Contacts of the helix formed by residues 1065 - 1088 (chain A) in PDB entry 1F5T
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 THR1065 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A GLY* 3.0 28.5 + - - +
1053A LEU* 3.1 5.2 + - - -
1054A VAL 3.8 17.0 - - - +
1055A VAL* 4.1 21.1 - - + -
1064A MET* 1.3 74.9 - - - +
1066A PRO* 1.3 77.3 - - - +
1067A THR* 3.5 4.3 + - - -
1068A GLY 2.8 12.5 + - - -
1069A ARG* 2.8 20.3 + - - +
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Residues in contact with PRO1066 (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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1064A MET 4.8 0.4 - - - +
1065A THR* 1.3 85.9 - - + +
1067A THR* 1.3 64.1 + - - +
1069A ARG* 3.3 7.3 + - + +
1070A THR* 2.9 27.6 + - - +
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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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1052A GLY 4.1 4.6 + - - -
1053A LEU* 3.7 20.4 - - + -
1065A THR* 3.1 8.9 + - - -
1066A PRO* 1.3 78.3 - - - +
1068A GLY* 1.3 65.4 + - - +
1070A THR* 2.9 17.6 + - - -
1071A LEU* 3.0 29.7 + - + +
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Residues in contact with GLY1068 (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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1012A LEU* 3.7 18.0 - - - +
1053A LEU* 3.5 27.5 - - - +
1064A MET* 4.2 7.2 - - - -
1065A THR* 2.8 13.3 + - - -
1067A THR* 1.3 80.5 - - - +
1069A ARG* 1.3 55.0 + - - +
1071A LEU 3.4 0.5 + - - -
1072A ALA* 2.9 28.9 + - - +
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Residues in contact with ARG1069 (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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1016A TYR* 4.9 11.2 - - + -
1019A GLU* 3.0 32.9 + - - -
1063A GLN* 5.6 3.4 + - - +
1064A MET* 3.4 49.2 + - + +
1065A THR 2.8 14.1 + - - +
1066A PRO* 3.7 9.6 - - + +
1068A GLY* 1.3 69.0 - - - +
1070A THR* 1.3 59.6 + - - +
1072A ALA* 3.4 1.8 + - + +
1073A THR* 2.6 40.6 + - - +
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Residues in contact with THR1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066A PRO 2.9 18.1 + - - -
1067A THR* 2.9 12.2 + - + -
1069A ARG* 1.3 78.5 - - - +
1071A LEU* 1.3 69.8 + - + +
1073A THR* 3.7 5.5 + - - -
1074A ALA* 3.2 20.8 + - + +
1077A ARG* 5.2 1.2 + - - -
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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
----------------------------------------------------------
1008A THR* 5.4 2.2 - - + -
1009A GLU* 6.1 2.7 - - + +
1012A LEU* 3.4 26.2 - - + -
1053A LEU* 4.0 28.0 - - + -
1067A THR* 3.0 19.4 + - + +
1068A GLY 3.8 0.4 - - - +
1070A THR* 1.3 79.9 - - + +
1072A ALA* 1.3 69.4 + - - +
1074A ALA* 2.8 10.0 + - + +
1075A VAL* 2.8 30.4 + - + +
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Residues in contact with ALA1072 (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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1012A LEU* 4.0 18.8 - - + +
1013A ARG* 5.0 2.6 - - - +
1016A TYR* 4.0 21.3 - - + -
1064A MET* 3.8 21.1 - - - -
1068A GLY 2.9 18.6 + - - +
1069A ARG* 3.5 5.4 - - - +
1071A LEU* 1.3 76.8 - - - +
1073A THR* 1.3 57.5 + - - +
1075A VAL* 3.2 5.0 + - - +
1076A MET* 2.8 32.0 + - - +
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Residues in contact with THR1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A TYR* 4.6 21.0 - - + +
1069A ARG* 2.6 29.7 + - - +
1070A THR* 3.9 5.4 + - - -
1072A ALA* 1.3 76.1 - - - +
1074A ALA* 1.3 55.0 + - - +
