Contacts of the helix formed by residues 115 - 139 (chain E) in PDB entry 2Q7M
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
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Residue Dist Surf HB Arom Phob DC
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90E TYR* 5.1 4.3 - - - -
93E VAL* 4.4 17.2 - - - +
114E PHE* 1.3 77.3 - - - +
116E LYS* 1.3 65.4 + - - -
117E ARG* 2.9 13.7 - - - -
118E ILE* 2.8 27.8 + - - +
119E ILE* 2.8 13.8 - - - +
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Residues in contact with LYS 116 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E ILE* 4.3 11.7 - - + -
114E PHE 2.5 14.4 + - - +
115E GLY* 1.3 69.8 - - - -
117E ARG* 1.3 55.9 + - - +
119E ILE* 2.8 21.4 - - - +
120E LEU* 2.8 21.7 + - - +
506E 2CS 2.6 93.2 + - + -
28F HIS* 5.9 2.2 + - - -
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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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115E GLY* 4.1 11.9 - - - -
116E LYS* 1.3 76.9 - - - +
118E ILE* 1.3 60.2 + - + +
120E LEU* 3.2 8.7 + - - +
121E PHE* 2.7 37.6 + - - +
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Residues in contact with ILE 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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86E ALA* 3.2 22.7 - - + +
89E MET* 3.3 14.1 - - + +
90E TYR* 2.8 58.6 - - + +
93E VAL* 4.0 11.0 - - + -
115E GLY* 2.8 19.5 + - - +
117E ARG* 1.3 76.7 - - + +
119E ILE* 1.3 53.8 + - - +
121E PHE* 2.8 13.9 + - - +
122E LEU* 2.7 47.4 + - + +
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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
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66E THR 4.9 4.3 - - - +
67E PHE* 4.3 14.6 - - + -
70E VAL* 4.0 20.9 - - + +
90E TYR* 3.5 34.1 - - + -
115E GLY 2.8 23.3 - - - +
116E LYS* 2.8 35.7 - - - +
118E ILE* 1.3 80.6 - - - +
120E LEU* 1.3 58.5 + - - +
122E LEU* 3.8 0.3 - - - +
123E PHE* 2.8 31.7 + - - +
506E 2CS 3.0 45.3 - - + +
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Residues in contact with LEU 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 LYS 2.8 23.4 + - - +
117E ARG* 3.2 10.1 - - - +
118E ILE 3.0 0.2 - - - -
119E ILE* 1.3 77.6 - - - +
121E PHE* 1.3 64.7 + - + +
123E PHE* 3.0 13.7 - - - +
124E LEU* 2.7 53.4 - - + +
506E 2CS 3.0 55.0 - - + -
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Residues in contact with PHE 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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82E PRO* 4.2 11.4 - - + -
85E PHE* 6.3 0.2 - + - -
86E ALA* 3.0 37.2 - - + -
117E ARG 2.7 17.0 + - - +
118E ILE* 2.8 9.8 + - - +
120E LEU* 1.3 79.0 - - + +
122E LEU* 1.3 60.9 + - + +
124E LEU* 2.6 29.3 + - + +
125E MET* 3.1 46.7 + - + -
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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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67E PHE* 3.9 27.4 - - + -
70E VAL* 3.5 35.7 - - + +
71E LEU* 4.0 8.7 - - - -
74E ALA* 2.8 14.8 - - - +
83E ALA* 3.8 6.5 - - - +
86E ALA* 3.3 22.0 - - + -
87E GLY* 4.1 10.1 - - - +
118E ILE* 2.7 30.2 + - + +
121E PHE* 1.3 73.2 - - + +
123E PHE* 1.3 55.0 + - - +
125E MET* 3.0 36.1 + - + -
126E SER* 2.6 21.6 + - - -
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Residues in contact with PHE 123 (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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70E VAL* 3.9 7.8 - - + +
119E ILE 2.8 8.7 + - - +
120E LEU 3.0 11.2 - - - +
122E LEU* 1.3 76.0 - - - +
124E LEU* 1.3 75.8 - - + +
126E SER* 3.1 9.1 + - - -
127E VAL* 2.9 39.0 + - + +
506E 2CS 3.0 31.0 - - + -
17F LEU* 3.3 42.8 - - + +
20F VAL* 3.6 15.3 - - + -
21F VAL* 3.5 21.1 - - + -
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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
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120E LEU* 2.7 56.7 + - + +
121E PHE* 2.6 20.2 + - + +
123E PHE* 1.3 89.7 - - + +
125E MET* 1.3 58.2 + - - -
127E VAL* 2.9 34.9 - - + +
128E ALA* 3.0 15.8 + - - +
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Residues in contact with MET 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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74E ALA* 3.4 22.7 - - + +
78E CYS* 3.1 31.9 - - - +
79E SER* 3.9 3.6 - - - -
82E PRO* 3.7 17.0 - - - -
83E ALA* 2.9 40.4 - - + +
121E PHE* 3.1 35.0 + - + -
122E LEU* 3.0 27.9 + - + +
124E LEU* 1.3 75.5 - - - +
126E SER* 1.3 62.0 + - - +
128E ALA* 2.8 24.0 + - - +
129E GLY 3.1 6.9 + - - -
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Residues in contact with SER 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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73E SER* 3.2 49.9 + - - -
74E ALA* 3.7 0.6 - - - +
77E LEU* 4.0 2.3 - - - +
122E LEU 2.6 17.7 + - - -
123E PHE* 3.1 14.4 + - - -
125E MET* 1.3 73.9 - - - +
127E VAL* 1.3 57.1 + - - -
128E ALA 3.0 4.5 - - - -
