Contacts of the helix formed by residues 35 - 53 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 1.3 97.6 - - + +
36G GLU* 1.3 66.3 + - - +
37G THR* 3.7 17.3 - - - +
38G HIS* 3.1 23.2 + - + +
39G GLN* 2.9 19.6 + - - +
96G LEU* 4.9 8.3 - - + -
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Residues in contact with GLU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU 3.9 0.4 + - - -
35G PRO* 1.3 70.6 - - - +
37G THR* 1.3 65.6 + - + +
39G GLN* 2.8 19.4 + - - +
40G MET* 2.9 14.0 + - - +
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Residues in contact with THR 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G PRO* 3.7 10.7 - - - +
36G GLU* 1.3 73.4 - - - +
38G HIS* 1.3 78.8 + - - -
40G MET* 3.1 9.1 + - - +
41G LEU* 2.9 27.3 + - - +
93G LEU* 6.2 5.4 - - + -
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Residues in contact with HIS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 4.1 6.6 - - + +
35G PRO* 3.1 30.0 + - + +
37G THR* 1.3 94.3 + - - +
39G GLN* 1.3 56.6 + - - +
41G LEU* 3.6 7.8 - - - +
42G LEU* 2.9 28.6 + - - +
93G LEU* 5.8 6.1 - - + -
94G ASP* 3.2 33.2 + - - -
96G LEU* 3.7 24.1 - - + +
97G ALA* 3.7 27.8 + - + +
100G ILE* 3.7 19.5 - - + +
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Residues in contact with GLN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 4.5 11.8 - - + +
35G PRO 2.9 11.6 + - - +
36G GLU* 2.8 13.5 + - - +
38G HIS* 1.3 75.8 - - - +
40G MET* 1.3 62.9 + - - +
42G LEU* 3.5 8.7 + - - +
43G GLN* 3.3 20.8 + - - +
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Residues in contact with MET 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLU 2.9 10.6 + - - +
37G THR* 3.5 10.8 - - - +
39G GLN* 1.3 75.8 - - - +
41G LEU* 1.3 59.2 + - - +
43G GLN* 3.1 8.1 + - - +
44G THR* 3.0 32.5 + - - +
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G THR 2.9 12.8 + - - +
38G HIS* 3.6 12.3 - - + +
40G MET* 1.3 72.9 - - - +
42G LEU* 1.3 66.4 + - - +
43G GLN 3.1 0.3 + - - -
44G THR* 3.2 10.8 + - + -
45G CYS* 3.0 38.9 + - - -
79G LEU* 4.9 3.1 - - + -
82G MET* 4.2 19.3 - - + -
93G LEU* 4.5 11.0 - - + -
97G ALA* 3.4 48.2 - - + +
100G ILE* 4.7 8.5 - - + -
101G ALA* 4.6 2.0 - - + -
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Residues in contact with LEU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 4.1 16.8 - - + -
38G HIS 2.9 17.2 + - - +
39G GLN* 3.6 9.4 - - - +
40G MET 3.3 0.2 - - - -
41G LEU* 1.3 77.2 - - - +
43G GLN* 1.3 65.4 + - - +
45G CYS* 3.5 2.0 + - - +
46G ARG* 3.0 66.3 + - - +
100G ILE* 3.6 29.6 - - + +
104G GLU* 4.0 16.6 - - + +
329G TRP* 5.9 3.4 - - + -
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Residues in contact with GLN 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLN 3.3 9.9 + - - +
40G MET* 3.1 12.6 + - - +
42G LEU* 1.3 84.9 - - - +
44G THR* 1.3 65.6 + - - +
46G ARG* 4.5 17.3 + - - +
47G ASP* 3.0 65.2 + - - +
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Residues in contact with THR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G MET* 3.0 14.5 + - - +
41G LEU* 3.5 14.0 - - + -
43G GLN* 1.3 75.9 - - - +
45G CYS* 1.3 61.2 + - - +
47G ASP* 3.3 7.2 + - - +
48G PHE* 2.9 28.5 + - + +
77G LEU* 4.8 24.5 - - + -