1076A MET* 3.3 7.4 + - + +
1077A ARG* 2.7 57.6 + - + +
1080A ARG* 6.4 0.4 - - - +
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Residues in contact with ALA1074 (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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1070A THR* 3.2 13.2 + - + +
1071A LEU* 2.8 15.3 + - + +
1073A THR* 1.3 77.9 - - - +
1075A VAL* 1.3 65.5 + - + +
1077A ARG* 2.9 34.9 + - - +
1078A LYS* 3.0 29.9 + - - +
1110A ASP* 6.0 0.7 - - - +
1113A GLU* 5.5 0.7 - - - +
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Residues in contact with VAL1075 (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 GLU* 3.7 51.8 - - + +
1012A LEU* 5.6 0.4 - - + -
1013A ARG* 4.3 11.2 - - + -
1071A LEU* 2.8 27.6 + - + +
1072A ALA* 3.6 6.3 - - - +
1074A ALA* 1.3 71.1 - - + +
1076A MET* 1.3 64.0 + - - +
1078A LYS* 3.0 13.4 + - - +
1079A HIS* 2.9 21.0 + - - +
1105A GLU* 4.1 27.2 - - + +
1106A HIS* 4.3 11.4 - - + +
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Residues in contact with MET1076 (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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1013A ARG* 3.6 23.1 - - + +
1016A TYR* 3.6 24.0 - - + -
1017A GLU* 3.6 31.2 - - + +
1020A GLU* 5.3 1.6 - - - +
1072A ALA 2.8 22.0 + - - +
1073A THR* 3.4 9.9 - - + +
1075A VAL* 1.3 73.2 - - - +
1077A ARG* 1.3 63.3 + - - +
1079A HIS* 3.2 37.6 + - + +
1080A ARG* 3.3 53.8 + - - +
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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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1070A THR 5.2 1.0 + - - -
1073A THR* 2.7 54.2 + - + +
1074A ALA* 3.3 27.6 - - - +
1076A MET* 1.3 71.5 - - - +
1078A LYS* 1.3 64.7 + - - +
1080A ARG* 3.3 13.9 + - - +
1081A LEU* 3.1 34.2 + - + +
1113A GLU* 3.0 31.4 + - - +
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Residues in contact with LYS1078 (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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1074A ALA* 3.0 23.9 + - - +
1075A VAL* 3.0 7.4 + - - +
1077A ARG* 1.3 73.5 - - - +
1079A HIS* 1.3 56.4 + - - +
1081A LEU* 3.7 1.6 - - - +
1082A ALA* 2.7 38.3 + - - +
1105A GLU* 3.6 26.0 - - - +
1108A MET* 3.4 53.5 + - + +
1109A SER 3.9 1.8 + - - -
1110A ASP* 3.0 28.6 + - - +
1113A GLU* 2.8 33.7 + - - +
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Residues in contact with HIS1079 (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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252A NI 3.5 9.6 - - + -
1013A ARG* 3.9 11.0 - - - +
1075A VAL 2.9 12.2 + - - +
1076A MET* 3.3 31.4 - - + +
1077A ARG 3.2 0.2 - - - -
1078A LYS* 1.3 78.0 - - - +
1080A ARG* 1.3 54.6 + - + +
1082A ALA* 3.3 3.6 - - - +
1083A GLU* 2.5 76.6 + - + +
1098A HIS* 2.6 34.0 - + - -
1101A ALA* 3.7 15.5 + - + -
1105A GLU* 3.6 28.2 + - - +
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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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1016A TYR* 4.4 7.1 + - - -
1020A GLU* 3.7 25.7 + - - -
1073A THR* 6.4 0.4 - - - +
1076A MET* 3.3 52.4 + - - +
1077A ARG* 3.8 8.9 - - - +
1078A LYS 3.3 0.4 - - - -
1079A HIS* 1.3 80.8 - - + +
1081A LEU* 1.3 56.6 + - + +
1082A ALA 3.0 1.6 - - - -
1083A GLU* 3.1 16.5 + - - +
1084A ARG* 2.7 40.6 + - - +
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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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1077A ARG* 3.1 30.5 + - + +
1078A LYS 3.8 3.8 - - - +
1080A ARG* 1.3 76.4 - - + +
