Contacts of the helix formed by residues 94 - 109 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F HIS* 3.1 24.6 + - - -
82F MET* 5.1 1.4 - - - +
83F ASP* 3.2 12.2 - - - +
93F LEU* 1.3 80.8 - - - +
95F TYR* 1.3 59.7 - - - +
96F LEU* 3.3 2.6 + - - +
97F ALA* 2.9 23.4 + - - +
98F TYR* 3.0 22.0 + - - +
336F ASP* 3.3 25.5 - - + +
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Residues in contact with TYR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASP* 3.6 28.2 + - + -
94F ASP* 1.3 68.3 - - - +
96F LEU* 1.3 58.3 + - - +
98F TYR* 3.6 35.2 - + + +
99F ALA* 2.9 27.5 + - - +
120F ASN* 4.5 4.9 + - + -
121F SER* 2.7 28.4 + - - -
125F GLY* 5.6 0.3 - - - -
270F MET* 3.5 32.5 - - + +
273F ILE* 4.1 20.1 - - + +
332F ALA* 3.6 17.0 - - + +
335F LYS* 3.6 41.7 - - + -
336F ASP* 2.7 20.5 + - - +
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 4.0 14.4 - - + -
35F PRO* 4.7 8.5 - - + -
38F HIS* 3.7 22.7 - - + +
94F ASP* 3.2 5.8 - - - +
95F TYR* 1.3 74.3 - - - +
97F ALA* 1.3 67.2 + - - +
99F ALA* 3.2 3.6 + - - +
100F ILE* 3.0 26.0 + - + +
329F TRP* 3.9 47.3 - - + +
332F ALA* 3.9 7.1 - - + +
333F MET* 4.2 25.6 - - + -
336F ASP* 3.0 17.4 + - - +
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F HIS* 3.6 18.6 + - + +
41F LEU* 3.5 24.5 - - + +
82F MET* 4.0 3.6 - - + -
93F LEU* 3.9 23.1 - - + -
94F ASP* 2.9 22.8 + - - +
96F LEU* 1.3 76.9 - - - +
98F TYR* 1.3 56.4 + - - +
100F ILE* 3.2 2.9 + - - +
101F ALA* 2.9 30.5 + - - +
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Residues in contact with TYR 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F MET* 3.7 20.3 - - + +
83F ASP* 5.7 0.9 - - + +
94F ASP 3.0 12.7 + - - +
95F TYR* 3.6 43.7 - + + +
96F LEU 3.3 0.2 - - - -
97F ALA* 1.3 74.7 - - - +
99F ALA* 1.3 59.3 + - - +
101F ALA* 4.0 0.2 - - - +
102F MET* 2.9 55.7 + - + +
116F MET* 4.3 6.3 - - + -
117F SER* 2.8 33.1 + - - -
120F ASN* 3.5 37.7 - - + -
121F SER* 2.9 26.7 + - - -
273F ILE* 5.2 1.3 - - + -
274F GLY* 3.7 15.6 - - - -
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TYR 2.9 18.1 + - - +
96F LEU* 3.2 7.8 + - - +
98F TYR* 1.3 79.6 - - - +
100F ILE* 1.3 62.6 + - - +
102F MET* 4.5 0.2 - - - -
103F GLU* 3.1 22.5 + - - +
273F ILE* 4.7 3.4 - - + -
277F SER* 3.5 27.9 - - - +
280F LEU* 5.7 0.7 - - - +
328F THR* 4.4 7.2 - - + -
329F TRP* 4.3 23.3 - - + +
332F ALA* 4.5 6.3 - - + -
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.5 37.5 - - + -
38F HIS* 3.8 23.6 - - + +
41F LEU* 4.6 4.7 - - + -
42F LEU* 3.7 45.5 - - + +
96F LEU* 3.0 17.2 + - + +
97F ALA* 3.6 6.3 - - - +
99F ALA* 1.3 76.2 - - - +
101F ALA* 1.3 63.1 + - - +
103F GLU* 3.4 6.4 + - - +
104F GLU* 3.2 22.7 + - + +
329F TRP* 4.1 23.3 - - + +
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Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.5 2.0 - - + -
45F CYS* 3.8 16.3 - - - +
79F LEU* 3.7 18.6 - - + -
82F MET* 3.5 33.9 - - + -
97F ALA 2.9 13.9 + - - +
98F TYR 4.0 0.2 - - - +
100F ILE* 1.3 74.3 - - - +
102F MET* 1.3 59.4 - - - +
104F GLU* 3.3 3.6 + - - +
105F ILE* 3.0 32.7 + - - +
116F MET* 4.0 3.8 - - + -
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Residues in contact with MET 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F TYR* 2.9 48.0 + - + +
