Contacts of the helix formed by residues 116 - 138 (chain E) in PDB entry 4O46
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 GLN 116 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLU* 3.2 32.3 - - + +
83D ARG* 5.0 3.1 - - - +
36E PRO* 4.8 17.6 - - - +
111E ASN 3.6 6.4 - - - +
112E CYS* 3.5 9.6 - - - +
113E SER* 2.7 49.6 + - - +
114E GLU 4.8 0.7 - - - -
115E THR* 1.4 71.8 - - - +
117E TYR* 1.4 62.4 + - - +
118E GLU* 3.5 2.7 - - - -
119E SER* 3.6 18.0 + - - +
120E LYS* 3.2 23.3 + - - +
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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
----------------------------------------------------------
83D ARG* 5.2 3.4 - - - +
114E GLU 4.4 8.3 - - - -
115E THR* 3.0 17.4 + - - +
116E GLN* 1.4 68.3 - - - +
118E GLU* 1.4 72.2 + - - +
120E LYS* 3.2 7.3 + - - +
121E VAL* 3.0 30.2 + - - +
160E ILE* 4.3 11.0 - - + -
164E HIS* 3.6 45.1 - + + -
165E MET* 5.0 6.3 - - + -
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Residues in contact with GLU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 2.9 43.1 + - - -
39E ASN* 6.0 0.2 - - - +
42E ARG* 5.0 7.4 - - - +
116E GLN* 3.5 0.7 - - - -
117E TYR* 1.4 79.1 + - - +
119E SER* 1.4 57.0 + - - +
121E VAL* 3.4 2.3 + - - +
122E PHE* 2.9 29.8 + - - +
165E MET* 3.8 28.9 - - + +
169E HIS* 3.8 24.5 + - + +
171E ILE* 4.1 14.8 - - + +
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Residues in contact with SER 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU* 5.3 1.4 + - - -
37E LEU 4.9 5.4 + - - -
42E ARG* 3.4 23.9 + - - +
112E CYS* 3.7 17.7 - - - -
116E GLN* 3.6 18.0 + - - +
117E TYR 3.4 0.2 - - - -
118E GLU* 1.4 73.8 - - - +
120E LYS* 1.4 59.1 + - - +
122E PHE* 3.2 7.4 + - - +
123E TYR* 2.9 48.4 + - - -
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Residues in contact with LYS 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ILE* 5.1 10.9 - - + +
112E CYS* 3.8 20.6 - - + -
113E SER 5.7 1.6 - - - +
116E GLN 3.2 16.6 + - - +
117E TYR* 3.6 7.9 - - - +
119E SER* 1.4 78.8 - - - +
121E VAL* 1.4 55.2 + - - +
123E TYR* 4.0 2.6 - - - +
124E LEU* 3.0 43.8 + - + +
156E GLU* 5.4 2.0 - - - +
160E ILE* 4.0 23.6 - - + -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E TYR 3.0 20.5 + - - +
118E GLU 3.9 3.6 - - - +
120E LYS* 1.4 70.2 - - - +
122E PHE* 1.4 56.2 + - - +
124E LEU* 3.8 0.9 - - - +
125E LYS* 2.8 37.0 + - - +
157E ALA* 3.7 33.0 - - + +
160E ILE* 3.7 21.3 - - + -
161E SER* 3.8 13.7 - - - +
165E MET* 3.8 11.0 - - - -
171E ILE* 3.8 19.5 - - + +
175E LEU* 3.9 21.8 - - + -
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Residues in contact with PHE 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ARG* 3.4 62.4 - - + +
43E ASN* 4.1 20.4 - - - -
46E SER* 3.8 21.8 - - - -
118E GLU 2.9 18.7 + - - +
119E SER* 3.5 4.9 - - - +
121E VAL* 1.4 75.3 - - - +
123E TYR* 1.4 64.1 + + - +
125E LYS* 3.5 13.3 + - + +
126E MET* 3.1 45.9 + - + +
171E ILE* 4.0 22.1 - - + +
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Residues in contact with TYR 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 3.6 18.7 + - - +
42E ARG* 3.4 34.9 - - + +
45E LEU* 4.8 5.4 - - + -
104E LEU* 3.6 23.3 - - + +
108E LEU* 3.5 51.3 - - + +
109E ILE* 3.6 20.8 - - + +
112E CYS* 3.7 15.9 - - - -
119E SER* 2.9 41.0 + - - +
120E LYS* 4.2 1.6 - - - +
122E PHE* 1.4 77.7 - + - +
124E LEU* 1.4 59.8 + - - +
126E MET* 3.2 6.8 + - - +
127E LYS* 2.9 27.4 + - - +
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Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ILE* 4.4 24.9 - - + -
