Contacts of the helix formed by residues 124 - 139 (chain E) in PDB entry 2V8W
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 SER 124 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E SER* 3.9 17.4 + - - -
120E GLN* 3.7 1.8 - - - +
123E ARG* 1.3 74.4 + - - +
125E ASP* 1.3 62.6 + - - +
126E LEU* 3.2 8.5 + - - -
127E ASP* 3.2 30.9 + - - +
128E ARG* 3.7 3.9 + - - +
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Residues in contact with ASP 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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117E LEU* 4.1 8.7 - - + -
120E GLN* 2.6 36.2 - - - +
123E ARG* 2.9 45.3 + - - +
124E SER* 1.3 70.5 + - - +
126E LEU* 1.3 59.0 + - - +
127E ASP 3.2 0.2 - - - -
128E ARG* 3.1 34.8 + - - +
129E PHE* 2.8 37.8 + - + +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E SER* 3.7 39.5 - - - +
83E SER* 3.9 13.5 - - - +
117E LEU* 3.7 19.5 - - + +
120E GLN* 4.1 3.4 - - - +
124E SER* 3.2 1.3 - - - -
125E ASP* 1.3 77.5 - - - +
127E ASP* 1.3 57.6 - - - +
129E PHE* 3.8 0.6 - - - -
130E TRP* 2.8 29.3 + - - +
154E VAL* 4.0 9.4 - - + -
156E VAL* 4.5 5.6 - - + -
161E ASP* 3.8 42.6 - - + +
163E ILE* 3.9 21.5 - - + -
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Residues in contact with ASP 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E TYR* 4.0 6.7 + - - +
81E LEU* 3.6 29.4 - - + +
82E SER* 3.4 13.3 + - - -
83E SER* 2.4 48.1 + - - -
124E SER* 3.2 18.2 + - - +
126E LEU* 1.3 76.3 - - - +
128E ARG* 1.3 57.4 + - - +
130E TRP* 4.0 4.4 - - - +
131E LEU* 3.0 33.0 + - - +
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Residues in contact with ARG 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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123E ARG* 4.6 10.3 - - - +
124E SER 3.7 2.2 + - - +
125E ASP* 3.1 42.1 + - - +
127E ASP* 1.3 80.8 - - - +
129E PHE* 1.3 91.8 + - + +
131E LEU* 4.0 5.1 - - - +
132E GLU* 3.1 25.7 + - + +
187E LEU 4.9 4.8 + - - -
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Residues in contact with PHE 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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115E ILE* 3.9 21.5 - - + -
117E LEU* 4.2 20.6 - - + -
125E ASP* 2.8 21.7 + - + +
126E LEU* 3.9 1.1 - - - +
128E ARG* 1.3 104.2 - - + +
130E TRP* 1.3 56.9 + - - +
132E GLU* 3.5 3.0 + - + +
133E THR* 2.7 37.9 + - - -
163E ILE* 3.8 15.0 - - + -
187E LEU* 3.6 35.2 - - + +
189E LEU* 3.8 30.5 - - + -
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Residues in contact with TRP 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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45E LEU* 4.8 4.1 - - + +
76E TYR* 4.6 13.1 - + - -
79E ILE* 6.3 0.6 - - - +
82E SER* 3.7 19.9 + - - +
91E TYR* 3.9 23.1 - + + +
92E SER 4.5 0.9 - - - -
93E LEU* 4.3 4.0 - - + -
126E LEU 2.8 19.6 + - - +
127E ASP* 4.0 4.0 - - - +
129E PHE* 1.3 73.7 - - - +
131E LEU* 1.3 61.2 + - - +
133E THR* 3.3 8.3 + - + -
134E LEU* 2.9 70.1 + - + +
152E ALA* 3.5 39.5 - - + -
153E VAL 3.7 17.7 - - - -
154E VAL* 3.5 35.9 - - + +
163E ILE* 3.5 20.1 - - + +
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E PHE* 4.0 17.5 - - + -
73E TRP* 3.8 36.1 - - + -
76E TYR* 3.8 30.1 - - + +
127E ASP 3.0 18.1 + - - +
128E ARG* 4.0 4.7 - - - +
130E TRP* 1.3 76.8 - - - +
132E GLU* 1.3 57.7 - - - +
134E LEU* 3.1 6.1 + - - +
135E LEU* 2.8 45.3 + - + +
60F MET* 4.4 15.5 - - + -
63F ARG* 5.2 3.6 - - - +
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ARG* 3.1 19.4 + - + +
129E PHE* 3.5 5.8 - - + +
131E LEU* 1.3 73.5 - - - +
133E THR* 1.3 65.8 + - - +
135E LEU* 3.3 5.8 + - - +
136E CYS* 3.0 27.3 + - - -
