Contacts of the strand formed by residues 32 - 38 (chain B) in PDB entry 2H1H
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 LYS 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET 3.0 10.0 + - - +
2B ARG* 3.4 14.3 - - + +
3B VAL* 3.0 25.5 + - - +
25B GLN* 4.8 5.5 + - - -
30B GLY* 3.5 18.6 - - - +
31B ILE* 1.3 81.3 + - - +
33B PHE* 1.3 63.7 + - - +
49B ALA 3.3 23.0 + - - -
50B ALA* 3.6 11.7 - - - +
52B GLU* 3.7 41.4 - - + +
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Residues in contact with PHE 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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3B VAL* 3.3 40.2 - - + +
5B ILE* 3.7 27.4 - - + -
21B LEU* 3.8 31.6 - - + -
24B ALA* 3.5 31.9 - - + -
31B ILE* 3.6 21.3 - - + -
32B LYS* 1.3 75.5 - - - +
34B ASP* 1.3 62.4 + - - +
50B ALA* 2.8 26.0 + - + +
51B VAL* 3.3 6.7 - - + +
52B GLU* 2.7 32.7 + - - -
148B PHE* 3.8 22.7 - + - -
152B LEU* 4.2 2.9 - - + -
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Residues in contact with ASP 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 ARG* 4.3 6.3 - - - +
3B VAL 2.9 5.7 + - - +
4B LEU* 3.8 7.4 - - + -
5B ILE* 2.7 28.7 + - - +
32B LYS 4.3 0.2 + - - -
33B PHE* 1.3 75.4 - - - +
35B TRP* 1.3 62.3 + - - +
52B GLU* 3.7 5.0 - - - +
53B ARG* 2.9 38.3 + - - +
55B ILE* 4.9 1.8 - - + -
85B LYS* 2.8 27.4 + - - -
87B TYR* 2.7 42.9 + - + +
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Residues in contact with TRP 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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4B LEU* 4.3 0.4 - - - +
5B ILE* 3.4 26.9 - - + -
7B LYS* 2.8 28.1 + - + +
14B VAL* 3.6 38.6 - - + -
17B THR* 3.7 23.3 - - + -
18B LEU* 3.9 20.9 - - + -
21B LEU* 3.8 23.6 - - + -
34B ASP* 1.3 76.9 - - - +
36B VAL* 1.3 81.0 + - - +
37B VAL* 3.4 9.4 + - + +
45B PRO* 3.5 31.0 - - + -
51B VAL* 3.9 14.8 - - + -
53B ARG 2.9 11.8 + - - +
54B VAL* 3.4 8.4 - - - +
55B ILE* 2.8 24.5 + - - -
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Residues in contact with VAL 36 (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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4B LEU* 3.8 24.2 - - + -
5B ILE 2.8 14.1 + - - +
6B VAL* 4.4 3.1 - - + -
7B LYS 3.3 17.3 + - - +
8B THR* 3.5 7.6 - - + +
35B TRP* 1.3 81.0 - - - +
37B VAL* 1.3 59.7 + - - +
55B ILE* 3.3 21.8 - - + +
57B VAL* 4.0 21.8 - - + -
78B PHE* 4.2 6.7 - - + -
82B LEU* 3.9 12.6 - - + -
103B VAL* 3.8 33.9 - - + -
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Residues in contact with VAL 37 (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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7B LYS 3.7 0.9 - - - +
8B THR* 3.6 16.4 - - - +
14B VAL* 3.7 23.8 - - + -
35B TRP* 3.9 10.5 - - + +
36B VAL* 1.3 76.0 - - - +
38B GLU* 1.3 74.2 + - - +
41B PHE* 4.1 13.2 - - + +
42B ALA* 3.5 18.6 - - + -
45B PRO* 4.4 4.9 - - + -
54B VAL* 3.4 31.2 - - + -
55B ILE 3.2 4.4 + - - -
56B PRO* 3.3 3.0 - - + +
57B VAL* 2.9 24.4 + - - -
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Residues in contact with GLU 38 (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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8B THR* 3.2 25.4 + - - +
9B SER* 3.6 19.4 + - - +
37B VAL* 1.3 80.2 - - - +
39B GLU* 1.3 74.3 + - - +
40B GLY 4.3 3.4 + - - +
41B PHE* 3.1 28.9 + - + -
42B ALA 3.3 8.5 + - - -
57B VAL* 3.2 21.8 - - - +
58B ALA* 3.8 6.0 - - - -
59B ILE* 3.4 24.3 + - - +
60B ARG* 3.5 27.6 + - - +
61B ARG* 5.6 0.3 + - - +
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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