Contacts of the helix formed by residues 114 - 136 (chain E) in PDB entry 2W8B
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 THR 114 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D GLU* 2.7 27.6 + - - -
335D GLN* 2.8 32.5 + - + +
336D ASP* 3.7 24.7 - - + +
349D VAL* 4.0 17.0 - - + -
378D GLU* 4.1 5.8 - - + -
113E GLY* 1.3 79.8 - - - +
115E PRO* 1.3 70.0 - - - +
117E TYR* 3.5 2.3 - - - +
118E ASN* 2.8 32.2 + - - +
150E LYS* 4.0 4.5 - - - -
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Residues in contact with PRO 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D MET* 3.8 5.7 - - + +
292D GLU* 4.9 0.4 - - - +
336D ASP* 4.8 0.2 - - - +
378D GLU* 3.2 32.3 - - + +
379D THR* 3.9 14.8 - - + -
423D PHE* 3.4 33.2 - - + -
114E THR* 1.3 89.6 - - - +
116E GLU* 1.3 63.8 + - + +
118E ASN* 3.3 8.1 + - - +
119E ILE* 3.4 15.6 + - - +
150E LYS* 3.9 15.2 + - + +
151E GLU* 3.4 22.9 - - - +
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Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D MET* 3.7 13.7 - - + +
204D SER* 2.7 30.8 + - - +
217D VAL* 3.9 7.6 - - - +
245D HIS* 2.8 28.6 + - - -
247D GLY 3.8 0.5 - - - -
248D ALA* 2.9 35.2 + - + +
268D LEU* 3.9 9.2 - - - +
291D THR* 3.9 9.8 + - - +
292D GLU* 3.4 25.3 + - + +
423D PHE* 5.4 0.2 - - + -
114E THR 3.5 0.4 - - - -
115E PRO* 1.3 78.1 - - + +
117E TYR* 1.3 63.7 + - - +
119E ILE* 3.4 17.6 - - - +
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Residues in contact with TYR 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.5 0.4 - - - +
289D ASN* 4.2 9.9 - - + -
291D THR* 3.9 12.3 - - + -
292D GLU* 3.0 18.9 + - - +
305D THR* 3.9 17.7 - - + -
307D ASP* 2.6 44.3 + - + +
312D PRO* 3.7 29.9 - - + +
335D GLN* 4.0 6.3 - - - +
114E THR* 3.3 17.8 + - - +
116E GLU* 1.3 76.2 - - - +
118E ASN* 1.4 70.2 + - - +
119E ILE 3.0 0.4 - - - -
120E SER* 2.9 53.1 + - - -
121E LEU* 4.4 17.6 - - + +
124E ARG* 4.2 10.0 + - - -
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Residues in contact with ASN 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ALA* 3.7 12.3 - - + +
110E ASP 3.2 18.4 + - - -
112E ARG 2.7 28.5 + - - +
113E GLY* 3.5 6.6 - - - -
114E THR 2.8 33.2 + - - +
115E PRO 3.3 4.8 + - - +
117E TYR* 1.4 81.4 - - - +
119E ILE* 1.3 65.2 + - - +
120E SER 3.1 0.2 - - - -
121E LEU* 3.1 27.0 + - - +
122E GLY 3.3 7.6 + - - -
149E GLY* 3.5 9.4 - - - -
150E LYS* 3.8 17.0 - - + +
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Residues in contact with ILE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D MET* 4.2 13.2 - - + -
219D PHE* 4.4 1.3 - - + -
245D HIS* 3.7 55.9 - - + +
268D LEU* 4.4 7.2 - - + -
115E PRO 3.4 9.2 + - - +
116E GLU* 3.4 19.5 - - - +
117E TYR 3.0 0.2 + - - -
118E ASN* 1.3 76.2 - - - +
120E SER* 1.3 63.4 + - - +
122E GLY 3.0 1.4 + - - -
123E GLU* 3.0 20.9 + - - +
147E SER* 2.8 38.8 + - - +
148E TYR* 3.9 5.2 - - - +
149E GLY* 3.7 21.5 - - - +
151E GLU* 5.3 0.2 - - + -
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Residues in contact with SER 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.0 10.4 - - - +
289D ASN* 3.4 37.8 + - - -
117E TYR* 2.9 43.1 + - - -
119E ILE* 1.3 80.0 - - - +
121E LEU* 1.3 57.9 + - - +
123E GLU* 3.2 8.8 + - - +
124E ARG* 3.0 34.9 + - - +
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Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ASP* 3.8 22.0 - - + +
78E TYR* 3.3 29.7 - - + +
