Contacts of the helix formed by residues 94 - 109 (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 ASP 94 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E HIS* 3.1 24.9 + - - -
82E MET* 5.1 2.4 - - - +
83E ASP* 3.6 10.8 - - - +
93E LEU* 1.3 79.2 - - - +
95E TYR* 1.3 58.9 + - - +
96E LEU* 3.2 4.1 + - - +
97E ALA* 2.8 23.9 + - - +
98E TYR* 3.1 21.3 + - - +
336E ASP* 3.5 25.3 - - + +
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Residues in contact with TYR 95 (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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83E ASP* 3.7 29.1 + - + -
94E ASP* 1.3 69.9 - - - +
96E LEU* 1.3 62.7 + - - +
98E TYR* 3.5 34.1 - + + +
99E ALA* 2.9 23.9 + - - +
120E ASN* 4.6 3.7 + - + -
121E SER* 2.7 33.1 + - - -
125E GLY* 5.8 0.2 - - - -
270E MET* 3.5 34.3 - - + +
273E ILE* 3.9 19.3 - - + -
332E ALA* 3.8 16.0 - - + +
335E LYS* 3.4 38.6 - - + -
336E ASP* 2.8 22.4 + - - +
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Residues in contact with LEU 96 (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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34E LEU* 4.1 17.3 - - + -
35E PRO* 5.0 7.2 - - + -
38E HIS* 4.0 17.5 - - + +
94E ASP* 3.2 5.8 + - - +
95E TYR* 1.3 75.9 - - - +
97E ALA* 1.3 62.3 + - - +
99E ALA* 3.2 4.9 + - + +
100E ILE* 3.1 25.6 + - + +
329E TRP* 3.8 53.2 - - + +
332E ALA* 3.9 6.9 - - + +
333E MET* 4.1 21.8 - - + -
336E ASP* 2.9 16.6 + - - +
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Residues in contact with ALA 97 (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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38E HIS* 3.4 15.5 + - + +
41E LEU* 3.4 33.9 - - + +
82E MET* 4.0 4.0 - - + -
93E LEU* 3.9 21.1 - - + -
94E ASP* 2.8 24.0 + - - +
96E LEU* 1.3 72.9 - - - +
98E TYR* 1.3 56.1 + - - +
100E ILE* 3.3 2.5 + - - -
101E ALA* 2.9 27.0 + - - +
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Residues in contact with TYR 98 (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 MET* 3.8 25.2 - - + +
83E ASP 5.7 0.4 - - - +
94E ASP 3.1 10.5 + - - +
95E TYR* 3.5 45.8 - + + +
96E LEU 3.3 0.4 - - - -
97E ALA* 1.3 79.7 - - - +
99E ALA* 1.3 59.4 + - - +
101E ALA* 3.8 0.2 - - - +
102E MET* 2.8 53.1 + - + +
116E MET* 4.4 0.9 - - + -
117E SER* 2.9 29.2 + - - -
120E ASN* 3.5 35.9 - - + -
121E SER* 2.7 29.3 + - - -
273E ILE* 5.2 1.6 - - + -
274E GLY* 3.7 14.0 - - - -
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Residues in contact with ALA 99 (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 2.9 13.3 + - - +
96E LEU 3.2 8.3 + - - +
98E TYR* 1.3 77.6 - - - +
100E ILE* 1.3 61.9 + - - +
102E MET* 4.5 0.2 - - - -
103E GLU* 3.1 25.8 + - - +
273E ILE* 4.5 8.5 - - + -
277E SER* 3.4 27.3 - - - +
280E LEU* 5.6 0.7 - - + +
328E THR* 4.1 15.9 - - + -
329E TRP* 4.4 13.9 - - + -
332E ALA* 4.5 4.3 - - + -
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Residues in contact with ILE 100 (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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34E LEU* 3.7 36.6 - - + -
38E HIS* 3.8 30.7 - - + +
41E LEU* 4.5 4.3 - - + -
42E LEU* 3.7 44.9 - - + +
96E LEU* 3.1 12.8 + - + +
97E ALA* 3.5 7.2 - - - +
99E ALA* 1.3 76.0 - - - +
101E ALA* 1.3 65.1 + - - +
103E GLU* 3.4 9.0 + - - +
104E GLU* 3.1 23.4 + - + +
329E TRP* 4.2 22.6 - - + +
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Residues in contact with ALA 101 (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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41E LEU* 4.8 1.3 - - + -
45E CYS* 3.8 28.5 - - - -
79E LEU* 4.2 2.0 - - + -
82E MET* 3.5 34.8 - - + -
97E ALA 2.9 11.7 + - - +
98E TYR 3.8 0.4 - - - +
100E ILE* 1.3 75.1 - - - +