120E LYS* 3.0 29.6 + - + +
123E TYR* 1.4 72.0 - - - +
125E LYS* 1.4 59.8 + - - +
127E LYS* 3.4 12.0 + - + +
128E GLY* 3.0 22.9 + - - -
153E ALA* 3.4 32.0 - - - +
156E GLU* 3.5 43.3 - - + +
157E ALA* 3.7 19.5 - - + +
160E ILE* 3.8 20.4 - - + -
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Residues in contact with LYS 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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121E VAL* 2.8 19.7 + - + +
122E PHE* 3.5 14.5 + - + +
124E LEU* 1.4 73.1 - - - +
126E MET* 1.4 63.4 + - - +
128E GLY* 3.2 2.8 + - - -
129E ASP* 2.9 52.8 + - - +
154E TYR* 3.7 9.1 - - + -
157E ALA* 4.2 0.4 - - - +
171E ILE* 4.9 6.3 - - + +
174E GLY* 3.8 17.3 - - - -
175E LEU* 3.9 43.5 - - + +
178E ASN* 3.5 18.7 - - - +
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Residues in contact with MET 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 4.5 17.9 - - + +
46E SER* 4.3 26.9 - - - +
49E TYR* 5.1 1.1 - - + -
100E VAL* 3.7 27.6 - - + -
104E LEU* 3.9 19.3 - - + -
122E PHE* 3.1 40.3 + - + +
123E TYR* 3.2 13.0 + - - +
125E LYS* 1.4 79.3 - - - +
127E LYS* 1.4 55.8 + - - +
129E ASP* 3.1 10.8 + - - +
130E TYR* 2.9 53.5 + - + +
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Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU* 3.6 21.7 - - + +
104E LEU* 3.7 7.7 - - + +
105E ASP* 3.6 27.9 - - - -
109E ILE* 3.8 20.9 - - + +
123E TYR 2.9 13.4 + - - +
124E LEU* 3.5 18.3 - - + +
125E LYS 3.3 0.2 - - - -
126E MET* 1.4 75.7 - - - +
128E GLY* 1.3 59.8 + - - +
130E TYR 3.6 0.2 + - - -
131E TYR* 3.2 51.3 + - + -
149E SER 5.4 1.6 - - - -
153E ALA* 3.8 16.4 - - + -
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Residues in contact with GLY 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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124E LEU 3.0 12.2 + - - -
125E LYS 3.2 4.4 + - - -
127E LYS* 1.3 75.6 - - - +
129E ASP* 1.4 56.7 + - - +
132E ARG* 3.0 17.0 + - - +
150E SER* 2.8 27.0 + - - -
153E ALA* 3.5 15.0 - - - +
154E TYR* 3.3 21.2 - - - -
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Residues in contact with ASP 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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125E LYS* 2.9 44.4 + - - +
126E MET* 3.4 12.6 - - - +
128E GLY* 1.4 74.4 - - - +
130E TYR* 1.3 61.6 + - + +
132E ARG* 3.1 10.3 + - - +
133E TYR* 2.9 51.1 + - + +
154E TYR* 2.6 25.3 + - - -
178E ASN* 2.7 25.2 + - - +
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Residues in contact with TYR 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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46E SER 4.1 4.0 + - - -
49E TYR* 3.3 7.6 - - - +
50E LYS* 3.2 33.1 + - + +
53E VAL* 3.7 23.6 - - + -
97E CYS* 3.6 22.1 - - + -
100E VAL* 3.7 36.3 - - + -
101E LEU* 4.1 23.8 - - + -
104E LEU* 5.0 0.2 - - + -
126E MET* 2.9 53.8 + - + +
129E ASP* 1.3 76.7 - - + +
131E TYR* 1.4 59.5 + - - +
133E TYR* 3.4 22.3 + + - -
134E LEU* 3.1 30.2 + - - +
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Residues in contact with TYR 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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98E GLN* 5.0 6.9 + - - -
101E LEU* 3.6 33.3 - - + +
105E ASP* 5.8 1.9 - - - -
127E LYS* 3.2 49.6 + - + +
130E TYR* 1.4 73.3 - - - +
132E ARG* 1.4 59.6 + - - +
134E LEU* 3.3 15.2 + - + +
135E ALA* 2.9 26.9 + - - +
146E VAL* 3.6 37.4 - - + +
149E SER* 3.6 38.7 + - - -
150E SER* 3.7 12.8 - - - -
