Contacts of the helix formed by residues 35 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LEU* 1.3 95.1 - - + +
36B GLU* 1.3 53.3 + - - +
37B THR* 3.7 17.3 - - - +
38B HIS* 3.1 20.6 + - + +
39B GLN* 2.7 31.9 + - - +
96B LEU* 5.0 9.0 - - + -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU 3.7 1.2 + - - -
35B PRO* 1.3 69.3 - - - +
37B THR* 1.3 60.9 + - + +
39B GLN* 3.5 9.6 - - - +
40B MET* 2.9 53.8 + - + +
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 3.7 8.7 - - - +
36B GLU* 1.3 76.7 - - + +
38B HIS* 1.3 76.7 + - - +
40B MET* 3.4 12.8 + - + +
41B LEU* 3.1 26.6 + - - +
93B LEU* 6.5 0.9 - - - -
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.6 20.6 - - + +
35B PRO* 3.1 23.5 + - + +
37B THR* 1.3 91.7 + - - +
39B GLN* 1.3 59.8 + - - +
41B LEU* 3.5 7.7 + - + +
42B LEU* 3.1 28.1 + - - +
93B LEU* 6.1 3.1 - - + -
94B ASP* 2.9 38.8 + - - -
96B LEU* 3.7 16.5 - - + +
97B ALA* 3.4 29.1 + - + +
100B ILE* 3.7 18.3 - - + +
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.7 9.3 - - + +
35B PRO 2.7 20.7 + - - +
36B GLU* 3.2 12.5 + - - +
38B HIS* 1.3 74.3 - - - +
40B MET* 1.3 60.7 + - + +
42B LEU* 3.6 8.7 + - - +
43B GLN* 3.5 19.1 + - - +
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 2.9 41.2 + - + +
37B THR* 3.8 11.2 - - + +
39B GLN* 1.3 75.8 - - + +
41B LEU* 1.3 61.0 + - - +
42B LEU 3.2 0.2 - - - -
43B GLN* 3.3 7.1 + - - +
44B THR* 3.0 32.0 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR 3.1 17.0 + - - +
38B HIS* 3.7 10.3 - - + +
39B GLN 3.4 0.2 - - - -
40B MET* 1.3 76.8 - - - +
42B LEU* 1.3 62.2 + - - +
44B THR* 3.4 9.3 + - + -
45B CYS* 3.1 43.8 + - - -
79B LEU* 4.8 3.4 - - + -
82B MET* 4.2 13.0 - - + -
93B LEU* 3.9 16.4 - - + -
97B ALA* 3.3 48.5 - - + +
100B ILE* 5.1 4.3 - - + -
101B ALA* 4.7 1.1 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 6.3 2.5 - - + -
38B HIS 3.1 17.0 + - - +
39B GLN* 3.7 8.5 - - - +
41B LEU* 1.3 77.9 - - - +
43B GLN* 1.3 68.6 + - - +
45B CYS* 3.3 3.3 + - - +
46B ARG* 2.8 57.9 + - - +
100B ILE* 3.7 29.6 - - + +
104B GLU* 4.0 16.1 - - + +
329B TRP* 5.9 5.8 - - + -
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Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN 3.5 9.6 + - - +
40B MET* 3.3 9.8 + - - +
42B LEU* 1.3 86.9 - - - +
44B THR* 1.3 59.0 + - - +
46B ARG* 4.3 17.7 - - - +
47B ASP* 2.8 66.6 + - - +
50B GLU* 5.8 0.6 + - - -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 3.0 16.5 + - - +
41B LEU* 3.4 13.7 + - + -
43B GLN* 1.3 75.5 - - - +
45B CYS* 1.3 62.9 + - - +
47B ASP* 3.8 6.3 - - - +
48B PHE* 2.9 27.2 + - - +
77B LEU* 4.8 25.1 - - + -
79B LEU* 6.6 0.2 - - + -
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Residues in contact with CYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.1 28.7 + - - +
