Contacts of the helix formed by residues 35 - 53 (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 PRO 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E LEU* 1.4 100.5 - - + +
36E GLU* 1.3 60.2 + - - +
37E THR* 4.4 5.4 - - + +
38E HIS* 3.2 29.3 + - + +
39E GLN* 2.9 25.2 + - - +
96E LEU* 5.0 7.0 - - + -
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Residues in contact with GLU 36 (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 3.9 0.4 + - - -
35E PRO* 1.3 71.7 - - - +
37E THR* 1.3 65.3 + - + +
39E GLN* 3.2 9.3 + - - +
40E MET* 3.0 24.5 + - - +
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Residues in contact with THR 37 (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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35E PRO* 4.4 4.0 - - + +
36E GLU* 1.3 79.4 - - + +
38E HIS* 1.3 76.2 + - - +
40E MET* 3.6 7.2 + - - +
41E LEU* 3.1 25.3 + - - +
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Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 4.1 5.1 - - + +
35E PRO* 3.2 36.0 + - + +
37E THR* 1.3 93.7 + - - +
39E GLN* 1.3 63.0 + - - +
41E LEU* 3.6 7.1 + - + +
42E LEU* 3.1 22.9 + - - +
94E ASP* 3.1 36.9 + - - -
96E LEU* 4.0 13.2 - - + +
97E ALA* 3.4 30.5 + - + +
100E ILE* 3.8 24.8 - - + +
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Residues in contact with GLN 39 (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* 4.6 12.3 - - + +
35E PRO 2.9 13.1 + - - +
36E GLU* 3.2 12.1 + - - +
38E HIS* 1.3 76.0 - - - +
40E MET* 1.3 61.7 + - - +
42E LEU* 3.2 9.7 + - - +
43E GLN* 3.1 21.5 + - - +
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Residues in contact with MET 40 (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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36E GLU 3.0 15.1 + - - +
37E THR* 3.8 7.2 - - - +
38E HIS 3.3 0.2 - - - -
39E GLN* 1.3 75.7 - - - +
41E LEU* 1.3 58.7 + - - +
43E GLN* 3.3 7.7 + - - +
44E THR* 3.0 33.4 + - - +
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Residues in contact with LEU 41 (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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37E THR 3.1 18.5 + - - +
38E HIS* 3.7 9.2 - - + +
40E MET* 1.3 75.6 - - - +
42E LEU* 1.3 63.1 + - - +
44E THR* 3.3 9.8 + - + -
45E CYS* 3.0 45.2 + - - -
79E LEU* 5.0 3.8 - - + -
82E MET* 4.1 16.6 - - + -
93E LEU* 4.4 11.7 - - + -
97E ALA* 3.4 49.6 - - + +
100E ILE* 4.5 9.0 - - + -
101E ALA* 4.9 0.2 - - + -
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Residues in contact with LEU 42 (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* 4.2 19.5 - - + -
38E HIS 3.1 13.6 + - - +
39E GLN* 3.2 11.6 + - - +
41E LEU* 1.3 77.7 - - - +
43E GLN* 1.3 63.6 + - - +
45E CYS 3.5 0.5 + - - -
46E ARG* 2.9 43.3 + - - +
100E ILE* 3.7 28.3 - - + -
103E GLU* 6.6 0.2 - - - -
104E GLU* 3.9 28.9 - - + +
329E TRP* 5.6 3.8 - - + -
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Residues in contact with GLN 43 (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 GLN 3.1 13.1 + - - +
40E MET* 3.7 9.6 - - - +
41E LEU 3.3 0.2 - - - -
42E LEU* 1.3 80.0 - - - +
44E THR* 1.3 58.0 + - - +
46E ARG* 4.3 18.4 - - - +
47E ASP* 2.9 67.3 + - - +
50E GLU* 5.9 0.2 + - - -
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Residues in contact with THR 44 (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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40E MET* 3.0 15.2 + - - +
41E LEU* 3.5 14.5 - - + +
43E GLN* 1.3 76.0 - - - +
45E CYS* 1.3 63.1 + - - +
47E ASP* 3.6 6.7 + - - +
48E PHE* 3.0 27.1 + - + +
77E LEU* 5.0 21.3 - - + -
79E LEU* 6.5 0.2 - - + -