101F ALA* 1.3 76.3 - - - +
103F GLU* 1.3 57.0 + - - +
105F ILE* 4.1 1.9 - - - +
106F SER* 2.8 58.0 + - - +
113F GLY* 3.2 29.6 - - - +
116F MET* 3.7 26.4 - - + +
117F SER* 3.8 13.7 - - - -
274F GLY 3.7 19.7 - - - +
277F SER* 3.6 17.0 - - - -
278F GLN* 3.9 8.1 - - + -
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ALA 3.1 17.3 + - - +
100F ILE* 3.7 7.0 - - - +
101F ALA 3.3 0.2 - - - -
102F MET* 1.3 77.1 - - - +
104F GLU* 1.3 69.0 + - - +
107F ARG* 3.0 27.7 + - + +
277F SER* 3.4 13.8 + - - +
280F LEU* 3.6 20.4 - - + +
281F GLY* 3.3 28.6 - - - +
284F GLN* 4.1 10.4 - - + +
325F ARG* 2.8 48.2 + - - +
329F TRP* 4.8 4.7 + - - -
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.8 32.2 - - + +
45F CYS* 3.7 28.0 - - + +
46F ARG* 3.0 54.2 + - - +
49F ALA* 3.4 18.1 - - - +
100F ILE* 3.2 14.7 + - + +
101F ALA 3.3 2.4 + - - +
103F GLU* 1.3 90.3 - - - +
105F ILE* 1.3 60.4 + - - +
107F ARG* 3.3 25.5 + - - +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F CYS* 4.3 15.3 - - + +
48F PHE* 3.9 29.4 - - + -
49F ALA* 4.7 0.9 - - + -
53F LEU* 3.2 15.6 - - + +
74F MET* 3.9 8.1 - - + -
79F LEU* 3.9 20.0 - - + -
101F ALA 3.0 21.0 + - - +
102F MET* 4.1 3.4 - - - +
104F GLU* 1.3 76.5 - - - +
106F SER* 1.3 58.6 + - - +
108F GLY 3.1 3.6 + - - -
109F CYS 2.9 23.2 + - - +
112F THR* 3.4 30.7 - - + -
113F GLY* 3.8 15.3 - - - +
116F MET* 3.8 19.3 - - - -
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Residues in contact with SER 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F MET* 2.8 31.3 + - - +
103F GLU 4.0 2.2 - - - -
105F ILE* 1.3 74.2 - - - +
107F ARG* 1.3 64.4 + - - +
108F GLY 3.2 0.6 + - - -
109F CYS 3.5 22.0 + - - -
110F ALA* 3.6 9.7 + - - +
113F GLY* 3.5 4.7 - - - -
278F GLN* 3.4 47.6 - - - +
281F GLY* 4.2 6.5 - - - -
282F ILE* 4.3 4.6 + - - +
285F THR* 5.0 1.2 - - - +
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ARG* 3.2 28.1 + - - +
49F ALA* 5.6 1.0 - - - +
50F GLU* 3.3 25.5 + - - +
54F PHE* 3.5 27.5 - - + -
103F GLU* 3.0 19.2 + - - +
104F GLU* 3.3 24.6 + - - +
106F SER* 1.3 76.7 - - - +
108F GLY* 1.3 59.2 + - - +
281F GLY* 3.4 15.4 - - - +
284F GLN* 3.9 17.9 - - - +
285F THR* 3.2 38.9 + - - +
288F ASP* 3.0 30.8 + - - +
380F ARG* 5.9 0.2 + - - -
381F HIS* 5.1 2.3 - - - -
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Residues in contact with GLY 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ALA* 4.3 2.9 - - - -
53F LEU* 3.8 17.9 - - - +
54F PHE* 3.6 28.9 + - - -
57F ALA* 3.5 19.6 - - - +
104F GLU 3.5 3.8 + - - -
105F ILE 3.1 6.7 + - - -
107F ARG* 1.3 81.0 - - - +
109F CYS* 1.3 62.5 + - - +
380F ARG* 4.5 3.5 + - - -
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Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.9 13.7 - - + +
56F ILE* 5.3 2.5 - - + -
57F ALA* 4.6 14.1 - - + -
60F VAL* 4.2 22.2 - - - -
67F PRO* 5.2 0.2 - - - -
105F ILE 2.9 13.6 + - - +
106F SER* 3.5 6.0 + - - -
108F GLY* 1.3 79.0 - - - +
110F ALA* 1.3 61.9 + - - +
111F SER* 3.8 12.6 - - - -
112F THR* 3.3 35.2 + - - +
113F GLY 3.1 22.0 + - - -
380F ARG* 5.2 2.5 - - - +
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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