Contacts of the helix formed by residues 35 - 53 (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 PRO 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F LEU* 1.4 101.5 - - + +
36F GLU* 1.3 65.4 + - - +
37F THR* 4.1 7.2 - - - +
38F HIS* 3.2 28.7 + - + +
39F GLN* 3.0 23.1 + - - +
96F LEU* 4.7 7.2 - - + -
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Residues in contact with GLU 36 (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 0.2 + - - -
35F PRO* 1.3 71.7 - - - +
37F THR* 1.3 65.4 + - + +
39F GLN* 3.3 17.0 + - - +
40F MET* 3.3 20.1 + - - +
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Residues in contact with THR 37 (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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35F PRO* 4.1 5.9 - - - +
36F GLU* 1.3 78.9 - - + +
38F HIS* 1.3 74.0 + - - +
40F MET* 3.5 8.1 + - - +
41F LEU* 3.2 23.2 + - - +
93F LEU* 6.4 2.7 - - - -
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Residues in contact with HIS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 4.1 5.3 - - + +
35F PRO* 3.2 32.4 + - + +
37F THR* 1.3 87.4 + - - +
39F GLN* 1.3 59.4 + - - +
41F LEU* 3.5 7.9 + - + +
42F LEU* 3.0 27.7 + - - +
93F LEU* 5.7 6.1 - - + -
94F ASP* 3.1 35.9 + - - -
96F LEU* 3.7 19.7 - - + +
97F ALA* 3.6 30.5 + - + +
100F ILE* 3.8 18.6 - - + +
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Residues in contact with GLN 39 (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* 3.3 32.3 + - + +
35F PRO 3.0 21.0 + - - +
36F GLU* 3.3 18.4 + - - +
37F THR 3.3 0.2 - - - -
38F HIS* 1.3 75.2 - - - +
40F MET* 1.3 62.8 + - - +
42F LEU* 3.4 6.5 + - - +
43F GLN* 3.3 21.7 + - - +
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Residues in contact with MET 40 (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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36F GLU 3.3 12.0 + - - +
37F THR* 3.7 11.2 - - - +
39F GLN* 1.3 72.5 - - - +
41F LEU* 1.3 64.8 + - - +
43F GLN* 3.4 6.2 + - - +
44F THR* 2.9 29.4 + - - +
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F THR 3.2 11.5 + - - +
38F HIS* 3.6 11.7 - - - +
39F GLN 3.3 0.2 - - - -
40F MET* 1.3 77.3 - - - +
42F LEU* 1.3 65.7 + - - +
44F THR* 3.3 9.4 + - + -
45F CYS* 3.0 41.4 + - - -
79F LEU* 4.7 4.3 - - + -
82F MET* 4.1 16.4 - - + -
93F LEU* 4.6 11.2 - - + -
97F ALA* 3.5 46.4 - - + +
100F ILE* 4.6 9.0 - - + -
101F ALA* 4.5 2.5 - - + -
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 4.1 20.4 - - + -
38F HIS 3.0 17.5 + - - +
39F GLN* 3.8 7.4 - - - +
40F MET 3.3 0.4 - - - -
41F LEU* 1.3 76.4 - - - +
43F GLN* 1.3 63.5 + - - +
45F CYS* 3.4 3.6 + - - +
46F ARG* 2.9 59.3 + - - +
100F ILE* 3.7 29.2 - - + -
104F GLU* 3.8 14.4 - - + +
329F TRP* 5.6 3.6 - - + -
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Residues in contact with GLN 43 (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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39F GLN 3.3 10.8 + - - +
40F MET* 3.8 8.7 - - - +
41F LEU 3.2 0.4 - - - -
42F LEU* 1.3 80.4 - - - +
44F THR* 1.3 60.5 + - - +
46F ARG* 3.3 20.9 + - - +
47F ASP* 2.7 70.9 + - - +
50F GLU* 5.5 0.2 + - - -
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Residues in contact with THR 44 (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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40F MET* 2.9 20.5 + - - +
41F LEU* 3.6 10.0 - - + -
43F GLN* 1.3 74.9 - - - +
45F CYS* 1.3 61.2 + - - +
47F ASP* 3.8 6.8 - - - +
48F PHE* 3.0 26.5 + - - +
77F LEU* 4.9 23.3 - - + -
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Residues in contact with CYS 45 (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* 3.0 28.3 + - - +