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Residues in contact with ARG 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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57E ARG* 4.4 4.2 - - - +
128E GLY 3.0 17.7 + - - +
129E ASP* 3.1 25.7 + - - +
131E TYR* 1.4 74.5 - - - +
133E TYR* 1.4 80.7 + - - +
135E ALA* 3.1 8.3 + - - +
136E GLU* 3.0 47.9 + - - +
150E SER* 3.8 9.6 + - - +
154E TYR* 2.9 15.9 + - - -
178E ASN* 3.4 21.2 + - - +
181E VAL* 3.8 23.1 - - - +
182E PHE* 3.8 32.1 - - + +
185E GLU* 6.3 0.2 - - - -
186E ILE* 3.7 20.1 - - + +
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Residues in contact with TYR 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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50E LYS* 3.3 26.7 - - + +
53E VAL* 4.0 15.7 - - + -
57E ARG* 3.4 47.6 + - - +
93E LEU* 3.8 16.8 - - + +
97E CYS* 3.8 10.3 - - - -
129E ASP* 2.9 40.4 + - + +
130E TYR* 3.7 43.0 - + - +
131E TYR 3.3 0.2 - - - -
132E ARG* 1.4 98.8 + - - +
134E LEU* 1.4 60.9 + - - +
136E GLU* 3.5 23.0 + - - +
137E VAL* 3.8 4.3 + - - +
178E ASN* 4.9 1.6 + - - -
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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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93E LEU* 4.9 0.7 - - + -
94E GLU* 3.7 37.4 - - + +
97E CYS* 3.7 20.0 - - + -
98E GLN* 3.6 22.2 - - - +
101E LEU* 3.8 23.8 - - + -
130E TYR 3.1 14.3 + - - +
131E TYR* 3.4 20.9 - - + +
132E ARG 3.2 0.2 - - - -
133E TYR* 1.4 75.7 - - - +
135E ALA* 1.4 56.3 + - - +
137E VAL* 3.4 9.4 + - - +
138E ALA* 3.1 28.3 + - + +
146E VAL* 3.9 18.4 - - + -
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Residues in contact with ALA 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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131E TYR 2.9 14.7 + - - +
132E ARG* 3.1 12.3 + - - +
134E LEU* 1.4 73.7 - - - +
136E GLU* 1.3 62.5 + - - +
137E VAL 3.3 1.0 + - - -
138E ALA* 3.4 17.0 + - - +
143E ARG* 3.7 13.8 + - - +
146E VAL* 3.7 12.1 - - + +
147E VAL* 3.8 29.8 - - + +
186E ILE* 4.1 17.2 - - + +
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Residues in contact with GLU 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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57E ARG* 3.1 44.5 + - - +
60E TRP* 3.5 21.5 - - + -
61E ARG* 4.6 5.1 + - - -
132E ARG* 3.0 33.1 + - - +
133E TYR* 3.5 15.7 - - - +
134E LEU 3.3 0.4 - - - -
135E ALA* 1.3 75.7 - - - +
137E VAL* 1.3 60.6 + - + +
138E ALA 4.9 0.9 - - - +
185E GLU* 6.0 1.0 - - - +
186E ILE* 3.9 17.5 - - + +
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Residues in contact with VAL 137 (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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60E TRP* 3.4 45.5 - - + +
90E GLU* 3.8 29.9 - - + +
93E LEU* 4.3 26.2 - - + -
94E GLU* 3.8 25.0 - - + +
133E TYR 4.2 8.3 - - - +
134E LEU* 3.4 13.7 - - - +
136E GLU* 1.3 79.7 - - + +
138E ALA* 1.3 64.1 + - - +
139E THR* 4.1 5.9 + - - +
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Residues in contact with ALA 138 (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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94E GLU* 5.4 4.3 - - - +
134E LEU* 3.1 17.7 + - + +
135E ALA 3.4 4.6 + - - +
136E GLU 4.9 0.9 - - - +
137E VAL* 1.3 80.9 - - + +
139E THR* 1.3 65.5 + - - +
142E LYS* 4.3 7.2 - - + -
143E ARG* 3.4 45.6 - - + +
146E VAL* 4.2 8.1 - - + -
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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