - - +
1117M GLY 3.0 19.1 + - - +
1118M GLU 3.7 1.1 - - - +
1119M ILE 3.1 0.4 - - - -
1120M ALA* 1.3 77.4 - - - +
1122M GLY* 1.3 62.1 + - - +
1124M ALA* 3.2 3.1 + - - +
1125M TYR* 3.1 21.3 + - - +
1263M ILE* 3.5 12.3 - - + +
1274M PHE* 4.1 4.9 - - + -
1278M SER* 3.2 9.6 - - - -
1279M PHE* 2.7 27.8 + - - +
1280M TYR* 2.9 31.7 + - - +
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Residues in contact with GLY1122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059M CYS* 4.2 4.9 - - - -
1061M HIS* 3.9 24.1 - - - +
1062M VAL* 4.1 12.5 - - - +
1118M GLU 3.3 4.8 + - - -
1119M ILE 3.2 6.1 + - - -
1121M ASP* 1.3 79.1 - - - +
1123M MET* 1.3 55.9 + - - +
1125M TYR* 3.2 4.3 + - - +
1126M LEU* 2.9 29.0 + - - +
1151M ILE* 4.2 7.4 - - - -
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Residues in contact with MET1123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119M ILE* 2.9 21.9 + - + +
1120M ALA 3.6 3.8 - - - +
1122M GLY* 1.3 73.9 - - - +
1124M ALA* 1.3 64.0 + - - +
1125M TYR 3.1 1.6 - - - -
1126M LEU* 3.5 19.8 - - + +
1127M ASN* 3.0 32.0 + - - +
1133M HIS* 4.0 11.4 - - + -
1136M LEU* 3.8 33.9 - - + -
1151M ILE* 4.2 9.6 - - + +
1194M ASP* 3.2 43.7 - - + +
1259M PHE* 3.5 28.0 - - + -
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Residues in contact with ALA1124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120M ALA 2.8 20.1 + - - +
1121M ASP 3.2 6.0 + - - +
1123M MET* 1.3 74.2 - - - +
1125M TYR* 1.3 56.5 + - - +
1127M ASN* 3.5 3.6 + - - +
1128M ALA* 3.0 28.8 + - - +
1259M PHE* 3.6 17.0 - - + +
1260M LEU* 3.5 34.2 - - + +
1263M ILE* 4.1 5.2 - - + -
1279M PHE* 3.8 7.3 - - + -
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Residues in contact with TYR1125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056M GLU 3.8 5.4 + - - -
1057M PHE* 3.5 22.7 - + + -
1058M ASN* 2.7 42.6 + - - +
1059M CYS* 3.5 27.6 - - + -
1062M VAL* 4.2 8.3 - - + -
1121M ASP 3.1 11.8 + - - +
1122M GLY 3.3 8.1 - - - +
1123M MET 3.1 0.2 - - - -
1124M ALA* 1.3 75.5 - - - +
1126M LEU* 1.3 69.4 + - + +
1128M ALA* 3.1 8.1 + - - +
1129M ASN* 2.8 47.5 + - - -
1279M PHE* 3.4 32.3 - + + -
1284M GLU* 3.4 28.4 + - - -
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Residues in contact with LEU1126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057M PHE* 3.6 43.1 - - + -
1062M VAL* 5.3 2.7 - - + -
1122M GLY 2.9 14.9 + - - +
1123M MET* 3.5 18.2 - - + +
1125M TYR* 1.3 78.3 - - + +
1127M ASN* 1.3 64.4 + - - +
1129M ASN* 3.2 14.7 + - - +
1130M LYS 3.4 0.2 + - - -
1131M PHE* 3.2 34.3 + - + +
1133M HIS* 3.6 48.7 - - + +
1151M ILE* 4.8 1.6 - - + -
1154M PHE* 3.8 14.4 - - + -
1157M THR* 5.2 1.1 - - + +
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Residues in contact with ASN1127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123M MET* 3.0 17.0 + - - +
1124M ALA* 4.1 5.4 - - - +
1126M LEU* 1.3 79.7 - - - +
1128M ALA* 1.3 60.7 + - - +
1130M LYS* 3.3 21.1 + - - +
1131M PHE 2.8 23.8 + - - +
1132M VAL* 4.5 0.4 - - - +
1133M HIS 5.0 0.2 - - - +
1160M ILE* 5.7 0.2 - - - +
1191M THR* 3.6 36.9 - - + +
1194M ASP* 3.9 15.4 + - - -
1259M PHE* 3.0 34.5 - - + -
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Residues in contact with ALA1128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124M ALA 3.0 17.9 + - - +
1125M TYR 3.1 6.0 + - - +
1127M ASN* 1.3 79.2 - - - +
1129M ASN* 1.3 61.3 + - - +
1130M LYS* 3.1 14.3 + - - +
1279M PHE* 3.6 25.1 - - + -
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Residues in contact with ASN1129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056M GLU* 5.0 15.3 - - + +
1057M PHE* 5.2 3.6 - - + -
1125M TYR* 2.8 59.1 + - - -
1126M LEU* 3.2 7.8 + - - +
1128M ALA* 1.3 77.9 - - - +
1130M LYS* 1.3 64.4 + - - +
1131M PHE* 3.1 30.7 - - + -
1159M ASP* 5.5 0.9 - - - +
1284M GLU* 4.5 6.0 + - - +
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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) + - + + + + + -
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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