1082A ALA* 1.3 57.5 + - - +
1084A ARG* 3.4 23.0 - - - +
1085A LEU* 3.0 28.4 + - - +
1108A MET* 4.2 9.4 - - + -
1113A GLU* 3.4 40.2 - - + +
1116A LEU* 3.8 18.2 - - + +
1117A VAL* 4.0 37.0 - - + +
1120A LEU* 4.3 2.5 - - + +
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Residues in contact with ALA1082 (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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1078A LYS 2.7 21.1 + - - +
1079A HIS* 3.3 5.2 - - - +
1081A LEU* 1.3 74.3 - - - +
1083A GLU* 1.3 66.6 + - - +
1084A ARG 3.0 1.3 - - - -
1085A LEU* 3.3 6.3 + - - +
1086A LEU* 3.1 28.5 + - - +
1101A ALA* 4.0 15.7 - - + +
1104A TRP* 4.2 26.0 - - + -
1105A GLU 4.9 1.1 - - - +
1108A MET* 4.8 10.8 - - - -
1116A LEU* 5.2 0.9 - - - -
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Residues in contact with GLU1083 (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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252A NI 1.9 47.1 - - - +
1079A HIS* 2.5 26.8 + - - +
1080A ARG* 3.5 12.1 - - - +
1082A ALA* 1.3 72.2 - - - +
1084A ARG* 1.3 65.3 + - - +
1086A LEU 3.6 0.3 + - - -
1087A THR* 3.3 15.8 + - - -
1097A VAL* 3.4 29.6 - - + +
1098A HIS* 2.0 15.9 + - - +
1101A ALA* 3.5 22.0 - - + +
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Residues in contact with ARG1084 (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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1080A ARG* 2.7 18.3 + - - +
1081A LEU* 3.4 29.0 - - - +
1082A ALA 3.0 0.4 - - - -
1083A GLU* 1.3 72.0 - - - +
1085A LEU* 1.3 57.6 + - - +
1086A LEU 2.9 1.3 - - - -
1087A THR* 2.6 29.0 + - - -
1088A ASP* 2.9 41.4 + - - +
1117A VAL* 5.7 3.4 + - - +
1120A LEU* 3.5 35.1 + - + +
1121A LYS* 5.8 1.2 - - - +
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Residues in contact with LEU1085 (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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1081A LEU 3.0 16.5 + - - +
1082A ALA* 3.6 7.6 - - - +
1084A ARG* 1.3 76.4 - - - +
1086A LEU* 1.3 60.8 + - + +
1089A ILE* 3.1 47.2 + - + +
1090A ILE* 3.2 33.3 + - + +
1104A TRP* 4.3 15.9 - - + -
1116A LEU* 3.2 38.6 - - + -
1120A LEU* 4.0 10.9 - - + +
2085B LEU* 4.5 9.6 - - + -
2090B ILE* 3.5 7.6 - - + -
2104B TRP* 5.6 2.9 - - + -
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Residues in contact with LEU1086 (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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1082A ALA 3.1 16.8 + - - +
1083A GLU 3.7 4.3 - - - +
1084A ARG 2.7 5.1 + - - -
1085A LEU* 1.3 74.7 - - - +
1087A THR* 1.3 55.6 + - - +
1090A ILE* 3.4 15.4 - - + +
1091A GLY 2.9 19.8 + - - -
1092A LEU* 3.1 20.9 + - + +
1097A VAL* 3.8 17.9 - - + +
1100A GLU* 3.7 32.3 - - + -
1101A ALA* 3.8 17.7 - - + +
1104A TRP* 3.6 42.6 - - + -
2112B VAL* 4.4 9.2 - - + -
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Residues in contact with THR1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083A GLU 3.3 8.3 + - - -
1084A ARG* 2.6 14.1 + - - -
1086A LEU* 1.3 73.3 - - - +
1088A ASP* 1.3 79.4 + - - +
1091A GLY* 3.4 18.5 + - - +
1092A LEU 4.4 3.1 + - - +
1094A ILE* 2.9 34.8 - - + +
1097A VAL* 3.7 11.4 - - - +
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Residues in contact with ASP1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A ARG* 2.9 44.7 + - - +
1087A THR* 1.3 92.7 - - - +
1089A ILE* 1.3 64.4 + - + +
1091A GLY* 4.5 0.9 + - - -
1120A LEU* 4.1 18.1 - - + +
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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