Contacts of the strand formed by residues 19 - 25 (chain J) in PDB entry 2BX5
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 19 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J LEU* 3.6 27.6 - - + -
13J ALA* 3.6 30.3 - - + -
17J ASP 3.4 1.6 + - - -
18J ARG* 1.3 87.7 - - - +
20J THR* 1.3 63.6 + - - +
21J ILE* 3.4 28.3 - - + -
74J THR* 3.8 0.9 - - - +
75J ILE* 3.0 35.9 + - + +
78J LEU* 3.8 25.1 - - + -
104J VAL* 4.4 3.4 - - + -
7K SER* 5.2 0.7 - - - -
8K PRO* 5.1 2.2 - - + -
22K THR* 5.6 0.2 - - - -
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Residues in contact with THR 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J PRO* 4.1 12.5 - - - +
11J LEU* 4.5 6.3 - - - +
18J ARG* 3.7 15.4 + - - -
19J VAL* 1.3 79.8 + - - +
21J ILE* 1.3 72.4 + - - +
22J THR* 5.1 0.2 - - + -
72J THR* 3.6 21.3 - - + -
73J LEU 3.9 4.3 - - - -
74J THR* 4.1 8.3 + - - +
8K PRO* 6.4 0.4 - - - +
20K THR* 3.5 49.3 + - + +
22K THR* 4.0 7.6 + - - -
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Residues in contact with ILE 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLN* 3.2 26.0 - - + +
7J SER 3.3 5.4 - - - +
11J LEU* 5.0 0.2 - - + -
19J VAL* 3.4 24.2 - - + -
20J THR* 1.3 78.5 - - - +
22J THR* 1.3 71.2 + - - +
35J TRP* 3.7 10.8 - - + -
72J THR* 2.8 36.8 - - - +
73J LEU* 3.1 32.2 + - + +
75J ILE* 4.2 13.9 - - + -
86J TYR* 4.8 10.1 - - + +
102J THR* 3.2 43.1 - - + +
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Residues in contact with THR 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J THR 3.8 0.7 - - - +
6J GLN* 3.1 9.1 - - - +
7J SER* 2.6 61.9 + - - -
8J PRO* 5.0 0.3 - - - +
20J THR* 5.8 0.2 - - - +
21J ILE* 1.3 77.2 - - - +
23J CYS* 1.3 62.4 + - - +
35J TRP* 4.1 1.1 - - - -
70J ASP* 4.7 8.3 - - - +
71J PHE 3.8 2.7 - - - +
72J THR* 4.2 13.7 - - + +
18K ARG* 3.3 31.4 + - + +
20K THR* 3.8 22.4 + - - +
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Residues in contact with CYS 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J MET* 3.9 29.6 - - - -
5J THR 3.6 2.9 - - - -
22J THR* 1.3 75.4 - - - +
24J ARG* 1.3 68.3 + - - +
33J LEU* 3.9 9.4 - - + -
35J TRP* 3.6 13.6 - - + -
69J THR 3.8 0.2 - - - +
70J ASP* 3.6 2.2 - - - +
71J PHE* 3.0 36.2 + - + +
88J CYS* 2.0 51.6 - - + -
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Residues in contact with ARG 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J MET* 3.7 1.2 - - - +
5J THR* 2.7 54.2 + - - +
23J CYS* 1.3 82.5 - - - +
25J ALA* 1.3 58.9 + - - +
26J SER 4.2 0.2 + - - -
69J THR* 2.9 34.2 + - + +
70J ASP* 3.1 35.6 + - - +
71J PHE* 5.5 0.4 - - - -
18K ARG* 5.1 10.5 - - - +
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Residues in contact with ALA 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ILE* 4.4 3.6 - - + -
3J GLN 3.8 2.5 - - - -
4J MET* 3.0 35.0 - - + -
5J THR* 5.4 0.2 - - - -
24J ARG* 1.3 74.1 - - - +
26J SER* 1.3 67.2 + - - +
27J GLN 2.8 23.4 - - - +
29J ILE* 4.0 13.9 - - + -
69J THR* 3.1 24.8 + - - +
71J PHE* 5.3 1.5 - - + -
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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