42B LEU* 3.9 1.8 - - - +
44B THR* 1.3 78.3 - - - +
46B ARG* 1.3 61.2 + - - +
48B PHE* 3.5 5.8 + - - +
49B ALA* 2.9 30.8 + - - +
79B LEU* 3.6 23.1 - - - -
101B ALA* 3.6 33.9 - - - +
104B GLU* 3.6 24.0 - - + +
105B ILE* 4.4 6.7 - - + +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 2.8 38.0 + - - +
43B GLN* 3.8 21.8 - - - +
45B CYS* 1.3 74.8 - - - +
47B ASP* 1.3 65.5 + - - +
49B ALA* 3.3 3.0 + - - +
50B GLU* 3.0 48.4 + - - +
103B GLU* 5.8 0.2 + - - -
104B GLU* 3.3 39.3 + - - +
107B ARG* 3.3 40.8 - - - +
284B GLN* 4.8 8.7 - - - +
288B ASP* 4.9 1.0 + - - -
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 2.8 58.3 + - - +
44B THR* 3.8 6.1 + - - +
46B ARG* 1.3 74.1 - - - +
48B PHE* 1.3 63.3 + - - +
50B GLU* 3.2 8.1 + - - +
51B LYS* 3.0 24.6 + - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B THR 2.9 20.0 + - - +
45B CYS* 3.7 6.1 - - - +
46B ARG 3.3 0.2 - - - -
47B ASP* 1.3 75.7 - - - +
49B ALA* 1.3 57.0 + - - +
51B LYS* 4.9 2.9 - - - -
52B GLU* 2.7 68.9 + - + +
53B LEU* 4.0 14.4 - - + -
70B GLN* 3.8 12.6 - - - -
73B LYS* 3.8 20.4 - - + -
74B MET* 3.5 32.3 - - + -
77B LEU* 3.5 29.6 - - + -
79B LEU* 4.9 1.6 - - + -
105B ILE* 3.9 15.0 - - + -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B CYS 2.9 21.0 + - - +
46B ARG* 3.3 5.6 + - - +
48B PHE* 1.3 72.2 - - - +
50B GLU* 1.3 59.4 + - + +
53B LEU* 2.9 31.0 + - + +
54B PHE* 2.8 35.9 + - + -
104B GLU 3.5 23.6 - - - +
105B ILE* 4.7 0.9 - - + -
107B ARG* 5.6 1.1 - - - +
108B GLY* 4.2 8.1 - - - -
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLN* 5.8 0.5 + - - -
46B ARG* 3.0 32.2 + - - +
47B ASP* 4.0 7.5 - - - +
49B ALA* 1.3 77.1 - - - +
51B LYS* 1.3 60.9 + - - +
54B PHE* 3.7 25.8 - - + +
55B PRO* 3.6 15.1 - - - +
107B ARG* 3.4 27.0 + - - +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP 3.0 16.1 + - - +
48B PHE* 4.0 3.4 - - - +
50B GLU* 1.3 76.7 - - - +
52B GLU* 1.3 88.7 + - + +
53B LEU 3.8 0.2 - - - -
55B PRO* 3.3 19.5 - - - +
73B LYS* 5.6 1.2 - - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 2.7 58.5 + - + +
51B LYS* 1.3 111.1 + - + +
53B LEU* 1.3 59.5 + - - +
55B PRO* 3.8 2.0 - - - -
56B ILE* 3.8 13.9 - - - +
70B GLN* 3.7 29.5 + - + +
73B LYS* 3.8 33.1 + - + +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.0 13.5 - - + -
49B ALA* 2.9 23.6 + - + +
52B GLU* 1.3 78.0 - - - +
54B PHE* 1.3 66.6 + - - +
55B PRO* 3.3 2.0 - - - +
56B ILE* 3.1 18.8 + - + +
57B ALA* 3.1 14.4 + - - +
70B GLN* 4.1 19.7 - - + -
74B MET* 4.8 0.2 - - - -
105B ILE* 3.4 57.0 - - + +
108B GLY 3.8 14.3 - - - +
109B CYS* 4.2 7.0 - - + +
112B THR* 3.8 26.2 - - + +
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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