Contacts of the helix formed by residues 115 - 135 (chain E) in PDB entry 4KYI
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 GLY 115 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ASP* 3.2 11.0 + - - -
113E ALA 3.1 2.2 - - - -
114E ARG* 1.3 77.6 - - - +
116E ASP* 1.3 60.5 + - - +
117E ARG 3.3 2.5 - - - -
118E PHE* 3.8 4.1 + - - +
119E ARG* 3.5 5.5 + - - +
266E GLN* 3.2 32.9 + - - +
275E PHE* 3.6 30.7 - - - -
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Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ASP* 2.8 19.4 - - - +
114E ARG* 3.0 39.1 + - - +
115E GLY* 1.3 73.4 - - - +
117E ARG* 1.3 55.5 - - - +
118E PHE 3.4 0.2 - - - -
119E ARG* 3.3 33.8 + - - +
120E ASN* 2.6 41.0 + - - -
190E ASP* 4.1 4.9 - - - +
194E ASN* 3.9 19.7 + - - +
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Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LYS 4.8 2.2 + - - -
103E LEU* 4.3 26.0 - - + +
104E LEU 3.8 14.1 + - - -
105E ASP* 3.2 38.7 + - - +
115E GLY 3.3 0.4 - - - -
116E ASP* 1.3 80.2 + - - +
118E PHE* 1.3 60.6 + - - +
119E ARG 3.2 0.2 - - - -
120E ASN* 3.4 2.2 + - - +
121E ILE* 2.9 37.1 + - + +
183E VAL* 5.2 9.9 + - - +
186E LEU* 3.4 50.8 + - + +
187E GLU* 4.6 15.8 - - - +
189E LEU* 4.9 1.7 - - + +
190E ASP* 3.7 28.8 + - - +
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Residues in contact with PHE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E MET* 4.1 34.3 - - + -
98E LEU 6.1 0.2 - - - -
100E ILE* 3.5 31.9 - - + -
103E LEU* 3.7 39.2 + - + +
115E GLY 3.8 9.0 + - - +
116E ASP 3.4 0.2 - - - -
117E ARG* 1.3 78.9 - - - +
119E ARG* 1.3 61.4 + - - +
121E ILE* 3.5 6.2 + - + +
122E LEU* 3.1 49.1 + - + +
265E VAL* 4.6 12.6 - - + -
266E GLN* 4.2 17.7 - - + -
269E GLY* 5.4 8.3 - - - -
275E PHE* 4.6 17.3 - + + -
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Residues in contact with ARG 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E GLY 3.5 12.7 + - - +
116E ASP* 3.3 23.3 + - - +
117E ARG 3.2 0.4 - - - -
118E PHE* 1.3 79.4 - - - +
120E ASN* 1.3 100.3 + - - +
122E LEU* 3.5 0.6 + - - -
123E ASP* 3.2 36.8 + - - +
194E ASN* 3.3 19.6 + - - +
198E THR* 5.9 5.4 - - - +
212E ARG* 3.8 25.5 - - - +
262E ALA* 3.2 39.7 - - - +
263E GLN* 4.1 18.4 - - + +
266E GLN* 4.1 9.6 - - + +
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Residues in contact with ASN 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASP 2.6 25.3 + - - +
117E ARG* 3.9 4.3 - - - +
118E PHE 3.4 0.2 - - - -
119E ARG* 1.3 100.7 + - - +
121E ILE* 1.3 64.9 + - - +
123E ASP* 3.4 6.2 + - - +
124E VAL* 3.2 27.9 + - - +
189E LEU* 4.1 13.7 - - + -
190E ASP* 3.7 24.4 + - - +
193E LEU* 3.3 35.2 - - + +
194E ASN* 3.5 14.2 + - - +
212E ARG* 4.4 0.7 + - - -
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Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E LEU* 4.2 16.6 - - + -
103E LEU* 3.7 25.8 - - + -
117E ARG* 2.9 24.4 + - + +
118E PHE* 3.7 10.8 - - + +
119E ARG 3.3 0.2 - - - -
120E ASN* 1.3 76.5 - - - +
122E LEU* 1.3 63.4 + - - +
124E VAL* 3.2 7.2 + - + +
125E ILE* 3.0 38.5 + - + +
