Contacts of the strand formed by residues 21 - 28 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F ASP* 4.4 2.2 - - - -
13F PRO* 4.0 7.1 - - - +
14F ILE* 3.3 29.5 + - + +
17F ILE* 3.5 22.1 - - + +
19F GLY 3.6 4.0 + - - -
20F HIS* 1.3 73.0 - - - +
22F ARG* 1.3 65.6 + - - +
23F ILE* 4.1 18.4 - - + -
37F SER* 3.7 21.1 - - - +
38F MET 3.4 24.7 - - - +
39F SER* 4.1 9.0 - - - +
40F THR* 5.0 1.8 - - - -
490F LEU* 3.8 23.8 - - + -
524F VAL* 4.1 15.5 - - + -
529F PRO* 4.6 0.4 - - + -
531F ILE* 3.7 14.4 - - + -
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E GLY 4.1 13.3 + - - -
89E GLY* 4.9 0.2 - - - -
10F VAL* 3.8 22.6 - - + +
11F VAL 3.5 4.7 - - - +
12F ASP* 3.1 42.4 + - + +
21F LEU* 1.3 76.8 - - - +
23F ILE* 1.3 62.8 + - - +
24F GLU* 2.7 35.1 + - + -
38F MET* 2.7 56.8 + - - +
40F THR* 4.1 4.5 - - + -
348F PHE* 3.5 35.8 - - - -
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Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE 3.8 0.5 - - - +
10F VAL* 3.2 3.8 - - - +
11F VAL* 2.6 40.6 + - + +
14F ILE* 3.4 33.0 - - + -
21F LEU* 4.1 14.8 - - + -
22F ARG* 1.3 75.6 - - - +
24F GLU* 1.3 65.2 + - - +
25F VAL* 3.7 24.2 - - + -
36F TRP 3.8 4.0 - - - +
37F SER* 4.3 20.2 - - - +
502F VAL* 5.1 4.7 - - + -
506F LEU* 3.9 16.8 - - + -
520F ILE* 4.0 13.4 - - + +
524F VAL* 3.7 20.9 - - + -
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Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS* 4.6 13.4 - - + +
9F ILE 3.4 5.4 - - - +
10F VAL* 4.2 11.4 - - + -
22F ARG* 2.7 36.9 + - - +
23F ILE* 1.3 77.6 - - - +
25F VAL* 1.3 64.3 + - - +
36F TRP* 3.0 46.0 + - + +
38F MET* 3.4 21.9 - - - +
348F PHE* 4.8 1.7 - - - +
349F HIS* 2.6 32.5 + - - -
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS* 2.9 11.4 - - - +
9F ILE* 2.8 63.9 + - + +
23F ILE* 3.7 20.9 - - + -
24F GLU* 1.3 79.4 - - - +
26F GLU* 1.3 57.9 - - - +
27F VAL* 3.8 14.6 - - + -
32F ILE* 4.1 13.7 - - + -
34F ASN 3.5 8.7 - - - +
35F ALA* 4.0 6.1 - - + -
36F TRP* 4.2 2.9 - - - -
506F LEU* 4.0 17.0 - - + -
520F ILE* 3.8 18.6 - - + -
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Residues in contact with GLU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASN 3.3 7.4 - - - +
8F LYS* 3.1 30.9 + - - +
25F VAL* 1.3 73.2 - - - +
27F VAL* 1.3 58.0 + - - +
32F ILE* 3.5 3.3 - - - -
33F LYS* 2.7 72.3 + - + +
34F ASN* 3.2 19.7 + - + +
36F TRP* 3.7 20.3 - - + -
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASN 2.7 30.1 + - - +
9F ILE* 3.8 31.2 - - + -
25F VAL* 3.8 14.8 - - + -
26F GLU* 1.3 82.7 - - - +
28F GLU* 1.3 66.5 + - - +
30F GLY* 3.8 12.8 - - - +
31F LYS 3.4 24.5 - - - +
32F ILE* 4.5 6.7 - - - -
33F LYS* 4.8 0.7 - - - +
511F ILE* 4.5 13.9 - - + -
514F PRO* 6.2 3.1 - - + -
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 1.3 77.1 - - - +
29F GLY* 1.3 65.5 + - - +
31F LYS* 3.1 21.1 + - + +
33F LYS* 3.6 40.0 - - + +
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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