Contacts of the helix formed by residues 47 - 53 (chain A) in PDB entry 2CG2
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 ALA 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP* 3.4 14.1 + - - +
46A ARG* 1.3 76.7 - - - +
48A ASP* 1.3 63.7 + - - +
50A GLU* 2.9 21.3 + - + +
51A ARG* 2.9 50.9 + - + +
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Residues in contact with ASP 48 (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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45A ASP* 4.9 0.8 + - - -
46A ARG 3.1 1.0 + - - -
47A ALA* 1.3 77.1 - - - +
49A PHE* 1.3 53.1 + - - +
51A ARG* 3.0 11.4 + - - +
52A ALA* 2.7 37.1 + - - +
97A ARG* 3.0 34.1 + - - +
101A LEU* 3.5 15.4 - - + +
346A TRP* 3.0 26.6 + - - +
348A ARG* 2.7 30.4 + - - -
399A TRP* 3.5 16.2 - - - +
400A TYR 5.3 0.2 + - - -
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Residues in contact with PHE 49 (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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46A ARG* 3.0 64.4 + - + +
48A ASP* 1.3 77.4 - - - +
50A GLU* 1.3 66.9 - - + +
52A ALA* 3.7 2.0 + - - +
53A ASP* 3.4 27.7 + - - +
97A ARG* 3.9 39.7 - - + -
100A LEU* 4.0 31.4 - - + -
101A LEU* 3.6 27.8 - - + -
104A LYS* 4.6 13.2 - - - +
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Residues in contact with GLU 50 (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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46A ARG* 2.9 32.8 + - - +
47A ALA* 2.9 17.2 + - - +
49A PHE* 1.3 81.2 - - + +
51A ARG* 1.3 59.1 + - + +
53A ASP* 3.5 3.7 + - - +
54A ARG* 3.0 30.2 + - - +
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Residues in contact with ARG 51 (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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45A ASP* 5.0 3.8 + - - -
47A ALA* 2.9 41.2 + - + +
48A ASP* 3.0 34.9 + - - +
50A GLU* 1.3 77.0 - - - +
52A ALA* 1.4 60.1 + - - +
54A ARG* 3.3 11.9 + - - +
118A ARG* 4.8 0.7 + - - -
346A TRP* 3.7 17.0 - - + +
347A PRO* 3.5 20.5 - - - +
348A ARG* 3.2 44.0 - - - +
349A TRP* 3.5 33.1 + - + +
353A GLU* 3.7 20.0 + - - +
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Residues in contact with ALA 52 (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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48A ASP 2.7 20.6 + - - +
49A PHE 4.2 2.0 - - - +
51A ARG* 1.4 71.6 - - - +
53A ASP* 1.3 59.3 + - - +
101A LEU* 3.9 16.2 - - + +
104A LYS* 3.5 29.0 - - + +
108A PHE* 3.2 12.5 - - - -
118A ARG* 2.8 30.1 + - - +
346A TRP* 4.0 14.8 - - + +
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Residues in contact with ASP 53 (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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49A PHE 3.4 17.2 + - - +
50A GLU* 4.3 3.6 - - - +
51A ARG 3.2 0.4 - - - -
52A ALA* 1.3 80.5 - - - +
54A ARG* 1.3 66.4 + - - +
55A GLY 3.3 0.5 + - - -
56A LEU* 3.2 25.4 + - + +
59A ARG* 3.3 33.1 + - - -
104A LYS* 3.9 18.1 + - - +
108A PHE* 4.2 2.5 - - - -
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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