79G LEU* 6.4 0.9 - - + -
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Residues in contact with CYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU* 3.0 28.2 + - - +
42G LEU* 3.9 2.0 - - - +
44G THR* 1.3 79.3 - - - +
46G ARG* 1.3 57.7 + - - +
48G PHE* 3.3 7.8 + - - +
49G ALA* 2.8 30.7 + - - +
79G LEU* 3.8 22.4 - - - -
101G ALA* 3.6 33.2 - - - +
104G GLU* 3.5 23.3 - - + +
105G ILE* 4.4 7.4 - - + +
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Residues in contact with ARG 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G LEU* 3.0 44.0 + - - +
43G GLN* 4.0 21.6 + - - +
45G CYS* 1.3 76.9 - - - +
47G ASP* 1.3 57.9 + - - +
49G ALA* 3.3 4.4 + - - +
50G GLU* 2.9 42.9 + - + +
104G GLU* 2.9 41.7 + - - +
107G ARG* 3.9 28.8 - - - +
284G GLN* 5.8 3.8 - - - +
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Residues in contact with ASP 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G GLN* 3.0 53.2 + - - +
44G THR* 3.7 5.6 - - - +
46G ARG* 1.3 74.3 - - - +
48G PHE* 1.3 60.1 + - - +
50G GLU* 3.9 6.2 - - - +
51G LYS* 3.0 32.5 + - - +
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Residues in contact with PHE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G THR 2.9 14.8 + - - +
45G CYS* 3.5 11.0 - - - +
47G ASP* 1.3 75.5 - - - +
49G ALA* 1.3 53.6 + - - +
51G LYS* 3.2 4.3 + - + -
52G GLU* 2.7 75.2 + - + +
53G LEU* 4.1 11.2 - - + -
70G GLN* 3.8 13.0 - - - -
73G LYS* 3.9 20.2 - - + -
74G MET* 3.3 35.7 - - + -
77G LEU* 3.5 29.4 - - + -
79G LEU* 4.9 1.6 - - + -
105G ILE* 3.9 17.3 - - + -
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G CYS 2.8 20.2 + - - +
46G ARG* 3.7 5.6 - - - +
48G PHE* 1.3 73.0 - - - +
50G GLU* 1.3 59.4 + - - +
53G LEU* 2.9 26.1 + - + -
54G PHE* 2.9 42.8 + - + -
104G GLU 3.5 24.7 - - - +
105G ILE* 4.7 0.9 - - + -
107G ARG* 5.5 1.1 - - - +
108G GLY* 4.3 6.7 - - - -
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Residues in contact with GLU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ARG* 2.9 38.0 + - + +
47G ASP* 3.9 7.6 - - - +
49G ALA* 1.3 77.8 - - - +
51G LYS* 1.3 61.6 + - - +
54G PHE* 3.7 23.3 - - + +
55G PRO* 3.6 14.9 - - - +
107G ARG* 4.7 4.5 - - - +
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Residues in contact with LYS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASP 3.0 19.4 + - - +
48G PHE* 3.7 3.8 - - + +
50G GLU* 1.3 78.3 - - - +
52G GLU* 1.3 82.0 + - + +
55G PRO* 3.3 17.9 - - - +
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Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G PHE* 2.7 57.5 + - + +
51G LYS* 1.3 102.0 - - + +
53G LEU* 1.3 59.0 + - + +
55G PRO* 3.8 3.6 - - - -
56G ILE* 3.5 22.2 - - - +
70G GLN* 3.7 22.7 + - + +
73G LYS* 3.7 32.0 - - - +
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G PHE* 4.1 13.7 - - + -
49G ALA* 2.9 22.0 + - - +
52G GLU* 1.3 83.1 - - - +
54G PHE* 1.3 65.3 + - - +
55G PRO* 3.3 2.2 - - - -
56G ILE* 3.1 10.8 + - + +
57G ALA* 3.0 24.1 + - - +
70G GLN* 4.1 20.0 - - + -
105G ILE* 3.4 55.0 - - + +
108G GLY 3.9 14.6 - - - -
109G CYS* 4.0 7.0 - - + +
112G THR* 3.9 23.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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