Contacts of the helix formed by residues 109 - 122 (chain E) in PDB entry 2VIG
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 CYS 109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E LEU* 4.0 14.8 - - + +
56E ILE* 5.4 1.8 - - + -
57E ALA* 4.4 13.9 - - + -
60E VAL* 4.1 23.1 - - - -
67E PRO* 5.3 0.2 - - - -
105E ILE 3.0 12.8 + - - +
106E SER* 3.6 4.8 + - - -
108E GLY* 1.3 80.6 - - - +
110E ALA* 1.3 67.5 + - - +
111E SER* 3.8 12.3 - - - -
112E THR* 3.3 34.7 + - - +
113E GLY 3.1 16.3 + - - -
380E ARG* 5.2 2.9 - - - +
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Residues in contact with ALA 110 (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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106E SER* 3.4 14.2 + - - +
109E CYS* 1.3 72.6 - - - +
111E SER* 1.3 61.8 + - - +
113E GLY* 3.3 1.7 + - - -
114E VAL* 3.1 9.5 + - - +
233E ILE* 4.1 6.5 - - + -
278E GLN* 3.0 24.0 + - - +
282E ILE* 3.8 27.6 - - + -
380E ARG* 5.4 2.8 - - - +
384E ASP* 3.2 35.0 + - + +
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Residues in contact with SER 111 (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 VAL* 4.1 5.0 - - - +
61E ASP* 6.0 0.2 - - - -
67E PRO* 5.3 0.7 - - - -
109E CYS* 3.3 12.6 - - - -
110E ALA* 1.3 74.6 - - - +
112E THR* 1.3 65.9 + - - +
114E VAL* 3.1 11.8 + - - +
115E ILE* 3.1 29.8 + - - +
233E ILE* 3.1 19.0 - - - +
234E ARG 3.4 0.5 + - - -
235E GLY* 2.9 39.9 + - - -
236E SER 3.8 4.3 - - - -
384E ASP* 5.1 0.4 + - - -
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Residues in contact with THR 112 (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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53E LEU* 3.7 14.6 - - + +
56E ILE* 5.3 0.2 - - - +
67E PRO* 3.7 15.1 - - - +
70E GLN* 5.6 0.9 - - + -
71E VAL* 4.9 8.5 - - + -
74E MET* 3.0 41.0 - - + +
105E ILE* 3.7 8.5 - - + -
109E CYS* 3.3 29.2 + - - +
111E SER* 1.3 76.4 - - - +
113E GLY* 1.3 62.8 + - - +
115E ILE* 3.3 11.8 + - - +
116E MET* 3.0 22.3 + - - +
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Residues in contact with GLY 113 (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 MET* 3.1 22.1 - - - +
105E ILE* 3.9 10.0 - - - +
106E SER* 3.6 21.1 - - - -
109E CYS 3.1 11.8 + - - -
110E ALA 3.5 5.6 - - - -
111E SER 3.1 1.0 - - - -
112E THR* 1.3 75.9 - - - +
114E VAL* 1.3 55.2 + - - +
116E MET* 3.5 0.6 + - - +
117E SER* 3.0 21.8 + - - -
278E GLN* 4.6 1.1 - - - -
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Residues in contact with VAL 114 (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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110E ALA 3.1 8.8 + - - +
111E SER* 3.1 14.5 + - - +
113E GLY* 1.3 72.7 - - - +
115E ILE* 1.3 62.1 + - - +
117E SER* 4.2 3.8 - - - -
118E VAL* 2.9 42.9 + - + +
187E THR* 4.3 7.4 - - + -
233E ILE* 4.3 9.0 - - + -
236E SER* 3.6 28.5 - - - +
275E ILE* 4.4 9.4 - - + -
278E GLN* 3.7 7.7 - - - +
391E TYR* 3.2 39.9 - - + +
392E GLU* 6.0 0.2 - - - +
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Residues in contact with ILE 115 (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 PHE* 3.7 22.7 - - + -
67E PRO* 3.9 23.3 - - + -
71E VAL* 4.1 24.9 - - + -
74E MET* 6.4 0.4 - - + -
80E LEU* 5.3 1.3 - - + -
111E SER 3.1 27.1 + - - +
112E THR* 3.5 7.2 - - - +
113E GLY 3.3 0.2 - - - -
114E VAL* 1.3 75.8 - - - +
116E MET* 1.3 62.5 + - - +
119E ASN* 3.2 21.1 + - - +
149E ILE* 4.2 19.7 - - + -
188E ASN* 3.6 32.6 + - - +
236E SER* 4.0 19.1 - - - +
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Residues in contact with MET 116 (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 MET* 3.7 27.3 - - + +
