Contacts of the strand formed by residues 45 - 50 (chain B) in PDB entry 2OQH
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 GLU 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ARG* 4.1 17.6 + - + -
38B VAL 3.2 7.6 - - - +
39B ARG* 3.2 38.4 + - + +
43B GLY 3.4 16.1 - - - +
44B VAL* 1.3 80.8 - - - +
46B GLY* 1.3 59.9 + - - +
47B TRP* 4.1 14.8 + - - +
110B LYS* 3.1 31.5 + - - +
359B GLU* 3.9 17.2 - - - +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL 3.7 0.3 - - - +
37B ARG* 3.3 6.2 - - - +
38B VAL* 2.8 35.0 + - - -
45B GLU* 1.3 74.6 - - - +
47B TRP* 1.3 63.0 + - - -
103B ALA* 3.3 24.7 - - - +
106B ASP* 3.4 5.6 - - - -
107B ALA* 3.8 11.5 - - - +
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TRP* 3.4 30.5 - + - -
35B VAL* 3.8 13.9 - - + -
36B VAL 3.4 9.4 - - - -
37B ARG* 3.4 38.8 - - + -
45B GLU* 4.1 15.1 + - - +
46B GLY* 1.3 78.3 - - - -
48B GLY* 1.3 59.1 + - - +
102B VAL* 3.7 0.2 - - - +
103B ALA* 3.4 14.0 + - - -
106B ASP* 2.8 20.5 + - - +
110B LYS* 3.9 12.9 - - - +
304B ILE* 4.1 10.8 - - + -
353B LEU* 3.3 23.7 - - + +
355B VAL* 5.8 3.6 - - + -
357B VAL* 3.5 37.9 - - + +
359B GLU* 3.7 30.4 + - + -
362B LEU* 3.7 20.6 - - + -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 3.5 6.0 - - - +
36B VAL 2.7 36.9 + - - +
47B TRP* 1.3 76.3 - - - +
49B GLU* 1.3 58.5 + - - +
99B ALA* 3.8 22.2 - - - -
102B VAL* 4.1 9.6 - - - -
103B ALA* 3.9 1.2 - - - +
304B ILE* 3.8 8.7 - - - -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 6.0 0.2 - - - +
33B ARG* 2.4 40.0 + - + +
34B THR 3.1 11.9 - - - +
35B VAL* 4.2 13.9 - - + -
48B GLY* 1.3 74.1 - - - +
50B THR* 1.3 61.5 + - - +
99B ALA* 4.5 4.4 - - - +
102B VAL* 5.2 1.4 - - - +
272B TYR* 3.4 22.9 - - - -
302B LEU* 3.1 16.5 - - - +
303B GLY 3.5 0.5 + - - -
304B ILE* 3.0 26.8 + - + +
305B ALA* 2.8 42.5 + - - +
333B ASP* 5.3 0.5 - - - +
334B ILE* 6.4 0.4 - - - -
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.3 20.5 + - - +
34B THR* 2.8 39.1 + - + +
49B GLU* 1.3 75.5 - - - +
51B MSE 1.3 65.7 + - - +
56B VAL* 3.5 29.6 - - + -
95B ALA* 2.9 35.4 + - - +
99B ALA* 3.8 15.7 - - + -
272B TYR* 4.0 15.6 - - - +
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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