Contacts of the strand formed by residues 34 - 41 (chain B) in PDB entry 2WJ7
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 VAL 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.6 5.0 - - - +
31B LEU* 3.1 36.2 + - + +
32B GLY 3.2 3.0 + - - -
33B ASP* 1.3 89.0 - - + +
35B ILE* 1.3 76.0 + - - +
36B GLU* 3.6 8.0 + - + +
58B LYS* 3.7 28.0 - - + -
59B TYR 3.3 12.8 - - - +
60B ARG* 5.3 7.4 - - + -
61B ILE* 5.3 0.2 - - - -
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 6.2 4.3 - - + -
28B VAL* 4.4 13.0 - - + -
29B LYS 3.8 3.6 - - - +
30B VAL* 4.5 15.9 - - + -
33B ASP 4.3 0.4 + - - -
34B VAL* 1.3 72.3 - - - +
36B GLU* 1.3 72.0 + - - +
37B VAL* 4.1 9.0 - - + -
57B ARG 3.5 0.9 - - - +
58B LYS* 3.1 6.8 - - - -
59B TYR* 2.9 64.8 + - + +
61B ILE* 3.9 26.2 - - + +
70B ILE* 4.2 11.4 - - + -
82B VAL* 3.7 29.4 - - + -
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Residues in contact with GLU 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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27B LYS 3.7 0.3 - - - +
28B VAL* 3.3 8.7 - - - +
29B LYS* 3.0 46.0 + - + +
31B LEU* 3.0 37.9 - - + +
34B VAL* 4.3 10.4 - - + +
35B ILE* 1.3 76.1 - - - +
37B VAL* 1.3 62.0 + - - +
38B HIS* 4.1 1.1 - - + +
56B HIS* 3.5 22.8 + - + -
57B ARG 3.3 4.7 - - - -
58B LYS* 3.9 26.9 + - + +
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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
----------------------------------------------------------
16B LEU* 4.3 11.4 - - + -
26B LEU* 4.9 3.1 - - + -
27B LYS 3.5 8.3 - - - +
28B VAL* 4.6 8.3 - - + -
35B ILE* 4.1 15.9 - - + -
36B GLU* 1.3 75.8 - - - +
38B HIS* 1.3 65.5 + - - +
55B PHE* 3.6 28.5 - - + -
56B HIS* 3.4 3.1 + - - -
57B ARG* 2.9 35.9 + - + -
59B TYR* 4.2 18.2 - - + -
80B LEU* 3.8 26.0 - - + -
82B VAL* 4.9 6.1 - - + -
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU 3.8 1.9 - - - +
26B LEU* 3.4 7.4 - - - +
27B LYS* 2.9 53.3 + - + +
36B GLU* 4.1 1.1 - - + -
37B VAL* 1.3 78.0 - - - +
39B GLY* 1.3 60.3 + - - +
40B LYS* 3.9 16.2 - - + +
54B GLU* 2.7 41.5 + - + -
55B PHE* 3.2 14.8 + - - -
56B HIS* 4.0 25.8 - + + +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.5 8.7 - - - -
25B GLU 3.5 7.9 - - - -
26B LEU* 3.9 6.3 - - - -
38B HIS* 1.3 75.9 - - - +
40B LYS* 1.3 62.0 + - - +
54B GLU* 3.2 3.6 - - - +
55B PHE* 2.9 52.3 + - - +
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Residues in contact with LYS 40 (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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21B PHE* 3.3 5.1 - - - -
25B GLU* 3.1 30.0 + - - +
38B HIS* 3.9 14.8 + - + +
39B GLY* 1.3 75.0 - - - +
41B HIS* 1.3 73.4 + - - +
42B GLU* 5.5 4.9 - - - +
53B ARG 3.3 10.8 - - - +
54B GLU* 3.1 36.3 + - + +
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Residues in contact with HIS 41 (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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20B HIS 3.4 12.6 + - - -
21B PHE* 3.9 6.9 - - + -
25B GLU* 3.6 23.6 - - - +
40B LYS* 1.3 83.3 - - - +
42B GLU* 1.3 86.3 + - - +
44B ARG* 3.5 28.8 + - - +
51B ILE 2.9 20.7 + - - -
52B SER* 3.3 5.4 - - - -
53B ARG* 2.6 74.1 + - + +
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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