42F LEU* 3.9 2.2 - - - +
44F THR* 1.3 77.2 - - - +
46F ARG* 1.3 60.2 + - - +
48F PHE* 3.7 5.9 - - - +
49F ALA* 2.9 30.3 + - - +
77F LEU* 6.3 0.4 - - - -
79F LEU* 3.7 35.2 - - - -
101F ALA* 3.8 20.6 - - - +
104F GLU* 3.7 22.7 - - + +
105F ILE* 4.3 7.5 - - + +
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Residues in contact with ARG 46 (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* 2.9 37.3 + - - +
43F GLN* 3.3 21.9 + - - +
45F CYS* 1.3 75.9 - - - +
47F ASP* 1.3 59.5 + - - +
49F ALA* 3.8 2.8 - - - +
50F GLU* 2.9 57.4 + - - +
104F GLU* 3.0 45.3 + - - +
107F ARG* 3.2 34.7 - - - +
284F GLN* 5.8 1.8 - - - +
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Residues in contact with ASP 47 (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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43F GLN* 2.7 55.2 + - - +
44F THR* 3.8 6.8 - - - +
46F ARG* 1.3 74.1 - - - +
48F PHE* 1.3 59.8 + - - +
50F GLU* 3.9 9.3 - - - +
51F LYS* 3.0 32.4 + - - +
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Residues in contact with PHE 48 (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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44F THR 3.0 18.7 + - - +
45F CYS* 3.7 5.8 - - - +
47F ASP* 1.3 73.7 - - - +
49F ALA* 1.3 60.9 + - - +
51F LYS* 4.5 4.3 - - - -
52F GLU* 2.7 60.0 + - + +
53F LEU* 3.9 20.9 - - + -
70F GLN* 3.7 13.7 - - - -
73F LYS* 3.8 20.2 - - + -
74F MET* 3.5 32.1 - - + -
77F LEU* 3.5 31.0 - - + -
79F LEU* 5.1 0.7 - - + -
105F ILE* 3.9 15.9 - - + -
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Residues in contact with ALA 49 (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 2.9 16.6 + - - +
46F ARG* 3.3 5.1 + - - +
48F PHE* 1.3 76.0 - - - +
50F GLU* 1.3 59.5 + - - +
53F LEU* 2.8 39.6 + - + -
54F PHE* 2.9 19.9 + - + -
104F GLU 3.4 26.9 - - - +
105F ILE* 4.6 2.0 - - + -
107F ARG* 5.6 1.3 - - - +
108F GLY* 4.3 13.9 - - - +
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Residues in contact with GLU 50 (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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43F GLN* 5.5 0.2 + - - -
46F ARG* 2.9 42.6 + - - +
47F ASP* 4.1 9.8 + - - +
49F ALA* 1.3 78.4 - - - +
51F LYS* 1.3 60.0 + - - +
54F PHE* 3.7 25.9 - - + +
55F PRO* 3.6 15.6 - - - +
107F ARG* 3.3 24.1 + - - +
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Residues in contact with LYS 51 (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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47F ASP 3.0 20.7 + - - +
48F PHE* 3.9 3.6 - - - +
50F GLU* 1.3 77.1 - - - +
52F GLU* 1.3 82.5 + - + +
55F PRO* 3.4 17.9 - - - +
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Residues in contact with GLU 52 (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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48F PHE* 2.7 57.1 + - + +
51F LYS* 1.3 105.3 + - + +
53F LEU* 1.3 58.9 + - + +
55F PRO* 3.9 3.8 - - - -
56F ILE* 3.7 14.7 - - - +
70F GLN* 3.7 24.9 + - + +
73F LYS* 3.7 32.8 + - + +
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Residues in contact with LEU 53 (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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48F PHE* 3.9 19.1 - - + -
49F ALA* 2.8 23.3 + - + +
52F GLU* 1.3 83.8 - - - +
54F PHE* 1.3 66.1 + - - +
55F PRO* 3.2 2.2 - - - +
56F ILE* 3.0 19.7 + - + +
57F ALA* 3.2 10.4 + - - +
70F GLN* 4.0 21.5 - - + -
105F ILE* 3.2 53.8 - - + +
108F GLY 3.8 14.1 - - - +
109F CYS* 3.9 9.3 - - + +
112F THR* 3.8 18.4 - - + +
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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