79E LEU* 3.4 26.0 - - + +
80E LEU* 3.9 12.8 - - + -
82E MET* 3.9 8.5 - - - -
98E TYR* 4.4 1.3 - - + -
101E ALA* 3.8 16.6 - - + -
102E MET* 3.8 41.1 - - + +
105E ILE* 3.8 16.4 - - + -
112E THR 3.0 16.0 + - - +
113E GLY 3.7 2.9 - - - +
115E ILE* 1.3 76.7 - - - +
117E SER* 1.3 57.0 + - - +
119E ASN* 3.4 1.3 + - - +
120E ASN* 2.6 48.3 + - - +
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Residues in contact with SER 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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98E TYR* 2.9 21.0 + - - -
102E MET* 3.8 10.7 - - - -
113E GLY 3.0 18.4 + - - -
114E VAL* 3.2 8.7 + - - -
116E MET* 1.3 75.6 - - - +
118E VAL* 1.3 60.5 + - - +
121E SER* 2.8 37.1 + - - -
122E LEU* 5.0 1.1 - - - -
271E GLY* 4.4 2.3 + - - -
274E GLY* 3.5 22.9 - - - -
275E ILE* 4.1 13.1 + - - +
392E GLU* 5.0 2.6 + - - -
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Residues in contact with VAL 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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114E VAL* 2.9 27.7 + - + +
117E SER* 1.3 73.8 - - - +
119E ASN* 1.3 66.4 + - - +
122E LEU* 3.1 33.7 + - + -
123E TYR 2.9 23.6 + - - -
150E GLY 3.8 9.9 - - - +
151E CYS* 3.9 15.3 - - - -
152E PHE* 4.5 3.1 - - + +
187E THR* 3.8 30.1 - - + +
188E ASN* 3.6 21.3 - - - +
392E GLU* 5.3 2.0 - - - +
501E FAD 4.8 2.2 - - - +
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Residues in contact with ASN 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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80E LEU* 2.8 35.5 + - + +
115E ILE 3.2 15.4 + - - +
116E MET* 3.9 4.0 - - - +
118E VAL* 1.3 82.1 - - - +
120E ASN* 1.3 56.3 + - - +
123E TYR* 3.6 9.1 - - - +
124E LEU* 3.0 39.8 + - - +
143E PHE 3.2 22.3 + - - +
149E ILE* 3.3 21.6 - - + +
150E GLY* 2.8 31.0 + - - +
188E ASN* 5.1 0.9 - - - +
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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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79E LEU 2.8 24.1 + - - +
80E LEU* 3.6 10.0 + - - +
81E ALA* 3.3 3.5 + - - -
82E MET* 3.0 33.1 + - - +
83E ASP* 4.6 1.9 + - - +
84E VAL* 6.0 0.2 - - - +
95E TYR* 4.6 4.6 + - + +
98E TYR* 3.5 27.3 - - + +
116E MET* 2.6 36.2 + - - +
119E ASN* 1.3 77.1 - - - +
121E SER* 1.3 60.2 + - - +
124E LEU* 3.6 6.5 - - - +
125E GLY* 3.2 23.6 + - - -
128E LEU* 5.9 0.2 - - - +
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Residues in contact with SER 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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95E TYR* 2.7 25.4 + - - -
98E TYR* 2.7 25.9 + - - -
117E SER* 2.8 17.7 + - - -
120E ASN* 1.3 74.8 - - - +
122E LEU* 1.3 63.7 + - - +
125E GLY* 3.4 16.2 - - - -
267E THR* 3.4 15.0 - - - +
270E MET* 3.6 8.4 + - - +
271E GLY* 3.6 27.1 - - - -
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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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117E SER 4.5 0.2 - - - +
118E VAL* 3.1 33.9 + - + +
121E SER* 1.3 79.6 - - - +
123E TYR* 1.3 60.7 + - - +
126E PRO* 3.1 19.7 - - - +
152E PHE* 3.2 48.4 - - + +
196E VAL* 4.5 1.2 - - - +
267E THR* 3.6 17.3 - - + +
268E LEU* 4.4 9.6 - - + -
271E GLY* 3.8 21.1 - - - -
392E GLU* 3.4 34.5 - - + +
501E FAD 4.9 7.4 - - + +
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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
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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