Contacts of the helix formed by residues 35 - 53 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LEU* 1.3 103.5 - - + +
36C GLU* 1.3 66.2 + - - +
37C THR* 3.9 15.3 - - - +
38C HIS* 3.3 18.9 + - + +
39C GLN* 3.0 20.5 + - - +
96C LEU* 4.6 7.4 - - + -
333C MET* 6.4 0.2 - - + -
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU 3.9 0.6 + - - -
35C PRO* 1.3 68.5 - - - +
37C THR* 1.3 68.8 + - + +
39C GLN* 3.0 10.0 + - - +
40C MET* 3.0 22.8 + - - +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PRO* 3.9 8.0 - - - +
36C GLU* 1.3 75.8 - - + +
38C HIS* 1.3 80.4 + - - +
40C MET* 3.1 8.7 + - - +
41C LEU* 2.9 29.1 + - - +
93C LEU* 6.3 3.8 - - - -
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.8 20.3 - - + +
35C PRO* 3.3 24.8 + - + +
36C GLU 3.2 0.8 - - - -
37C THR* 1.3 105.5 + - - +
39C GLN* 1.3 55.2 + - - +
41C LEU* 3.6 8.0 - - - +
42C LEU* 3.0 28.1 + - - +
93C LEU* 6.0 4.3 - - + -
94C ASP* 3.0 35.9 + - - -
96C LEU* 3.8 20.2 - - + +
97C ALA* 3.5 31.6 + - + +
100C ILE* 3.9 10.0 - - + +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.7 11.4 - - + +
35C PRO 3.0 12.0 + - - +
36C GLU* 3.0 13.3 + - - +
38C HIS* 1.3 74.5 - - - +
40C MET* 1.3 63.6 - - - +
42C LEU* 3.4 8.6 + - - +
43C GLN* 3.1 21.7 + - - +
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU 3.0 11.2 + - - +
37C THR* 3.5 10.3 - - - +
39C GLN* 1.3 73.6 - - - +
41C LEU* 1.3 56.2 + - - +
43C GLN* 2.9 8.8 + - - +
44C THR* 2.8 37.4 + - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C THR 2.9 16.1 + - - +
38C HIS* 3.6 9.4 - - - +
40C MET* 1.3 74.8 - - - +
42C LEU* 1.3 62.7 + - - +
44C THR* 3.3 10.2 + - + -
45C CYS* 2.9 38.3 + - - +
79C LEU* 4.9 2.9 - - + -
82C MET* 4.2 18.6 - - + -
93C LEU* 4.3 10.3 - - + -
97C ALA* 3.3 52.3 - - + +
100C ILE* 4.6 7.6 - - + -
101C ALA* 4.6 1.8 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.3 18.6 - - + -
38C HIS 3.0 17.6 + - - +
39C GLN* 3.5 9.4 - - - +
40C MET 3.2 0.4 - - - -
41C LEU* 1.3 75.5 - - - +
43C GLN* 1.3 67.4 + - - +
45C CYS* 3.3 4.9 + - - +
46C ARG* 2.9 62.7 + - - +
100C ILE* 3.8 26.2 - - + -
104C GLU* 3.9 15.2 - - + +
329C TRP* 5.7 2.9 - - + -
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Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN 3.1 12.2 + - - +
40C MET* 2.9 11.7 + - - +
42C LEU* 1.3 83.2 - - - +
44C THR* 1.3 60.2 + - - +
46C ARG* 4.5 13.5 + - - +
47C ASP* 2.9 66.8 + - - +
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C MET* 2.8 19.7 + - - +
41C LEU* 3.6 13.0 - - + -
43C GLN* 1.3 71.4 - - - +
45C CYS* 1.3 61.7 + - - +
47C ASP* 3.4 6.3 + - - +
48C PHE* 2.9 28.8 + - + +
77C LEU* 4.8 23.1 - - + -
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Residues in contact with CYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 2.9 27.3 + - - +