130E ILE* 2.9 35.5 + - - +
17F LEU* 3.9 14.6 - - - +
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Residues in contact with VAL 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 PHE* 2.9 31.7 + - + +
124E LEU* 2.9 50.9 - - + +
126E SER* 1.3 75.8 - - - +
128E ALA* 1.3 62.6 + - - +
130E ILE* 3.9 11.2 - - + +
131E PHE* 3.5 20.3 + - - +
17F LEU* 4.9 4.4 - - + +
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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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78E CYS* 4.5 7.2 - - - -
124E LEU 3.0 16.4 + - - +
125E MET* 2.8 17.0 - - - +
126E SER 3.0 1.0 - - - -
127E VAL* 1.3 74.3 - - - +
129E GLY* 1.3 68.5 + - - +
130E ILE 3.0 0.4 - - - -
131E PHE* 2.7 39.7 + - + -
132E ASN* 2.9 3.8 + - - +
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Residues in contact with GLY 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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77E LEU* 2.9 24.2 + - - -
78E CYS* 4.4 1.3 - - - +
125E MET 3.1 6.7 + - - -
128E ALA* 1.3 79.3 - - - +
130E ILE* 1.3 55.8 + - - +
132E ASN* 3.4 14.9 - - - +
133E TYR* 2.6 37.6 + - - +
6F VAL* 5.9 2.0 - - - -
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Residues in contact with ILE 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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77E LEU* 3.9 23.5 + - + +
126E SER 2.9 23.3 + - - +
127E VAL* 3.9 15.0 - - + +
128E ALA 3.0 0.4 + - - -
129E GLY* 1.3 75.9 - - - +
131E PHE* 1.3 66.6 + - + +
133E TYR* 3.8 13.8 - - - +
134E TYR* 3.8 15.7 + - + -
6F VAL* 6.1 0.7 - - - -
10F VAL* 3.6 20.7 - - + +
13F ALA* 4.0 4.7 - - + -
14F ILE* 3.1 50.9 - - + +
17F LEU* 4.2 8.5 - - + -
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Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E VAL 3.7 12.6 - - - +
128E ALA* 2.7 33.3 + - + -
130E ILE* 1.3 82.1 - - + +
132E ASN* 1.3 65.0 + - + +
133E TYR 2.9 4.7 - - - -
134E TYR* 2.5 41.4 + - + +
135E LEU* 3.3 37.3 - - + +
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Residues in contact with ASN 132 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E ALA 2.9 12.0 + - - +
129E GLY* 3.4 14.1 - - - +
131E PHE* 1.3 94.0 - - + +
133E TYR* 1.3 64.3 + - - +
135E LEU* 3.3 16.4 + - + +
136E ILE* 2.8 44.5 + - - +
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E GLY 2.6 22.7 + - - +
130E ILE* 3.8 4.3 - - - +
132E ASN* 1.3 76.2 + - - +
134E TYR* 1.3 98.2 + + - +
135E LEU 3.0 4.7 - - - -
136E ILE* 3.1 8.5 + - + +
137E PHE* 2.9 32.9 + + + +
3F GLN* 2.9 56.4 + - - +
6F VAL* 4.0 20.4 - - + -
7F GLY* 3.1 25.5 + - - -
10F VAL* 3.8 18.2 - - + -
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Residues in contact with TYR 134 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E ILE* 4.0 11.0 - - + -
131E PHE* 2.5 22.4 + - + +
133E TYR* 1.3 106.3 - + - +
135E LEU* 1.3 61.7 + - + -
137E PHE* 3.6 16.8 - + + -
138E PHE* 2.9 32.0 + - + +
10F VAL* 3.3 26.6 - - + +
11F LEU* 3.9 11.8 - - - +
14F ILE* 4.5 9.3 - - + +
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Residues in contact with LEU 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 PHE* 3.3 44.6 - - + +
132E ASN* 3.4 16.4 - - + +
133E TYR 3.0 0.2 - - - -
134E TYR* 1.3 82.5 - - + +
136E ILE* 1.3 58.5 + - + +
137E PHE 3.0 1.6 - - - -
138E PHE* 2.8 5.7 + - + -
139E PHE* 2.4 62.7 + - + +
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Residues in contact with ILE 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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132E ASN* 2.8 52.9 - - - +
133E TYR* 3.1 6.9 + - + +
135E LEU* 1.3 77.3 - - + +
137E PHE* 1.3 59.1 + - - +
139E PHE 4.6 4.9 - - - -
140E GLY* 4.3 19.9 + - - +
3F GLN* 3.5 31.0 + - + +
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Residues in contact with PHE 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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133E TYR* 2.9 29.1 + + + +
134E TYR* 3.6 21.8 - + - -
136E ILE* 1.3 77.4 - - - +
138E PHE* 1.3 97.2 + + - +
140E GLY 5.5 0.2 - - - -
3F GLN* 3.5 17.9 - - - +
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Residues in contact with PHE 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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134E TYR* 2.9 20.0 + - + +
135E LEU* 2.8 1.4 + - + -
137E PHE* 1.3 109.8 - + - +
139E PHE* 1.3 100.4 + + + +
140E GLY 4.2 0.4 - - - -
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Residues in contact with PHE 139 (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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135E LEU* 2.4 64.2 + - + +
136E ILE* 4.6 0.9 - - - -
138E PHE* 1.3 110.8 - + + +
140E GLY* 1.3 56.7 + - - +
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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
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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