Contacts of the strand formed by residues 21 - 28 (chain J) in PDB entry 2FRV
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 LEU 21 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J ASP* 4.4 1.8 - - - -
13J PRO* 4.0 7.1 - - - +
14J ILE* 3.3 29.7 + - + +
17J ILE* 3.5 22.6 - - + +
19J GLY 3.6 3.4 + - - -
20J HIS* 1.3 74.5 - - - +
22J ARG* 1.3 67.8 + - - +
23J ILE* 4.1 16.6 - - + -
37J SER* 3.7 20.6 - - - +
38J MET 3.4 24.9 - - - +
39J SER* 4.1 9.0 - - - +
40J THR* 5.0 1.6 - - - -
490J LEU* 3.8 24.2 - - + -
524J VAL* 4.1 15.9 - - + -
529J PRO* 4.6 0.2 - - + -
531J ILE* 3.7 13.7 - - + -
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Residues in contact with ARG 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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88I GLY 4.1 13.3 + - - -
89I GLY* 4.9 0.2 - - - -
10J VAL* 3.8 23.7 - - + +
11J VAL 3.5 5.2 - - - +
12J ASP* 3.1 40.9 + - + +
21J LEU* 1.3 75.9 - - - +
23J ILE* 1.3 62.3 + - - +
24J GLU* 2.7 35.1 + - + -
38J MET* 2.7 58.4 + - - +
40J THR* 4.1 4.0 - - + -
348J PHE* 3.5 37.5 - - - -
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Residues in contact with ILE 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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9J ILE 3.8 0.7 - - - +
10J VAL* 3.2 4.2 - - - +
11J VAL* 2.6 41.0 + - + +
14J ILE* 3.4 31.9 - - + -
21J LEU* 4.1 15.7 - - + -
22J ARG* 1.3 76.8 - - - +
24J GLU* 1.3 66.6 + - - +
25J VAL* 3.7 23.3 - - + -
36J TRP 3.8 3.8 - - - +
37J SER* 4.3 20.0 - - - +
502J VAL* 5.1 5.2 - - + -
506J LEU* 3.9 16.6 - - + -
520J ILE* 4.0 13.9 - - + -
524J VAL* 3.7 20.4 - - + -
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Residues in contact with GLU 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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8J LYS* 4.6 13.3 - - + +
9J ILE 3.4 5.8 - - - +
10J VAL* 4.2 11.0 - - + +
22J ARG* 2.7 37.9 + - - +
23J ILE* 1.3 77.1 - - - +
25J VAL* 1.3 64.2 + - - +
36J TRP* 3.0 46.5 + - + +
38J MET* 3.4 22.4 - - - +
348J PHE* 4.8 1.6 - - - -
349J HIS* 2.6 31.0 + - - -
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Residues in contact with VAL 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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8J LYS* 2.9 12.5 - - - +
9J ILE* 2.8 64.2 + - + +
23J ILE* 3.7 20.6 - - + -
24J GLU* 1.3 79.1 - - - +
26J GLU* 1.3 60.3 + - - +
27J VAL* 3.8 14.6 - - + -
32J ILE* 4.1 13.9 - - + -
34J ASN 3.5 8.3 - - - +
35J ALA* 4.0 6.5 - - + -
36J TRP* 4.2 1.8 - - - -
506J LEU* 4.0 16.8 - - + -
520J ILE* 3.8 18.6 - - + -
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Residues in contact with GLU 26 (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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7J ASN 3.3 7.9 - - - +
8J LYS* 3.1 31.2 + - - +
25J VAL* 1.3 73.2 - - - +
27J VAL* 1.3 60.1 + - - +
32J ILE* 3.5 3.6 - - - -
33J LYS* 2.7 72.5 + - + +
34J ASN* 3.2 20.6 + - + +
36J TRP* 3.7 20.0 - - + -
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Residues in contact with VAL 27 (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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7J ASN 2.7 30.0 + - - +
9J ILE* 3.8 32.3 - - + -
25J VAL* 3.8 15.3 - - + -
26J GLU* 1.3 82.3 - - - +
28J GLU* 1.3 65.4 + - - +
30J GLY* 3.8 13.5 - - - +
31J LYS 3.4 24.9 - - - +
32J ILE* 4.5 6.1 - - - -
33J LYS* 4.8 1.1 - - - +
511J ILE* 4.5 13.2 - - + -
514J PRO* 6.2 2.9 - - + -
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Residues in contact with GLU 28 (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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27J VAL* 1.3 78.2 - - - +
29J GLY* 1.3 66.4 + - - +
31J LYS* 3.1 21.3 + - + +
33J LYS* 3.6 39.9 + - + +
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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