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Residues in contact with CYS 45 (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* 3.0 30.2 + - - +
42E LEU* 4.0 1.3 - - - +
44E THR* 1.3 79.2 - - - +
46E ARG* 1.3 61.1 + - - +
48E PHE* 3.6 6.8 - - - +
49E ALA* 2.8 31.4 + - - +
79E LEU* 4.0 22.0 - - - -
101E ALA* 3.8 31.9 - - - +
104E GLU* 3.6 21.8 - - + +
105E ILE* 4.4 8.8 - - + +
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Residues in contact with ARG 46 (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* 2.9 28.2 + - - +
43E GLN* 3.7 20.2 - - - +
45E CYS* 1.3 76.5 - - - +
47E ASP* 1.3 57.1 + - - +
49E ALA* 3.3 4.0 + - - +
50E GLU* 3.0 55.1 + - - +
104E GLU* 3.4 28.2 - - - +
107E ARG* 4.1 13.9 - - - +
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Residues in contact with ASP 47 (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 GLN* 2.9 48.3 + - - +
44E THR* 3.8 6.5 + - - +
46E ARG* 1.3 76.1 - - - +
48E PHE* 1.3 54.8 + - - +
50E GLU* 3.5 11.3 + - - +
51E LYS* 2.9 31.4 + - - +
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Residues in contact with PHE 48 (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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44E THR 3.0 18.9 + - - +
45E CYS* 3.6 7.9 - - - +
46E ARG 3.3 0.2 - - - -
47E ASP* 1.3 74.1 - - - +
49E ALA* 1.3 62.3 + - - +
51E LYS* 3.3 3.5 + - - -
52E GLU* 2.8 67.3 + - + +
53E LEU* 4.0 15.9 - - + -
70E GLN* 3.9 12.8 - - - -
73E LYS* 3.9 21.1 - - + -
74E MET* 3.5 30.3 - - + -
77E LEU* 3.4 31.2 - - + -
79E LEU* 5.1 1.1 - - + -
105E ILE* 4.0 15.3 - - + -
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Residues in contact with ALA 49 (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 2.8 18.4 + - - +
46E ARG* 3.8 4.9 - - - +
48E PHE* 1.3 72.9 - - - +
50E GLU* 1.3 58.7 + - - +
53E LEU* 2.9 43.9 + - + -
54E PHE* 2.9 21.7 + - + -
104E GLU 3.3 27.1 - - - +
105E ILE* 4.5 0.4 - - - -
107E ARG* 5.5 1.6 - - - +
108E GLY* 4.3 9.2 - - - -
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Residues in contact with GLU 50 (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 GLN* 5.9 0.3 + - - -
46E ARG* 3.0 33.3 + - - +
47E ASP* 4.0 10.7 - - - +
49E ALA* 1.3 79.7 - - - +
51E LYS* 1.3 62.8 + - - +
54E PHE* 3.6 28.5 - - + +
55E PRO* 3.6 14.2 - - - +
107E ARG* 3.4 23.9 + - - +
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Residues in contact with LYS 51 (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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47E ASP 2.9 18.5 + - - +
48E PHE* 4.0 2.7 - - + +
50E GLU* 1.3 78.2 - - - +
52E GLU* 1.3 84.6 + - + +
55E PRO* 3.4 17.7 - - - +
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Residues in contact with GLU 52 (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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48E PHE* 2.8 54.4 + - + +
51E LYS* 1.3 106.7 + - + +
53E LEU* 1.3 58.3 + - + +
55E PRO* 3.8 3.1 - - - -
56E ILE* 3.5 28.9 - - - +
70E GLN* 3.8 17.4 + - + +
73E LYS* 3.8 33.7 + - - +
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Residues in contact with LEU 53 (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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48E PHE* 4.0 12.3 - - + -
49E ALA* 2.9 27.4 + - - +
52E GLU* 1.3 78.9 - - - +
54E PHE* 1.3 65.9 + - - +
55E PRO* 3.3 1.6 - - - -
56E ILE* 3.0 20.1 + - + +
57E ALA* 3.1 14.4 + - - +
70E GLN* 4.0 25.6 - - + -
105E ILE* 3.6 49.1 - - + +
108E GLY 3.9 15.7 - - - -
109E CYS* 4.0 4.7 - - + +
112E THR* 3.7 24.7 - - + +
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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