Contacts of the helix formed by residues 56 - 64 (chain F) 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 ILE 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F GLU 3.7 11.0 - - - +
53F LEU* 3.0 21.8 + - + +
55F PRO* 1.3 82.7 - - + +
57F ALA* 1.3 66.1 + - - +
58F ALA 3.3 2.9 - - - -
59F GLN* 3.2 11.4 + - - +
60F VAL* 2.9 33.9 + - + +
67F PRO* 4.0 6.5 - - + -
70F GLN* 3.4 43.5 - - + +
109F CYS* 5.3 2.7 - - - -
112F THR* 5.1 1.8 - - - +
503F EDO 3.9 33.9 - - - +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU 3.2 6.9 + - - +
54F PHE* 3.7 9.4 + - + +
56F ILE* 1.3 78.7 - - - +
58F ALA* 1.3 63.7 + - - +
60F VAL* 3.4 6.7 + - - +
61F ASP* 3.1 25.1 + - - +
108F GLY 3.5 21.5 - - - +
109F CYS* 4.6 10.7 - - + -
380F ARG* 3.4 34.1 - - - +
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Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE 5.0 1.2 + - - -
55F PRO 5.4 1.0 + - - +
56F ILE 3.3 0.6 - - - -
57F ALA* 1.3 78.6 - - - +
59F GLN* 1.3 57.8 + - - +
61F ASP* 3.6 4.1 - - - +
62F LYS* 2.8 32.8 + - - +
374F THR 5.8 4.3 - - - +
380F ARG* 4.3 14.7 - - - +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F PRO 5.8 0.7 - - - +
56F ILE* 3.2 13.2 + - - +
58F ALA* 1.3 76.9 - - - +
60F VAL* 1.3 56.7 + - - +
62F LYS* 4.3 6.7 - - - +
63F GLU* 2.7 71.7 + - - +
65F LEU* 4.2 12.9 - - + +
503F EDO 3.7 20.7 - - - -
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Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ILE* 2.9 42.3 + - + +
57F ALA* 3.7 7.4 - - - +
59F GLN* 1.3 74.5 - - - +
61F ASP* 1.3 61.3 + - - +
64F HIS* 3.0 25.5 + - - -
65F LEU* 3.0 27.6 + - - +
67F PRO* 4.3 8.3 - - + -
109F CYS* 4.2 8.7 - - - -
111F SER* 4.0 15.0 - - - +
235F GLY* 3.4 30.1 + - - +
503F EDO 4.1 13.0 - - - -
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Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ALA 3.1 15.6 + - - +
58F ALA* 3.6 4.4 - - - +
60F VAL* 1.3 82.8 - - + +
62F LYS* 1.3 69.6 + - - +
64F HIS* 3.5 3.3 + - - -
234F ARG* 3.3 47.4 + - - +
235F GLY 5.1 0.4 - - - +
379F GLU* 4.7 1.0 - - - +
380F ARG* 3.6 22.5 - - - +
383F ARG* 2.9 44.8 + - - -
384F ASP* 4.6 4.7 - - - +
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ASP* 4.6 13.9 + - - +
58F ALA 2.8 21.8 + - - +
59F GLN* 4.0 6.7 - - - +
61F ASP* 1.3 79.1 - - - +
63F GLU* 1.3 71.9 + - + +
64F HIS* 3.5 11.6 + - - -
234F ARG* 5.0 3.7 + - - +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLN* 2.7 58.0 + - + +
62F LYS* 1.3 85.4 - - + +
64F HIS* 1.3 72.2 + - - +
65F LEU* 3.2 22.4 - - + +
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL 3.0 9.6 + - - -
61F ASP 3.5 2.0 + - - -
62F LYS 3.4 15.4 + - - -
63F GLU* 1.3 78.5 - - - +
65F LEU* 1.3 58.4 + - - +
66F PHE 4.0 1.4 + - - -
227F LYS* 5.0 9.5 + - - +
228F GLU 5.1 4.3 - - - -
229F ASP* 3.2 29.3 + - - -
230F LYS* 4.6 7.4 + - - -
234F ARG* 3.3 63.2 + - + +
235F GLY 5.0 0.3 - - - +
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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