42C LEU* 3.7 2.7 - - - +
44C THR* 1.3 80.9 - - - +
46C ARG* 1.3 59.6 + - - +
48C PHE* 3.5 6.5 + - - +
49C ALA* 3.0 28.4 + - - +
79C LEU* 3.8 24.9 - - - -
101C ALA* 3.5 33.9 - - - +
104C GLU* 3.7 23.6 - - + +
105C ILE* 4.5 7.4 - - + +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 2.9 41.8 + - - +
43C GLN* 4.0 16.7 + - - +
45C CYS* 1.3 72.9 - - - +
47C ASP* 1.3 66.7 + - - +
49C ALA* 3.3 4.6 + - - +
50C GLU* 3.0 31.9 + - + +
103C GLU* 5.9 0.2 + - - -
104C GLU* 3.2 41.6 + - - +
107C ARG* 3.6 37.6 - - - +
284C GLN* 5.3 5.7 - - - +
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Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLN* 2.9 51.5 + - - +
44C THR* 3.7 6.2 - - - +
46C ARG* 1.3 74.8 - - - +
48C PHE* 1.3 67.1 + - - +
50C GLU* 3.3 5.3 + - - +
51C LYS* 2.8 27.7 + - - +
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR 2.9 17.6 + - - +
45C CYS* 3.6 8.1 - - - +
47C ASP* 1.3 76.3 - - - +
49C ALA* 1.3 56.2 + - - +
51C LYS* 4.6 4.5 - - + -
52C GLU* 2.7 71.9 + - + +
53C LEU* 4.2 10.5 - - + -
70C GLN* 3.9 12.1 - - - -
73C LYS* 3.8 22.9 - - + -
74C MET* 3.4 35.2 - - + -
77C LEU* 3.5 30.1 - - + -
79C LEU* 5.0 2.5 - - + -
105C ILE* 3.9 15.9 - - + -
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C CYS 3.0 15.2 + - - +
46C ARG* 3.6 6.3 - - - +
47C ASP 3.2 0.2 - - - -
48C PHE* 1.3 77.1 - - - +
50C GLU* 1.3 58.1 + - - +
53C LEU* 2.9 22.7 + - + -
54C PHE* 2.9 42.5 + - + -
104C GLU 3.2 27.6 - - - +
105C ILE* 4.7 0.7 - - + -
107C ARG* 5.4 1.6 - - - +
108C GLY* 4.4 5.4 - - - -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ARG* 3.0 31.4 + - + +
47C ASP* 3.9 4.5 - - - +
49C ALA* 1.3 76.1 - - - +
51C LYS* 1.3 63.8 + - - +
54C PHE* 3.6 24.4 - - + +
55C PRO* 3.6 14.7 - - - +
107C ARG* 4.6 5.4 - - - +
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASP 2.8 22.3 + - - +
48C PHE* 3.8 3.6 - - - +
50C GLU* 1.3 74.1 - - - +
52C GLU* 1.3 82.4 + - + +
55C PRO* 3.4 17.5 - - - +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 2.7 56.6 + - + +
51C LYS* 1.3 104.9 + - + +
53C LEU* 1.3 58.6 + - - +
55C PRO* 3.8 3.1 - - - -
56C ILE* 3.6 26.2 - - - +
70C GLN* 3.7 21.6 + - + +
73C LYS* 3.6 27.9 + - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 4.2 10.5 - - + -
49C ALA* 2.9 20.3 + - - +
52C GLU* 1.3 84.9 - - - +
54C PHE* 1.3 64.8 + - - +
55C PRO* 3.2 2.0 - - - -
56C ILE* 3.0 20.7 + - + +
57C ALA* 3.0 14.0 + - - +
70C GLN* 4.1 20.6 - - + -
105C ILE* 3.4 55.0 - - + +
108C GLY* 3.9 14.8 - - - +
109C CYS* 4.0 6.1 - - + +
112C THR* 3.7 26.0 - - + +
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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