Contacts of the strand formed by residues 32 - 37 (chain D) in PDB entry 3RKR
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 ARG 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D GLY* 6.0 0.2 - - - -
7D GLN 2.7 15.6 + - - +
8D VAL* 3.4 12.8 - - + +
9D ALA 2.9 24.5 + - - -
30D GLY 3.8 1.8 + - - -
31D ALA* 1.3 70.0 - - - +
33D VAL* 1.3 60.9 + - - +
34D VAL* 3.5 5.7 + - - +
56D GLU* 2.9 66.1 + - + +
57D ALA* 4.5 4.7 - - - +
58D GLU* 3.3 16.5 + - - +
81D HIS* 2.9 43.2 + - - -
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.4 4.9 - - + +
11D VAL* 4.0 17.7 - - + -
23D ALA* 3.7 20.2 - - + +
26D LEU* 4.1 7.0 - - + -
27D GLY* 3.4 33.7 - - - +
31D ALA* 3.5 11.0 - - + +
32D ARG* 1.3 70.7 - - - +
34D VAL* 1.3 62.6 + - - +
35D LEU* 3.3 29.0 + - + +
50D ILE* 4.2 9.6 - - + -
56D GLU 3.1 11.5 + - - +
57D ALA* 3.4 3.3 - - - -
58D GLU 3.3 20.0 + - - +
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 4.7 8.7 - - + -
9D ALA 2.9 13.9 + - - +
10D VAL* 3.5 12.2 - - + +
11D VAL* 3.0 26.0 + - - +
32D ARG* 3.5 9.4 + - - +
33D VAL* 1.3 70.0 - - - +
35D LEU* 1.3 60.0 + - - +
58D GLU* 3.7 23.6 - - - +
60D HIS* 3.4 33.0 - - + +
73D PHE* 4.0 11.9 - - + -
77D VAL* 3.9 32.3 - - + -
81D HIS* 5.2 1.8 - - + -
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.8 3.6 - - + -
14D ALA* 4.0 9.0 - - + -
23D ALA* 3.6 21.1 - - + -
33D VAL* 3.4 33.2 - - + +
34D VAL* 1.3 73.7 - - - +
36D THR* 1.3 63.8 + - - +
43D LEU* 3.7 22.0 - - + +
46D VAL* 4.1 5.4 - - + -
47D GLU* 3.9 32.1 - - + +
50D ILE* 4.1 4.7 - - + -
57D ALA* 4.4 2.7 - - + -
58D GLU 2.8 15.1 + - - +
59D SER* 3.6 18.8 - - - +
60D HIS* 3.0 29.3 + - - +
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Residues in contact with THR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 5.1 1.0 - - - +
11D VAL 3.2 15.2 + - - -
12D THR* 3.9 24.2 - - + +
13D GLY 3.4 4.2 + - - +
14D ALA* 3.0 23.6 + - - +
35D LEU* 1.3 76.0 + - - +
37D ALA* 1.3 73.1 + - - +
43D LEU* 3.7 4.6 - - - +
60D HIS 3.4 4.5 + - - -
62D CYS* 3.9 26.6 - - + +
64D LEU* 4.6 9.9 - - + -
73D PHE* 3.5 30.5 - - - -
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY 5.1 1.3 - - - +
14D ALA 5.1 0.2 - - - +
15D SER* 4.4 8.3 - - - -
36D THR* 1.3 83.4 - - - +
38D ARG* 1.3 61.5 + - - +
39D ASP* 3.2 17.0 - - - +
42D LYS* 4.7 0.9 - - + -
43D LEU* 3.8 13.8 - - + +
60D HIS 3.4 4.2 + - - -
61D ALA* 3.2 5.4 - - - -
62D CYS 2.8 27.8 + - - -
241D SO4 2.9 27.6 - - - +
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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