Contacts of the helix formed by residues 35 - 53 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D LEU* 1.3 97.1 - - + +
36D GLU* 1.3 66.8 + - - +
37D THR* 3.9 8.7 - - + +
38D HIS* 3.0 30.3 + - + +
39D GLN* 2.9 19.6 + - - +
96D LEU* 4.8 7.9 - - + -
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU 3.7 1.4 + - - -
35D PRO* 1.3 70.5 - - - +
37D THR* 1.3 62.8 + - + +
39D GLN* 3.2 10.5 + - - +
40D MET* 3.0 44.4 + - + +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 3.9 7.2 - - + +
36D GLU* 1.3 85.0 - - + +
38D HIS* 1.3 77.0 + - - +
40D MET* 3.4 10.3 + - - +
41D LEU* 3.1 25.6 + - - +
93D LEU* 6.5 0.9 - - - -
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Residues in contact with HIS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.9 21.3 - - + +
35D PRO* 3.0 26.5 + - + +
37D THR* 1.3 100.3 + - - +
39D GLN* 1.3 59.2 + - - +
41D LEU* 3.7 7.2 + - - +
42D LEU* 3.1 27.0 + - - +
93D LEU* 6.2 3.1 - - + -
94D ASP* 3.1 35.5 + - - -
96D LEU* 3.7 22.1 - - + +
97D ALA* 3.6 30.1 + - + +
100D ILE* 4.0 11.4 - - + +
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.7 12.9 - - + +
35D PRO 2.9 12.0 + - - +
36D GLU* 3.4 13.9 - - - +
38D HIS* 1.3 75.2 - - - +
40D MET* 1.3 64.5 + - + +
42D LEU* 3.4 8.0 + - - +
43D GLN* 3.2 22.5 + - - +
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 3.0 33.1 + - + +
37D THR* 3.4 8.7 + - - +
38D HIS 3.4 0.2 - - - -
39D GLN* 1.3 74.5 - - + +
41D LEU* 1.3 63.9 + - - +
43D GLN* 3.7 5.9 + - - +
44D THR* 2.8 30.3 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D THR 3.1 17.2 + - - +
38D HIS* 3.8 8.5 - - - +
39D GLN 3.3 0.2 - - - -
40D MET* 1.3 75.4 - - - +
42D LEU* 1.3 67.1 + - - +
44D THR* 3.2 9.4 + - + -
45D CYS* 2.9 43.4 + - - -
79D LEU* 4.8 2.2 - - + -
82D MET* 4.2 17.9 - - + -
93D LEU* 4.3 10.5 - - + -
97D ALA* 3.3 50.0 - - + +
100D ILE* 4.7 8.1 - - + -
101D ALA* 4.5 1.1 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.3 18.8 - - + -
38D HIS 3.1 15.4 + - - +
39D GLN* 3.7 7.9 - - - +
40D MET 3.4 0.2 - - - -
41D LEU* 1.3 79.2 - - - +
43D GLN* 1.3 60.0 + - + +
45D CYS* 3.3 3.0 + - - +
46D ARG* 2.7 47.1 + - + +
100D ILE* 3.7 27.4 - - + -
104D GLU* 3.8 27.6 - - - +
329D TRP* 5.8 2.7 - - + -
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN 3.2 13.8 + - - +
40D MET* 3.9 6.3 - - - +
41D LEU 3.2 0.4 - - - -
42D LEU* 1.3 83.5 - - + +
44D THR* 1.3 56.3 + - - +
46D ARG* 4.2 13.6 - - - +
47D ASP* 2.8 71.9 + - - +
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET* 2.8 24.6 + - - +
41D LEU* 3.5 11.6 - - + -
43D GLN* 1.3 74.7 - - - +
45D CYS* 1.3 61.7 + - - +
47D ASP* 3.4 7.1 + - - +
48D PHE* 2.9 28.9 + - - +
77D LEU* 5.0 23.6 - - + -
79D LEU* 6.5 0.7 - - + -
