Contacts of the strand formed by residues 28 - 35 (chain B) in PDB entry 2R2Q
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 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 6.2 4.0 - - - -
97A ASP* 4.8 9.7 + - - -
21B ILE* 5.3 1.2 - - - +
22B ARG* 5.9 1.7 - - - -
25B TYR* 3.3 28.1 + - + +
26B PRO 3.4 4.1 - - - +
27B ASP* 1.3 86.8 - - + +
29B VAL* 1.3 69.8 + - - +
30B PRO* 4.4 3.3 - - - +
50B LEU* 3.4 53.1 - - + +
51B VAL 3.3 6.1 - - - +
52B PRO* 3.6 32.1 - - + -
53B SER* 4.9 0.2 - - - -
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Residues in contact with VAL 29 (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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22B ARG* 6.0 0.7 - - - +
28B ARG* 1.3 78.8 - - - +
30B PRO* 1.3 67.3 - - + +
31B VAL* 3.6 14.3 - - + +
49B TYR 3.6 1.7 - - - +
50B LEU* 3.6 3.7 - - - -
51B VAL* 2.8 42.9 + - + +
53B SER* 4.4 15.0 - - - -
91B MET* 4.1 28.5 - - + +
92B GLY* 4.5 5.6 - - - +
95B TYR* 3.8 37.2 - - + -
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Residues in contact with PRO 30 (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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18B GLY* 4.8 7.2 - - - +
21B ILE* 3.7 34.8 - - + -
22B ARG* 5.2 5.2 - - + +
28B ARG 4.4 1.6 - - - +
29B VAL* 1.3 86.2 - - + +
31B VAL* 1.3 61.8 + - - +
49B TYR 3.7 5.2 - - - +
50B LEU* 4.3 3.8 - - + -
95B TYR* 3.8 15.4 - - + +
103B TYR 3.3 22.4 - - - +
104B PHE* 3.6 25.7 - - + -
105B LEU 3.1 22.0 + - - -
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Residues in contact with VAL 31 (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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29B VAL* 3.6 20.2 - - + +
30B PRO* 1.3 79.9 - - - +
32B ILE* 1.3 68.6 + - - +
33B VAL* 3.9 11.0 - - + -
47B ARG 3.6 0.5 - - - +
48B LYS* 3.4 3.3 - - - +
49B TYR* 2.7 42.7 + - + +
51B VAL* 3.6 19.1 - - + -
60B PHE* 4.2 6.7 - - + -
91B MET* 3.8 14.4 - - + -
104B PHE* 4.2 1.2 - - - -
105B LEU* 3.3 21.3 - - + +
107B VAL* 3.6 26.9 - - + -
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Residues in contact with ILE 32 (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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3B PHE* 4.1 2.1 - - + -
5B TYR* 3.7 34.8 - - + -
31B VAL* 1.3 77.4 - - - +
33B VAL* 1.3 59.3 + - - +
34B GLU* 3.7 29.4 - - + +
47B ARG* 3.2 7.6 - - + +
48B LYS* 3.9 18.4 - - + -
104B PHE* 3.7 28.9 - - + -
105B LEU 2.8 8.2 + - - +
106B TYR* 3.4 34.9 - - + -
107B VAL* 2.8 32.6 + - - +
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Residues in contact with VAL 33 (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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31B VAL* 3.9 6.5 - - + -
32B ILE* 1.3 77.0 - - - +
34B GLU* 1.3 70.4 + - - +
44B LEU* 5.0 4.9 - - + +
46B LYS 4.1 4.5 - - - +
47B ARG* 2.9 22.6 + - - +
49B TYR* 3.7 19.7 - - + -
60B PHE* 3.5 37.2 - - + -
64B ILE* 4.2 19.1 - - + -
78B PHE* 5.0 1.1 - - + -
107B VAL* 3.3 18.2 - - + +
109B TYR* 3.7 27.3 - - + -
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Residues in contact with GLU 34 (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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2B GLY 4.8 0.3 - - - +
3B PHE* 3.6 25.7 - - + +
4B GLN* 2.8 31.5 + - - +
5B TYR* 2.8 36.3 + - - +
32B ILE* 3.7 5.7 - - + +
33B VAL* 1.3 79.7 - - - +
35B LYS* 1.3 68.5 + - - +
43B ASP* 5.8 0.2 - - - -
44B LEU* 6.1 1.1 - - - -
47B ARG* 3.5 21.2 - - + -
107B VAL 3.0 6.7 + - - -
108B ALA* 3.2 6.9 - - - -
109B TYR* 2.9 31.9 + - - -
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Residues in contact with LYS 35 (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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34B GLU* 1.3 78.9 - - - +
36B ALA* 1.3 84.6 + - - +
37B PRO* 3.4 19.2 + - - +
39B ALA* 3.3 29.1 + - + +
41B VAL 3.1 27.4 - - - +
42B PRO 3.9 7.4 - - - +
43B ASP* 3.9 28.6 + - - +
44B LEU 5.7 0.2 - - - +
108B ALA* 5.2 0.2 - - - -
109B TYR* 3.5 33.1 + - + +
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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