Contacts of the helix formed by residues 35 - 53 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 1.3 103.8 - - + +
36A GLU* 1.3 64.3 + - - +
37A THR* 3.2 9.4 - - - +
38A HIS* 3.3 30.2 + - + +
39A GLN* 3.0 19.1 + - - +
96A LEU* 5.2 5.2 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 3.6 1.5 + - - -
35A PRO* 1.3 71.6 - - - +
37A THR* 1.3 58.9 + - + +
39A GLN* 3.0 11.2 + - - +
40A MET* 2.9 28.9 + - - +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.5 8.7 - - + +
36A GLU* 1.3 79.3 - - + +
38A HIS* 1.3 80.0 + - - -
40A MET* 3.3 8.3 + - - +
41A LEU* 3.0 27.0 + - - +
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Residues in contact with HIS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.7 27.4 - - + +
35A PRO* 3.3 22.3 + - + +
37A THR* 1.3 94.4 + - - +
39A GLN* 1.3 57.3 + - - +
41A LEU* 3.6 8.4 - - + +
42A LEU* 2.9 28.9 + - - +
94A ASP* 3.3 31.8 + - - -
96A LEU* 4.1 11.5 - - + +
97A ALA* 3.7 31.2 + - + +
100A ILE* 3.8 16.0 - - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.7 12.0 - - + +
35A PRO 3.0 13.6 + - - +
36A GLU* 3.0 13.7 + - - +
38A HIS* 1.3 74.7 - - - +
40A MET* 1.3 64.6 + - - +
42A LEU* 3.4 8.2 + - - +
43A GLN* 3.2 21.8 + - - +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU 2.9 12.4 + - - +
37A THR* 3.3 11.9 + - - +
39A GLN* 1.3 71.4 - - - +
41A LEU* 1.3 61.7 + - - +
43A GLN* 2.9 9.2 + - - +
44A THR* 2.8 34.2 + - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR 3.0 13.0 + - - +
38A HIS* 3.6 11.0 - - + +
40A MET* 1.3 79.4 - - - +
42A LEU* 1.3 63.7 + - - +
44A THR* 3.3 9.6 + - + -
45A CYS* 3.0 46.3 + - - -
79A LEU* 4.8 3.4 - - + -
82A MET* 4.2 16.6 - - + -
93A LEU* 4.4 10.8 - - + -
97A ALA* 3.4 49.1 - - + +
100A ILE* 4.7 6.1 - - + -
101A ALA* 4.7 1.8 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.5 15.7 - - + -
38A HIS 2.9 18.8 + - - +
39A GLN* 3.6 9.2 - - - +
40A MET 3.2 0.2 - - - -
41A LEU* 1.3 74.7 - - - +
43A GLN* 1.3 64.5 + - + +
45A CYS* 3.4 1.3 + - - -
46A ARG* 2.9 61.6 + - - +
100A ILE* 3.8 25.6 - - + -
104A GLU* 3.9 17.9 - - - +
329A TRP* 5.9 3.6 - - + -
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN 3.2 9.7 + - - +
40A MET* 2.9 10.6 + - - +
42A LEU* 1.3 82.9 - - + +
44A THR* 1.3 59.6 + - - +
46A ARG* 4.2 21.2 + - - +
47A ASP* 2.8 71.5 + - - +
50A GLU* 5.3 0.2 + - - -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 2.8 19.1 + - - +
41A LEU* 3.6 14.3 - - + -
43A GLN* 1.3 77.4 - - - +
45A CYS* 1.3 61.9 + - - +
47A ASP* 3.6 5.7 - - - +
48A PHE* 2.9 28.4 + - + +
77A LEU* 5.2 21.8 - - + -
79A LEU* 6.5 0.4 - - + -
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Residues in contact with CYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.0 30.4 + - - +
42A LEU* 3.9 1.8 - - - +
44A THR* 1.3 77.9 - - - +
46A ARG* 1.3 61.6 + - - +
48A PHE* 3.5 6.3 + - - +
49A ALA* 2.8 30.7 + - - +
79A LEU* 3.9 22.0 - - - -
101A ALA* 3.9 30.5 - - - +
104A GLU* 3.6 23.4 - - + +
105A ILE* 4.5 8.9 - - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 2.9 37.2 + - - +
43A GLN* 3.8 20.1 + - - +
45A CYS* 1.3 77.6 - - - +
47A ASP* 1.3 57.1 + - - +
49A ALA* 3.2 4.8 + - - +
50A GLU* 2.8 56.4 + - - +
104A GLU* 2.8 41.7 + - - +
107A ARG* 3.3 39.1 - - - +
284A GLN* 5.9 0.8 - - - +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN* 2.8 53.3 + - - +
44A THR* 3.6 6.1 + - - +
46A ARG* 1.3 77.1 - - - +
48A PHE* 1.3 52.1 + - - +
50A GLU* 3.3 11.9 + - - +
51A LYS* 2.7 39.3 + - - +
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 2.9 18.1 + - + +
45A CYS* 3.7 6.7 - - - +
47A ASP* 1.3 75.6 - - - +
49A ALA* 1.3 55.9 + - - +
51A LYS* 4.5 4.3 - - + -
52A GLU* 2.6 72.3 + - + +
53A LEU* 4.1 10.3 - - + -
70A GLN* 3.9 13.9 - - - -
73A LYS* 3.9 22.0 - - + -
74A MET* 3.5 35.4 - - + -
77A LEU* 3.7 26.5 - - + -
79A LEU* 4.9 2.5 - - + -
105A ILE* 3.9 16.2 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A CYS 2.8 21.9 + - - +
46A ARG* 3.5 5.8 - - - +
48A PHE* 1.3 72.0 - - - +
50A GLU* 1.3 59.1 + - - +
53A LEU* 2.9 43.5 + - + -
54A PHE* 3.0 27.7 + - + -
104A GLU* 3.4 24.7 - - - +
105A ILE* 4.8 0.7 - - + -
107A ARG* 5.5 1.3 - - - +
108A GLY* 4.4 2.2 - - - -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN* 5.3 0.2 + - - -
46A ARG* 2.8 40.2 + - - +
47A ASP* 3.8 12.2 - - - +
49A ALA* 1.3 79.2 - - - +
51A LYS* 1.3 60.7 + - - +
54A PHE* 3.7 21.3 - - + +
55A PRO* 3.6 15.9 - - - +
107A ARG* 3.3 24.5 + - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP 2.7 22.5 + - - +
48A PHE* 3.9 2.7 - - - +
50A GLU* 1.3 74.6 - - - +
52A GLU* 1.3 82.5 + - + +
55A PRO* 3.6 14.6 - - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 2.6 58.8 + - + +
51A LYS* 1.3 106.3 + - + +
53A LEU* 1.3 59.2 - - + +
55A PRO* 3.8 4.0 - - - +
56A ILE* 3.4 26.9 - - - +
70A GLN* 3.7 16.0 + - + +
73A LYS* 3.8 30.5 + - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.1 10.3 - - + -
49A ALA* 2.9 18.6 + - - +
52A GLU* 1.3 82.2 - - - +
54A PHE* 1.3 70.6 + - - +
55A PRO* 3.2 1.8 - - - -
56A ILE* 2.9 21.3 + - + +
57A ALA* 3.1 13.5 + - - +
70A GLN* 4.0 21.1 - - + -
105A ILE* 3.4 56.5 - - + +
108A GLY* 3.9 15.9 - - - -
109A CYS* 4.1 5.2 - - + +
112A THR* 3.9 25.4 - - + +
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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