176E ILE* 4.5 12.5 - - + +
179E LEU* 4.0 17.0 - - + -
180E THR* 4.1 15.7 - - + -
186E LEU* 4.7 2.0 - - + -
189E LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E MET* 3.7 29.4 - - + -
81E ILE* 5.8 0.4 - - + -
118E PHE* 3.1 36.2 + - + +
119E ARG* 3.7 4.5 - - - +
121E ILE* 1.3 77.6 - - + +
123E ASP* 1.3 51.5 + - - +
125E ILE* 3.0 18.3 + - + +
126E TYR* 2.7 65.0 + - + +
262E ALA* 3.7 22.2 - - + +
265E VAL* 3.6 26.2 - - + -
266E GLN 4.2 4.7 - - - +
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Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ARG* 3.2 19.6 + - - +
120E ASN* 3.6 12.9 - - - +
121E ILE 3.3 0.4 - - - -
122E LEU* 1.3 78.0 - - - +
124E VAL* 1.3 56.9 + - - +
126E TYR* 4.0 7.8 - - - +
127E MET* 2.9 31.9 + - - +
159E TYR* 2.9 39.3 + - + -
193E LEU* 4.3 9.2 - - + +
212E ARG* 3.4 23.2 + - - -
213E LEU* 4.8 4.5 + - - +
260E SER* 4.3 2.8 + - - -
262E ALA* 3.4 20.0 + - - +
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ASN 3.2 16.4 + - - +
121E ILE* 3.5 9.2 - - + +
122E LEU 3.1 0.4 - - - -
123E ASP* 1.3 74.1 - - - +
125E ILE* 1.3 63.9 + - - +
127E MET* 3.3 9.5 - - + +
128E MET* 3.0 25.3 + - - +
159E TYR* 6.1 0.2 - - + -
163E LEU* 4.7 11.0 - - + -
170E ILE* 3.6 37.7 - - + -
176E ILE* 3.6 17.3 - - + -
179E LEU* 6.1 3.4 - - + -
189E LEU* 3.8 26.9 - - + -
193E LEU* 4.1 7.2 - - + -
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Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E MET* 4.5 0.9 - - + -
81E ILE* 4.2 16.6 - - + -
84E VAL* 5.5 0.8 - - + +
86E MET* 3.7 26.2 - - + +
94E LEU* 3.7 29.8 - - + -
98E LEU* 3.9 7.6 - - + -
121E ILE* 3.0 29.5 + - + +
122E LEU* 3.0 22.5 + - + +
124E VAL* 1.3 76.7 - - - +
126E TYR* 1.3 67.4 + - + +
128E MET* 3.8 2.1 - - - +
129E GLN* 3.4 21.8 + - - +
176E ILE* 3.8 25.1 - - + -
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Residues in contact with TYR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E SER* 2.8 43.9 + - - -
81E ILE* 4.6 8.5 - - + -
84E VAL* 4.8 15.3 - - + -
122E LEU* 2.7 53.5 + - + +
123E ASP* 4.0 9.0 - - - +
125E ILE* 1.3 78.4 - - + +
127E MET* 1.3 60.5 + - - +
128E MET 3.3 0.2 + - - -
129E GLN* 3.3 1.7 + - - +
130E MET* 2.9 41.8 + - - +
213E LEU* 3.9 15.7 - - + -
261E ILE* 3.6 36.3 - - + -
262E ALA* 3.6 13.7 - - + -
265E VAL* 3.4 13.2 - - - +
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Residues in contact with MET 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ASP 2.9 23.2 + - - +
124E VAL* 3.3 13.7 - - - +
126E TYR* 1.3 76.9 - - - +
128E MET* 1.3 68.1 + - + +
130E MET* 4.7 1.3 - - - +
131E LYS* 3.1 30.9 + - + +
156E ILE* 3.7 25.7 - - + +
159E TYR* 3.6 32.5 - - + -
160E GLU* 3.6 31.4 - - + +
163E LEU* 3.9 23.1 - - + -
170E ILE* 5.0 8.7 - - - +
213E LEU* 3.7 15.8 - - + +
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E MET* 4.9 2.2 - - + -
90E ASP* 5.1 0.9 - - - +
124E VAL 3.0 19.3 + - - +
125E ILE* 3.8 5.8 - - - +
126E TYR 3.2 0.2 - - - -
127E MET* 1.3 85.1 - - + +
129E GLN* 1.3 84.9 + - + +
131E LYS* 3.7 5.8 + - - +
132E LYS* 3.3 44.7 + - + +
170E ILE* 4.1 16.8 - - + +
171E ASN* 4.3 6.7 - - - -