109E ALA* 4.1 12.3 - - + -
110E ASP 5.8 0.7 - - - +
112E ARG 5.0 3.6 - - - +
117E TYR* 4.4 17.3 - - + +
118E ASN* 3.1 36.2 + - - +
120E SER* 1.3 79.0 - - - +
122E GLY* 1.3 62.7 + - - +
124E ARG* 3.5 15.9 + - - +
125E ARG* 3.2 43.9 + - - +
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Residues in contact with GLY 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E GLY* 3.3 27.7 - - - -
108E HIS* 3.7 11.1 + - - -
118E ASN 3.3 5.8 + - - -
119E ILE 3.0 3.2 + - - -
121E LEU* 1.3 77.7 - - - +
123E GLU* 1.3 58.1 + - - +
125E ARG* 3.5 1.7 + - - +
126E ALA* 3.0 23.6 + - - +
147E SER* 3.3 20.0 - - - -
149E GLY* 4.9 0.2 - - - -
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Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ARG* 3.6 19.6 + - - +
245D HIS* 3.7 10.0 + - - +
263D SER* 2.5 40.1 + - - +
266D GLY 4.7 9.4 - - - +
267D SER* 4.7 2.9 - - - -
268D LEU* 4.9 3.2 - - - +
289D ASN* 5.0 1.4 - - - +
119E ILE* 3.0 19.0 + - - +
120E SER* 3.2 9.9 + - - +
122E GLY* 1.3 74.7 - - - +
124E ARG* 1.3 58.0 + - + +
126E ALA* 3.7 0.9 - - - +
127E ASN* 2.7 38.2 + - - +
145E ILE* 3.7 20.8 - - + +
147E SER* 3.4 20.1 + - - -
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Residues in contact with ARG 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D SER* 6.0 0.6 - - - +
289D ASN* 3.3 18.5 - - - +
307D ASP* 3.0 29.2 + - - +
78E TYR* 3.3 57.3 + - + +
117E TYR* 4.3 5.9 + - - -
120E SER* 3.0 21.0 + - - +
121E LEU* 3.8 12.0 - - - +
122E GLY 3.3 0.2 - - - -
123E GLU* 1.3 79.3 - - + +
125E ARG* 1.3 57.1 + - - +
127E ASN* 3.4 6.0 + - - +
128E ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 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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73E PHE* 3.4 54.1 - - + +
74E ASP 3.5 19.4 + - - -
76E ASP* 3.6 23.8 + - - +
77E LYS 3.3 10.3 + - - -
78E TYR* 4.0 13.3 - - + -
108E HIS 2.9 27.0 + - - -
109E ALA* 3.5 18.6 - - - +
110E ASP 4.5 0.4 - - - +
121E LEU* 3.2 24.7 + - - +
122E GLY 3.9 4.0 - - - +
123E GLU 3.3 0.2 - - - -
124E ARG* 1.3 74.2 - - - +
126E ALA* 1.3 65.2 + - - +
128E ALA* 3.2 5.6 + - - +
129E VAL* 3.2 18.5 + - - +
167E ARG* 3.5 24.2 - - - +
168E ARG 4.2 6.1 - - - +
169E ALA* 4.2 5.4 - - + -
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Residues in contact with ALA 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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105E VAL* 3.7 41.2 - - + +
107E GLY 4.2 8.1 - - - +
122E GLY 3.0 18.3 + - - +
123E GLU 3.9 3.4 - - - +
125E ARG* 1.3 75.7 - - - +
127E ASN* 1.3 58.6 + - - +
129E VAL* 3.1 7.1 + - - +
130E LYS* 2.9 25.4 + - - +
145E ILE* 3.9 19.5 - - + -
169E ALA* 4.2 2.6 - - - +
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Residues in contact with ASN 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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244D ARG* 4.4 21.7 - - - +
123E GLU 2.7 22.9 + - - +
124E ARG* 3.8 6.5 - - - +
126E ALA* 1.3 70.4 - - - +
128E ALA* 1.3 60.9 + - - +
130E LYS* 3.1 24.8 + - - +
131E MET* 2.8 52.3 + - - +
145E ILE* 4.8 4.2 - - + +
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Residues in contact with ALA 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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73E PHE* 4.5 0.9 - - + -
78E TYR 2.9 30.3 - - - +
79E ASP* 4.6 1.3 - - - -
80E ILE* 3.8 19.7 - - + +
124E ARG 2.9 11.1 + - - +
