Contacts of the strand formed by residues 5 - 14 (chain A) in PDB entry 2CHR
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 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.6 1.1 - - - -
4A ASP* 1.3 85.6 - - + +
6A ILE* 1.3 65.8 + - - +
7A GLU* 4.0 1.8 - - + -
36A VAL 3.7 0.5 - - - -
37A TYR* 2.9 41.8 + - + +
76A LEU* 3.5 10.5 - - + -
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Residues in contact with ILE 6 (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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3A ILE* 3.6 17.9 - - + -
5A ALA* 1.3 72.8 - - - +
7A GLU* 1.3 61.7 + - - +
34A VAL* 3.7 26.7 - - + -
35A ARG 4.0 2.5 - - - -
36A VAL* 3.5 28.7 - - + +
67A VAL* 5.1 4.8 - - + +
68A GLU* 5.8 3.1 - - - +
72A ALA* 4.5 24.6 - - + +
75A LEU* 3.6 41.7 - - + -
76A LEU* 3.5 13.0 - - + +
104A VAL* 4.5 13.2 - - + -
108A LEU* 5.3 0.9 - - + -
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Residues in contact with GLU 7 (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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5A ALA* 4.0 2.8 - - + -
6A ILE* 1.3 75.0 - - - +
8A ALA* 1.3 73.3 + - - +
9A VAL* 4.1 13.3 - - + +
34A VAL* 3.4 5.9 - - - +
35A ARG* 2.8 40.5 + - + +
37A TYR* 3.0 38.3 + - + +
67A VAL* 6.1 0.2 - - - -
68A GLU* 6.2 0.4 - - - -
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Residues in contact with ALA 8 (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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7A GLU* 1.3 82.0 - - - +
9A VAL* 1.3 66.9 + - - +
32A VAL* 4.4 9.2 - - + -
33A ILE 3.3 11.7 - - - +
34A VAL* 3.9 18.4 - - + -
35A ARG 4.7 0.2 - - - +
64A LYS* 4.5 5.5 - - + +
67A VAL* 4.3 17.3 - - + -
68A GLU* 3.3 31.1 + - + +
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Residues in contact with VAL 9 (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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7A GLU* 4.1 13.9 - - + +
8A ALA* 1.3 80.8 - - - +
10A ILE* 1.3 65.6 + - - +
11A VAL* 3.8 17.0 - - + -
32A VAL* 3.4 3.5 - - - -
33A ILE* 3.0 52.6 + - + +
35A ARG* 3.3 24.2 - - - +
64A LYS* 4.9 3.4 - - - -
363A VAL* 3.9 9.2 - - + -
367A ALA* 5.2 4.9 - - + -
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Residues in contact with ILE 10 (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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9A VAL* 1.3 75.2 - - - +
11A VAL* 1.3 65.0 + - - +
12A ASP* 3.8 8.1 - - - +
31A TYR 3.4 15.5 - - - +
32A VAL* 4.1 5.4 - - + -
60A ALA* 3.5 35.7 - - + +
61A GLU* 4.1 8.1 - - - +
64A LYS* 3.6 28.3 - - + +
367A ALA* 3.0 27.3 - - - +
368A ARG 2.9 26.5 - - - +
369A VAL* 3.8 27.6 - - + +
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Residues in contact with VAL 11 (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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9A VAL* 3.8 16.8 - - + -
10A ILE* 1.3 82.7 - - - +
12A ASP* 1.3 63.8 + - - +
13A VAL* 4.8 2.7 - - + -
30A SER* 3.7 0.9 - - - -
31A TYR* 2.9 52.1 + - + +
33A ILE* 4.2 13.7 - - + -
334A LEU* 4.0 24.9 - - + -
363A VAL* 3.7 33.7 - - + +
366A TYR* 4.6 4.7 - - + -
367A ALA* 3.9 9.0 - - - +
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Residues in contact with ASP 12 (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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10A ILE* 3.8 2.1 - - - +
11A VAL* 1.3 74.0 - - - +
13A VAL* 1.3 63.4 + - - +
14A PRO* 4.0 2.8 - - - +
28A GLN* 3.6 21.0 - - - +
29A GLN 3.9 3.4 - - - -
30A SER* 3.3 26.4 - - - +
366A TYR* 3.2 28.6 - - + +
368A ARG* 2.8 43.6 + - + +
369A VAL 3.8 2.1 - - - +
370A SER* 2.7 30.4 + - - -
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Residues in contact with VAL 13 (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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11A VAL 3.8 3.6 + - - +
12A ASP* 1.3 77.2 - - - +
14A PRO* 1.3 68.9 - - + +
28A GLN* 3.9 1.3 - - - -
29A GLN* 2.8 44.0 + - - +
31A TYR* 4.3 15.0 - - + -
330A LEU* 3.6 30.2 - - + +
332A ASP* 3.9 26.0 - - + +
334A LEU* 3.7 29.6 - - + -
366A TYR* 4.3 12.6 - - + -
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Residues in contact with PRO 14 (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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12A ASP 4.0 4.9 - - - +
13A VAL* 1.3 95.1 - - + +
15A THR* 1.3 64.7 + - - +
27A HIS 4.2 4.9 - - - +
28A GLN* 3.8 23.6 - - + +
330A LEU* 3.5 3.9 - - - +
331A ALA* 3.0 34.0 + - + +
332A ASP* 6.0 0.4 - - + -
366A TYR* 4.1 14.8 - - + -
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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