Contacts of the helix formed by residues 56 - 64 (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 ILE 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLU 3.4 12.1 - - - +
53A LEU* 2.9 24.0 + - + +
55A PRO* 1.3 83.5 - - + +
57A ALA* 1.3 59.9 + - - +
58A ALA 3.4 1.8 - - - -
59A GLN* 3.0 18.8 + - - +
60A VAL* 2.8 37.5 + - + +
67A PRO* 4.1 15.3 - - + -
70A GLN* 3.3 48.9 - - + +
109A CYS* 5.4 2.5 - - + -
112A THR* 5.1 1.1 - - - +
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Residues in contact with ALA 57 (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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53A LEU 3.1 8.2 + - - +
54A PHE* 3.6 9.8 + - + +
56A ILE* 1.3 77.1 - - - +
58A ALA* 1.3 63.3 + - - +
60A VAL* 3.5 7.6 + - - +
61A ASP* 3.1 24.9 + - - +
108A GLY 3.5 17.9 - - - +
109A CYS* 4.5 10.3 - - + -
380A ARG* 3.4 34.2 + - - +
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Residues in contact with ALA 58 (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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54A PHE 4.9 1.4 + - - -
55A PRO 5.5 0.8 + - - +
56A ILE 3.4 0.4 - - - -
57A ALA* 1.3 76.8 - - - +
59A GLN* 1.3 58.5 + - - +
61A ASP* 3.6 5.9 - - - +
62A LYS* 2.8 31.2 + - - +
374A THR 5.8 3.8 - - - +
380A ARG* 4.2 13.0 - - - +
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Residues in contact with GLN 59 (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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55A PRO 5.6 1.4 - - - +
56A ILE* 3.0 20.6 + - + +
58A ALA* 1.3 77.0 - - - +
60A VAL* 1.3 65.1 + - + +
62A LYS* 4.4 4.9 - - - +
63A GLU* 3.0 58.6 + - - +
65A LEU* 3.8 17.4 - - + +
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Residues in contact with VAL 60 (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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56A ILE* 2.8 35.3 + - + +
57A ALA* 3.8 6.5 - - - +
59A GLN* 1.3 72.5 - - + +
61A ASP* 1.3 59.6 + - - +
64A HIS* 3.1 10.0 + - - -
65A LEU* 3.0 45.8 + - + +
67A PRO* 4.0 22.4 - - + -
109A CYS* 4.1 19.5 - - - -
111A SER* 4.1 5.2 - - - +
235A GLY* 3.6 28.4 + - - +
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Residues in contact with ASP 61 (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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57A ALA 3.1 18.7 + - - +
58A ALA* 3.6 4.2 - - - +
60A VAL* 1.3 79.2 - - + +
62A LYS* 1.3 70.1 + - - +
63A GLU 3.4 0.3 + - - -
64A HIS 3.6 3.5 + - - -
234A ARG* 3.2 46.5 + - - +
235A GLY 5.2 0.2 - - - +
374A THR* 6.1 0.5 - - - +
379A GLU* 4.7 0.7 - - - +
380A ARG* 3.6 20.9 - - - +
383A ARG* 2.8 45.4 + - - -
384A ASP* 4.7 4.7 - - - +
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Residues in contact with LYS 62 (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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58A ALA 2.8 23.3 + - - +
59A GLN* 3.3 4.9 + - - +
61A ASP* 1.3 79.9 - - - +
63A GLU* 1.3 72.0 + - + +
64A HIS* 3.7 10.7 + - - -
234A ARG* 4.9 4.8 + - - +
229B ASP* 5.3 10.1 + - - +
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Residues in contact with GLU 63 (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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59A GLN* 3.0 48.7 + - - +
62A LYS* 1.3 91.2 - - + +
64A HIS* 1.3 75.7 + - - +
65A LEU* 3.2 18.8 - - + +
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Residues in contact with HIS 64 (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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60A VAL 3.1 7.8 + - - -
61A ASP 3.6 1.4 + - - -
62A LYS 3.5 12.8 + - - -
63A GLU* 1.3 81.7 + - - +
65A LEU* 1.3 60.3 + - - +
66A PHE 3.7 2.1 + - - -
227A LYS* 5.0 11.9 + - + +
228A GLU 5.0 4.5 - - - -
229A ASP* 3.3 29.0 + - - -
230A LYS* 4.5 7.1 + - - -
234A ARG* 3.3 64.4 + - + +
235A GLY* 4.7 0.7 - - - +
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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