186E ARG* 2.2 67.0 + - + +
187E LEU* 3.8 17.5 - - + -
56F ARG* 3.1 29.9 - - - +
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Residues in contact with THR 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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129E PHE 2.7 22.5 + - - -
130E TRP* 3.3 14.8 + - + -
132E GLU* 1.3 71.9 - - - +
134E LEU* 1.3 60.4 + - - +
136E CYS* 3.2 14.6 + - - +
137E LEU* 3.2 14.0 + - - +
152E ALA* 3.5 31.0 - - + -
163E ILE* 3.5 11.9 - - + +
165E ILE* 4.0 13.7 - - + -
183E TYR* 2.9 37.0 + - + +
187E LEU* 4.6 0.8 - - - +
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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
----------------------------------------------------------
45E LEU* 5.2 4.7 - - + -
72E PHE* 3.7 34.3 - - + -
76E TYR* 4.0 14.8 - - + -
93E LEU* 3.7 31.6 - - + -
130E TRP* 2.9 67.1 + - + +
131E LEU* 3.1 7.6 + - - +
133E THR* 1.3 75.6 - - - +
135E LEU* 1.3 59.5 + - - +
137E LEU* 3.3 8.0 + - + +
138E ILE* 2.9 33.8 + - - +
152E ALA* 5.3 0.2 - - + -
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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
----------------------------------------------------------
72E PHE* 4.0 18.2 - - + -
73E TRP* 4.2 6.5 - - + -
131E LEU* 2.8 28.9 + - + +
132E GLU* 3.7 8.3 - - - +
134E LEU* 1.3 74.1 - - - +
136E CYS* 1.3 59.0 + - - +
138E ILE* 4.0 16.8 - - + -
139E GLY* 3.0 27.7 + - - -
141E SER* 3.9 2.3 + - - -
186E ARG* 4.0 13.1 + - - +
56F ARG* 4.1 18.2 - - + -
59F LEU* 3.4 35.0 - - + +
60F MET* 3.7 28.5 - - - -
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Residues in contact with CYS 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 GLU* 3.0 14.7 + - - -
133E THR* 3.2 10.3 + - - +
135E LEU* 1.3 73.5 - - - +
137E LEU* 1.3 64.7 + - + +
140E GLU* 3.2 1.9 + - - -
141E SER* 3.1 38.8 + - - +
142E PHE* 3.7 28.4 - - + -
165E ILE* 5.0 2.0 - - + -
183E TYR* 4.6 9.0 - - - -
186E ARG* 3.3 51.4 - - - +
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Residues in contact with LEU 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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43E TRP* 3.5 35.6 - - + -
93E LEU* 3.7 24.5 - - + +
133E THR 3.2 15.8 + - - +
134E LEU* 3.3 7.4 + - + +
136E CYS* 1.3 77.8 - - - +
138E ILE* 1.3 66.4 + - - +
140E GLU* 3.0 17.7 + - - +
142E PHE* 4.4 12.6 - - + -
149E VAL* 3.6 24.7 - - + -
151E GLY 3.7 2.5 - - - -
152E ALA* 3.6 40.2 - - + +
165E ILE* 4.4 11.0 - - + -
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Residues in contact with ILE 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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39E LEU* 3.5 35.0 - - + +
40E GLN 4.9 1.2 + - - -
43E TRP* 3.9 13.8 + - + +
66E PHE* 3.9 19.3 - - + -
69E VAL* 4.9 4.7 - - + -
72E PHE* 3.7 38.4 - - + -
93E LEU* 3.9 22.7 - - + -
134E LEU 2.9 21.8 + - - +
135E LEU* 4.0 13.7 - - + -
137E LEU* 1.3 78.7 - - - +
139E GLY* 1.3 61.7 + - - +
140E GLU* 3.2 10.7 + - - +
52F ILE 5.1 0.5 - - - +
54F TYR* 4.8 1.6 - - - -
59F LEU* 4.0 22.4 - - + -
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Residues in contact with GLY 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 3.0 18.8 + - - -
136E CYS 4.0 0.4 - - - -
138E ILE* 1.3 76.8 - - - +
140E GLU* 1.3 70.3 + - - +
141E SER* 3.5 3.7 + - - -
52F ILE 4.7 0.2 - - - -
53F ILE* 3.5 4.6 - - - +
54F TYR* 3.0 46.0 + - - +
59F LEU* 3.9 8.3 - - - -
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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
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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