125E ARG* 3.2 10.5 + - - +
127E ASN* 1.3 74.3 - - - +
129E VAL* 1.3 57.9 + - - +
131E MET* 3.5 8.7 + - - +
132E TYR* 3.0 29.6 + - - +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E VAL* 3.9 27.8 - - + -
73E PHE* 4.7 0.2 - - + -
80E ILE* 4.0 12.8 - - + -
88E LEU* 4.1 7.9 - - + -
105E VAL* 3.8 17.3 - - + -
125E ARG 3.2 10.7 + - - +
126E ALA 3.1 9.9 + - - +
128E ALA* 1.3 78.8 - - - +
130E LYS* 1.3 63.8 + - - +
132E TYR* 3.2 3.6 + - - +
133E LEU* 3.0 40.6 + - + +
169E ALA* 3.9 15.0 - - + -
171E LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 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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244D ARG* 4.3 15.1 - - - +
105E VAL* 5.0 0.4 - - + +
126E ALA 2.9 14.4 + - - +
127E ASN* 3.1 22.0 + - - +
129E VAL* 1.3 79.5 - - - +
131E MET* 1.3 58.7 + - - +
133E LEU* 3.4 2.6 + - - +
134E GLN* 2.8 65.8 + - - +
140E ALA* 4.0 15.1 - - - +
143E ILE* 3.5 49.5 - - + +
145E ILE* 3.9 17.7 - - + -
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Residues in contact with MET 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ASN* 2.8 46.1 + - - +
128E ALA* 3.7 7.6 - - - +
130E LYS* 1.3 70.3 - - - +
132E TYR* 1.3 67.7 + - - +
134E GLN* 3.2 23.6 + - + +
135E GLY* 2.9 20.1 + - - -
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Residues in contact with TYR 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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80E ILE* 4.1 30.3 - - + -
85E ALA* 3.4 28.6 - - + +
88E LEU* 3.5 31.4 - - + -
89E ASP* 2.6 32.3 + - - -
128E ALA 3.0 18.6 + - - +
129E VAL 3.2 4.9 + - - +
131E MET* 1.3 76.3 - - - +
133E LEU* 1.3 67.5 + - + +
135E GLY* 3.1 12.6 + - - -
136E LYS* 3.2 34.6 + - + +
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Residues in contact with LEU 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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88E LEU* 3.4 37.7 - - + +
91E HIS* 4.2 8.5 - - + -
92E ALA* 3.9 17.7 - - + +
95E LEU* 4.6 4.0 - - + -
103E VAL* 4.3 15.7 - - + -
105E VAL* 4.9 0.4 - - + -
129E VAL* 3.0 36.7 + - + +
130E LYS* 3.8 4.0 - - - +
132E TYR* 1.3 77.9 - - + +
134E GLN* 1.3 60.9 + - - +
136E LYS* 2.9 21.1 + - - +
138E VAL* 3.1 23.9 + - + +
143E ILE* 3.9 24.0 - - + -
171E LEU* 4.3 9.6 - - + -
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Residues in contact with GLN 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 LYS* 2.8 59.7 + - - +
131E MET* 3.2 25.6 + - + +
133E LEU* 1.3 75.2 - - - +
135E GLY* 1.3 58.7 + - - +
137E GLY* 2.8 21.1 + - - -
138E VAL 3.3 21.3 + - - +
140E ALA* 3.1 26.5 - - - +
143E ILE* 4.0 6.1 - - + -
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Residues in contact with GLY 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E MET 2.9 14.4 + - - -
132E TYR* 3.1 6.9 + - - -
134E GLN* 1.3 75.2 - - - +
136E LYS* 1.3 72.6 + - - +
137E GLY 3.2 2.2 + - - -
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Residues in contact with LYS 136 (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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89E ASP* 3.7 25.9 + - + +
92E ALA* 3.5 20.5 - - + +
96E ARG* 2.9 26.8 + - - +
132E TYR* 3.2 35.5 + - + +
133E LEU* 2.9 12.2 + - - +
135E GLY* 1.3 100.6 - - - +
137E GLY* 1.3 59.0 + - - +
138E VAL 3.6 0.3 + - - -
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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