172E ASN* 3.4 46.0 - - - +
173E VAL* 3.6 21.3 - - + -
176E ILE* 4.4 5.6 - - + -
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Residues in contact with GLN 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 3.5 40.8 - - + +
85E GLY 4.0 3.2 + - - -
86E MET* 3.7 28.3 - - + +
87E ASP* 4.3 4.3 + - - +
90E ASP* 4.6 4.9 - - - +
125E ILE 3.4 13.1 + - - +
126E TYR 3.3 3.2 + - - +
128E MET* 1.3 93.2 - - + +
130E MET* 1.3 60.9 + - - +
131E LYS 3.1 4.7 - - - -
132E LYS* 3.0 30.8 + - - +
133E HIS* 3.1 39.2 + - + +
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Residues in contact with MET 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 3.5 18.8 - - + -
126E TYR* 2.9 19.7 + - - +
127E MET 4.5 1.3 - - - +
129E GLN* 1.3 74.8 - - - +
131E LYS* 1.3 59.1 + - - +
133E HIS* 4.0 0.7 - - - -
134E LEU* 3.3 25.6 + - - +
152E LEU* 4.6 5.6 - - + -
156E ILE* 4.2 7.8 - - + +
213E LEU* 3.6 37.7 - - + -
217E ASP* 3.8 30.7 - - + +
218E LEU* 3.7 27.8 - - + -
221E LEU* 4.0 27.8 - - + +
261E ILE* 4.6 7.2 - - + -
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Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E MET* 3.1 23.3 + - + +
128E MET* 3.7 6.3 - - - +
129E GLN 3.1 0.2 - - - -
130E MET* 1.3 77.1 - - - +
132E LYS* 1.3 66.0 + - + +
134E LEU* 3.1 13.0 + - + +
135E GLU* 2.9 49.2 + - + +
156E ILE* 3.7 30.7 - - + +
160E GLU* 3.2 36.6 - - - +
170E ILE 5.8 2.5 - - - +
171E ASN* 6.2 1.8 - - - +
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Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ASP* 5.8 3.0 - - - +
90E ASP* 4.2 16.4 + - - -
128E MET* 3.3 34.4 - - + +
129E GLN* 3.0 22.2 + - - +
131E LYS* 1.3 77.9 - - + +
133E HIS* 1.3 64.5 + - + +
135E GLU* 3.6 22.9 + - - +
136E SER* 3.7 10.2 + - - -
171E ASN 5.5 5.8 - - - +
172E ASN* 6.4 0.2 - - - -
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Residues in contact with HIS 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL 3.1 27.4 + - - -
85E GLY* 3.4 23.6 + - - -
129E GLN* 3.1 32.2 + - - +
130E MET 4.2 0.2 - - - +
131E LYS 3.2 0.4 - - - -
132E LYS* 1.3 77.4 - - + +
134E LEU* 1.3 61.5 + - - +
136E SER* 2.7 27.8 + - - +
137E VAL* 3.8 2.1 + - - +
221E LEU* 3.9 24.5 - - + +
225E LEU* 3.6 17.1 - - + +
232E LEU* 3.8 24.3 - - + +
233E ILE* 3.7 14.9 - - + +
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Residues in contact with LEU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E MET 3.3 12.9 + - - +
131E LYS* 3.1 11.8 + - + +
133E HIS* 1.3 76.9 - - - +
135E GLU* 1.3 57.6 + - + +
136E SER 3.1 1.8 - - - -
137E VAL* 3.2 28.8 + - + +
149E TYR* 3.6 27.3 + - + +
152E LEU* 3.9 28.0 - - + -
153E LYS* 3.9 20.6 - - + +
156E ILE* 3.6 27.1 - - + -
221E LEU* 4.7 4.3 - - + -
224E LEU* 3.5 31.9 - - + -
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A LYS* 5.8 4.0 - - - +
131E LYS* 2.9 47.5 + - + +
132E LYS* 3.9 14.8 - - - +
133E HIS 3.3 0.6 - - - -
134E LEU* 1.3 77.8 - - + +
136E SER* 1.3 58.1 + - - +
137E VAL 3.4 4.4 - - - +
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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