Contacts of the strand formed by residues 10 - 13 (chain J) in PDB entry 3CMA
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 VAL 10 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J ALA* 3.5 4.9 - - - +
9J ASP* 1.3 88.3 - - + +
11J ILE* 1.3 66.2 + - - +
12J VAL* 4.1 21.8 - - + -
29J GLN* 3.8 22.4 - - - +
34J GLU* 3.7 25.8 - - + +
35J THR 3.0 7.3 + - - +
36J VAL* 3.4 9.3 - - + -
37J ALA 3.0 24.4 + - - -
114J GLU* 3.8 21.3 - - - +
116J LEU* 5.1 0.9 - - + -
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Residues in contact with ILE 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J ALA* 4.3 13.5 - - + +
9J ASP 5.7 0.2 - - - -
10J VAL* 1.3 78.3 - - - +
12J VAL* 1.3 61.5 + - - +
37J ALA* 3.4 8.7 - - + +
39J VAL* 3.9 20.6 - - + -
107J ASN* 4.6 1.8 - - - +
109J TYR* 3.4 44.2 - - + -
111J GLU* 4.3 28.5 - - + +
112J ASP 5.2 0.2 - - - -
113J GLY* 2.9 24.4 - - - +
114J GLU* 2.8 29.5 + - - +
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Residues in contact with VAL 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J VAL* 4.1 14.3 - - + -
11J ILE* 1.3 74.9 - - - +
13J ASP* 1.3 74.0 + - - +
14J ALA 3.7 1.3 + - - +
22J VAL* 4.0 19.3 - - + -
26J VAL* 4.5 2.5 - - + -
29J GLN* 5.4 1.3 - - - +
36J VAL* 4.2 11.9 - - + -
37J ALA 2.9 10.5 + - - +
38J VAL* 4.6 9.6 - - + -
39J VAL* 2.9 32.1 + - - +
113J GLY* 4.1 2.0 - - - -
114J GLU* 3.4 4.3 - - + +
116J LEU* 3.5 49.6 - - + +
119J THR* 6.0 0.2 - - - +
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Residues in contact with ASP 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 1.3 77.0 - - - +
14J ALA* 1.3 63.3 + - - +
15J ARG* 2.9 44.2 + - - +
17J CYS* 3.4 16.3 - - - -
39J VAL* 4.1 2.9 - - - -
40J ASN* 3.1 19.5 + - - +
107J ASN* 5.6 0.3 - - - +
112J ASP* 5.3 2.4 - - - +
113J GLY* 3.5 27.2 + - - +
114J GLU 2.7 14.0 + - - +
115J VAL* 4.1 14.9 - - + +
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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