Contacts of the strand formed by residues 9 - 13 (chain D) in PDB entry 4OQB
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 TYR 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D LYS* 3.7 7.3 - - - +
8D LEU* 1.3 108.2 - - + +
10D ARG* 1.3 64.9 + - - +
35D MET* 5.0 1.1 - - + -
36D ALA 3.4 17.3 - - - +
37D ILE* 3.7 24.1 - - + +
38D MET* 4.9 1.3 - - - +
57D PHE* 3.7 22.9 - + + -
62D HIS* 3.9 27.1 + + + +
63D SER 5.1 2.0 + - - -
64D ILE* 3.7 28.7 - - + +
70D GLU* 4.3 18.7 + - + -
71D VAL* 3.9 20.2 - - + -
72D ASP* 3.2 23.5 + - - +
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Residues in contact with ARG 10 (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 TYR* 1.3 79.6 - - - +
11D VAL* 1.3 71.7 + - - +
12D GLU* 2.7 33.5 + - - +
15D LYS* 4.7 4.0 - - - +
35D MET* 3.4 3.1 - - - +
36D ALA* 2.7 45.0 + - + +
38D MET* 4.6 17.0 - - + -
49D PRO* 5.8 0.2 - - + -
51D TRP* 3.9 20.2 - - + -
71D VAL* 3.9 3.3 - - - +
72D ASP* 3.1 34.7 + - + -
73D GLY* 3.2 22.2 - - - +
76D GLU* 5.9 1.6 - - - +
305D LYS* 4.1 7.9 - - - +
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Residues in contact with VAL 11 (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 ARG* 1.3 79.4 + - - +
12D GLU* 1.3 67.9 + - - +
33D LEU* 3.9 23.6 - - + -
34D ARG 3.4 14.1 - - - +
35D MET* 3.7 19.1 - - + -
51D TRP* 4.9 0.2 - - - -
71D VAL* 3.4 21.8 - - + -
72D ASP 2.9 17.6 + - - +
73D GLY* 3.6 20.5 - - - +
74D PHE* 4.0 5.6 - - + +
77D LEU* 3.7 23.8 - - + -
85D VAL* 4.7 5.8 - - + -
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Residues in contact with GLU 12 (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 ARG* 2.7 39.4 + - - +
11D VAL* 1.3 76.8 - - - +
13D TYR* 1.3 71.5 + - - +
15D LYS* 3.2 28.0 + - - +
33D LEU* 3.8 1.8 - - - +
34D ARG* 2.8 64.0 + - - +
51D TRP* 3.3 26.9 - - + -
73D GLY 5.4 0.2 - - - -
77D LEU* 4.1 11.9 - - - -
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Residues in contact with TYR 13 (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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12D GLU* 1.3 81.8 - - - +
14D ALA* 1.3 66.7 + - - +
15D LYS* 3.0 9.7 + - - +
31D ASP* 4.2 22.7 - - + +
32D SER 3.5 2.7 - - - -
33D LEU* 4.1 33.9 - - + -
76D GLU 5.7 0.2 - - - -
77D LEU* 3.9 16.1 - - + +
78D ARG* 3.0 31.2 + - + +
81D ASP* 2.6 33.4 + - - +
246D TRP* 3.8 35.0 - + - -
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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