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Residues in contact with CYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 2.9 32.1 + - - +
42D LEU 3.6 3.8 - - - +
44D THR* 1.3 76.8 - - - +
46D ARG* 1.3 61.3 + - - +
48D PHE* 3.2 6.8 + - - +
49D ALA* 2.8 31.9 + - - +
79D LEU* 3.8 19.5 - - - -
101D ALA* 3.6 33.9 - - - +
104D GLU* 3.6 20.9 - - + +
105D ILE* 4.5 6.8 - - + +
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 2.7 27.7 + - + +
43D GLN* 3.7 16.2 - - - +
45D CYS* 1.3 73.4 - - - +
47D ASP* 1.3 67.3 + - - +
49D ALA* 3.3 3.7 + - - +
50D GLU* 3.0 51.3 + - - +
104D GLU* 3.4 29.1 - - - +
107D ARG* 4.2 13.2 - - - +
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Residues in contact with ASP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLN* 2.8 54.3 + - - +
44D THR* 3.7 6.2 - - - +
46D ARG* 1.3 72.0 - - - +
48D PHE* 1.3 61.8 + - - +
50D GLU* 3.7 12.0 + - - +
51D LYS* 3.2 25.3 + - - +
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 2.9 18.6 + - + +
45D CYS* 3.2 6.0 + - - +
47D ASP* 1.3 75.2 - - - +
49D ALA* 1.3 62.0 + - - +
51D LYS* 3.3 2.1 + - - -
52D GLU* 2.7 67.0 + - + +
53D LEU* 3.9 22.4 - - + -
70D GLN* 3.9 14.6 - - + -
73D LYS* 4.0 18.6 - - + -
74D MET* 3.5 32.1 - - + -
77D LEU* 3.8 28.0 - - + -
79D LEU* 4.7 2.9 - - + -
105D ILE* 3.9 14.6 - - + -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D CYS 2.8 18.3 + - - +
46D ARG* 3.8 4.5 - - - +
48D PHE* 1.3 75.0 - - - +
50D GLU* 1.3 57.8 + - - +
53D LEU* 2.9 39.6 + - + -
54D PHE* 2.9 20.5 + - + -
104D GLU 3.5 26.2 - - - +
105D ILE* 4.6 0.9 - - + -
107D ARG* 5.6 1.6 - - - +
108D GLY* 4.1 14.8 - - - +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ARG* 3.0 43.6 + - - +
47D ASP* 4.1 11.0 - - - +
49D ALA* 1.3 77.2 - - - +
51D LYS* 1.3 60.3 + - - +
54D PHE* 3.7 25.2 - - + +
55D PRO* 3.5 16.3 - - - +
107D ARG* 3.5 16.6 + - - +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASP 3.2 18.4 + - - +
48D PHE* 3.9 2.5 - - - +
50D GLU* 1.3 77.6 - - - +
52D GLU* 1.3 85.7 + - + +
55D PRO* 3.4 16.9 - - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 2.7 56.7 + - + +
51D LYS* 1.3 106.0 - - + +
53D LEU* 1.3 60.1 + - + +
55D PRO* 3.9 2.7 - - - -
56D ILE* 3.5 22.2 - - - +
70D GLN* 3.7 19.7 + - + +
73D LYS* 3.4 35.7 + - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.9 15.5 - - + -
49D ALA* 2.9 17.2 + - - +
52D GLU* 1.3 84.1 - - - +
54D PHE* 1.3 65.6 + - - +
55D PRO* 3.3 2.5 - - - -
56D ILE* 3.1 11.6 + - + +
57D ALA* 3.0 23.9 + - - +
70D GLN* 4.1 17.5 - - + -
105D ILE* 3.6 53.8 - - + +
108D GLY 3.9 15.5 - - - -
109D CYS* 4.1 5.2 - - + +
112D THR* 3.6 28.5 - - + +
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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