102E MET* 1.3 65.6 + - - +
104E GLU* 3.2 3.5 + - - +
105E ILE* 2.9 27.4 + - + +
116E MET* 3.8 9.2 - - + -
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Residues in contact with MET 102 (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* 2.8 45.3 + - + +
101E ALA* 1.3 72.8 - - - +
103E GLU* 1.3 58.9 + - - +
105E ILE* 3.8 2.2 - - - +
106E SER* 2.8 57.7 + - - +
113E GLY* 3.1 31.6 - - - +
116E MET* 3.8 24.6 - - + +
117E SER* 3.8 16.6 - - - -
274E GLY 3.7 18.4 - - - +
277E SER* 3.5 19.5 - - - -
278E GLN* 3.8 9.0 - - + -
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Residues in contact with GLU 103 (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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42E LEU* 6.6 0.2 - - - -
99E ALA 3.1 14.7 + - - +
100E ILE* 3.6 7.0 - - - +
101E ALA 3.3 0.4 - - - -
102E MET* 1.3 78.1 - - - +
104E GLU* 1.3 75.5 + - - +
107E ARG* 3.1 22.6 + - + +
277E SER* 3.5 17.0 + - - +
280E LEU* 3.7 18.8 - - + +
281E GLY* 3.3 20.0 - - - +
284E GLN* 4.2 8.1 - - + +
325E ARG* 2.8 46.9 + - - +
329E TRP* 4.7 6.8 + - - -
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Residues in contact with GLU 104 (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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42E LEU* 3.9 45.3 - - + +
45E CYS* 3.6 26.0 - - + -
46E ARG* 3.4 27.8 - - - +
49E ALA* 3.3 19.7 - - - +
100E ILE 3.1 15.9 + - - +
101E ALA 3.8 1.8 - - - +
103E GLU* 1.3 89.2 - - - +
105E ILE* 1.3 61.3 + - - +
107E ARG* 3.4 30.0 + - - +
108E GLY 3.6 0.2 + - - -
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Residues in contact with ILE 105 (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 CYS* 4.4 15.3 - - + +
48E PHE* 4.0 13.9 - - + -
53E LEU* 3.6 22.1 - - + +
74E MET* 3.9 8.7 - - + -
79E LEU* 3.9 22.4 - - + -
101E ALA 2.9 22.5 + - - +
102E MET 3.8 3.1 - - - +
104E GLU* 1.3 74.8 - - - +
106E SER* 1.3 58.7 + - - +
108E GLY 3.1 4.0 + - - -
109E CYS 3.0 23.0 + - - +
112E THR* 3.7 29.2 - - + -
113E GLY* 3.9 15.3 - - - +
116E MET* 3.8 20.2 - - - -
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Residues in contact with SER 106 (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* 2.8 32.8 + - - +
103E GLU 4.1 2.5 - - - -
105E ILE* 1.3 73.2 - - - +
107E ARG* 1.3 64.5 + - - +
109E CYS 3.6 10.2 + - - -
110E ALA* 3.4 22.1 + - - +
113E GLY* 3.6 4.9 - - - -
278E GLN* 3.3 46.6 - - - +
281E GLY* 4.1 7.3 - - - -
282E ILE* 4.4 3.9 + - - +
285E THR* 5.1 1.4 - - - +
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Residues in contact with ARG 107 (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 ARG* 4.1 19.8 + - - +
49E ALA* 5.5 0.8 - - - +
50E GLU* 3.4 26.1 + - - +
54E PHE* 3.8 27.3 - - + -
103E GLU* 3.1 19.3 + - - +
104E GLU* 3.4 23.9 + - - +
106E SER* 1.3 76.4 - - - +
108E GLY* 1.3 59.1 + - - +
281E GLY* 3.3 16.7 - - - +
284E GLN* 4.1 17.3 - - - +
285E THR* 3.2 37.8 + - - +
288E ASP* 3.1 27.4 + - - +
380E ARG* 5.8 0.2 + - - -
381E HIS* 5.2 1.9 - - - -
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Residues in contact with GLY 108 (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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49E ALA* 4.3 2.9 - - - -
53E LEU* 3.9 15.8 - - - +
54E PHE* 3.6 29.3 + - - -
57E ALA* 3.4 19.4 - - - +
104E GLU 3.6 3.2 + - - -
105E ILE 3.1 6.8 + - - -
107E ARG* 1.3 81.3 - - - +
109E CYS* 1.3 61.7 + - - +
380E ARG* 4.6 4.0 + - - -
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Residues in contact with CYS 109 (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* 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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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