Contacts of the helix formed by residues 56 - 64 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E GLU 3.5 15.9 - - - +
53E LEU* 3.0 19.5 + - + +
55E PRO* 1.3 84.5 - - + +
57E ALA* 1.3 62.0 + - - +
58E ALA 3.3 2.7 - - - -
59E GLN* 3.3 12.9 + - - +
60E VAL* 2.9 47.3 + - + +
67E PRO* 4.1 6.1 - - + -
70E GLN* 3.2 50.3 - - + +
109E CYS* 5.4 2.9 - - - -
112E THR* 5.3 0.7 - - - +
502E EDO 4.2 14.1 - - - +
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Residues in contact with ALA 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU 3.1 7.7 + - - +
54E PHE* 3.6 9.5 + - - +
56E ILE* 1.3 77.8 - - - +
58E ALA* 1.3 62.2 + - - +
60E VAL* 3.7 6.8 - - - +
61E ASP* 3.1 24.9 + - - +
108E GLY 3.4 26.0 - - - +
109E CYS* 4.4 10.8 - - + -
380E ARG* 3.6 29.4 - - - +
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Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PHE 5.0 1.2 + - - -
55E PRO 5.4 1.0 + - - -
56E ILE 3.3 0.4 - - - -
57E ALA* 1.3 77.8 - - - +
59E GLN* 1.3 53.1 + - - +
61E ASP* 3.6 4.9 - - - +
62E LYS* 2.7 37.3 + - - +
374E THR 5.9 3.1 - - - +
380E ARG* 4.2 14.8 - - - +
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Residues in contact with GLN 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E PRO 5.5 1.4 + - - +
56E ILE* 3.3 14.9 + - - +
58E ALA* 1.3 75.9 - - - +
60E VAL* 1.3 59.8 + - - +
62E LYS* 4.3 7.2 - - - -
63E GLU* 2.8 62.3 + - - +
65E LEU* 3.8 15.4 - - + +
502E EDO 3.8 21.1 + - - -
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ILE* 2.9 44.4 + - + +
57E ALA* 3.7 6.1 - - - +
59E GLN* 1.3 73.8 - - - +
61E ASP* 1.3 58.6 + - + +
64E HIS* 3.0 10.6 + - - -
65E LEU* 3.0 48.7 + - - +
67E PRO* 4.3 7.9 - - + -
109E CYS* 4.1 19.7 - - - -
111E SER* 4.1 5.2 - - - +
235E GLY* 3.6 19.4 + - - +
502E EDO 4.0 14.8 - - - -
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Residues in contact with ASP 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ALA 3.1 15.2 + - - +
58E ALA* 3.6 4.8 - - - +
60E VAL* 1.3 81.5 - - + +
62E LYS* 1.3 68.6 + - - +
63E GLU 3.5 0.2 + - - -
64E HIS 3.7 2.8 + - - -
111E SER* 6.0 0.2 - - - -
234E ARG* 3.2 47.3 + - - +
235E GLY 5.0 0.7 - - - +
379E GLU* 4.8 0.7 - - - +
380E ARG* 3.6 22.9 - - - +
383E ARG* 2.9 44.2 + - - -
384E ASP* 4.6 4.6 - - - +
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Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ALA 2.7 23.5 + - - +
59E GLN* 3.2 5.6 + - - +
61E ASP* 1.3 79.3 - - - +
63E GLU* 1.3 74.8 + - + +
64E HIS* 3.6 10.2 + - - -
234E ARG* 5.0 4.8 + - - +
229F ASP* 5.3 9.2 + - - -
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Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLN* 2.8 49.7 + - + +
62E LYS* 1.3 90.9 - - + +
64E HIS* 1.3 74.0 + - - +
65E LEU* 3.3 15.4 - - + +
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Residues in contact with HIS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E VAL 3.0 9.8 + - - -
61E ASP 3.7 4.5 + - - -
62E LYS 3.4 13.9 + - - -
63E GLU* 1.3 82.0 - - - +
65E LEU* 1.3 60.1 + - - +
66E PHE 3.8 2.1 + - - -
227E LYS* 4.9 10.4 + - - -
228E GLU 5.0 7.1 + - - -
229E ASP* 3.3 28.6 + - - -
230E LYS* 4.6 5.2 + - - -
234E ARG* 3.4 57.9 + - + +
235E GLY 4.8 1.0 - - - +
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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