Contacts of the strand formed by residues 21 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ASP* 4.4 2.0 - - - -
13B PRO* 4.0 7.2 - - - +
14B ILE* 3.3 29.0 + - + +
17B ILE* 3.5 22.8 - - + +
19B GLY 3.6 3.8 + - - -
20B HIS* 1.3 73.0 - - - +
22B ARG* 1.3 66.7 + - - +
23B ILE* 4.1 17.3 - - + -
37B SER* 3.7 20.0 - - - +
38B MET 3.4 25.8 - - - +
39B SER* 4.1 9.2 - - - +
40B THR* 5.0 1.6 - - - -
490B LEU* 3.8 24.2 - - + -
524B VAL* 4.1 15.7 - - + -
529B PRO* 4.6 0.4 - - + -
531B ILE* 3.7 12.8 - - + -
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Residues in contact with ARG 22 (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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88A GLY 4.1 12.5 + - - -
10B VAL* 3.8 23.1 - - + +
11B VAL 3.5 4.9 - - - -
12B ASP* 3.1 42.0 + - + +
21B LEU* 1.3 75.7 - - - +
23B ILE* 1.3 63.5 + - - +
24B GLU* 2.7 35.9 + - + -
38B MET* 2.7 57.2 + - - +
40B THR* 4.1 3.8 - - + -
348B PHE* 3.5 37.1 - - - -
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Residues in contact with ILE 23 (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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9B ILE 3.8 0.9 - - - +
10B VAL* 3.2 4.0 - - - +
11B VAL* 2.6 41.1 + - + +
14B ILE* 3.4 32.8 - - + -
21B LEU* 4.1 15.3 - - + -
22B ARG* 1.3 76.7 - - - +
24B GLU* 1.3 65.0 + - - +
25B VAL* 3.7 24.2 - - + -
36B TRP 3.8 4.0 - - - +
37B SER* 4.3 20.6 - - - +
502B VAL* 5.1 4.7 - - + -
506B LEU* 3.9 15.9 - - + -
520B ILE* 4.0 13.7 - - + -
524B VAL* 3.7 21.1 - - + -
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Residues in contact with GLU 24 (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 LYS* 4.6 13.0 - - + +
9B ILE 3.4 6.1 - - - +
10B VAL* 4.2 10.1 - - + +
22B ARG* 2.7 38.0 + - - +
23B ILE* 1.3 77.1 - - - +
25B VAL* 1.3 64.8 + - - +
36B TRP* 3.0 47.0 + - + +
38B MET* 3.4 22.0 - - - +
348B PHE* 4.8 1.7 - - - -
349B HIS* 2.6 33.0 + - - -
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Residues in contact with VAL 25 (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 LYS* 2.9 12.7 - - - +
9B ILE* 2.8 63.9 + - + +
23B ILE* 3.7 20.9 - - + -
24B GLU* 1.3 78.5 - - - +
26B GLU* 1.3 59.4 + - - +
27B VAL* 3.8 14.8 - - + -
32B ILE* 4.1 13.5 - - + -
34B ASN 3.5 8.3 - - - +
35B ALA* 4.0 6.5 - - + -
36B TRP* 4.2 2.2 - - - -
506B LEU* 4.0 16.8 - - + -
520B ILE* 3.8 18.2 - - + -
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Residues in contact with GLU 26 (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 ASN 3.3 7.6 - - - +
8B LYS* 3.1 32.1 + - - +
25B VAL* 1.3 72.2 - - - +
27B VAL* 1.3 60.1 + - - +
32B ILE* 3.5 4.0 - - - -
33B LYS* 2.7 72.1 + - + +
34B ASN* 3.2 20.1 + - + +
36B TRP* 3.7 20.3 - - + -
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Residues in contact with VAL 27 (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 ASN 2.7 29.5 + - - +
9B ILE* 3.8 31.0 - - + -
25B VAL* 3.8 14.6 - - + -
26B GLU* 1.3 82.5 - - - +
28B GLU* 1.3 65.6 + - - +
30B GLY* 3.8 13.7 - - - +
31B LYS 3.4 24.5 - - - +
32B ILE* 4.5 6.3 - - - -
33B LYS* 4.8 1.1 - - - +
511B ILE* 4.5 13.7 - - + -
514B PRO* 6.2 3.1 - - + -
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Residues in contact with GLU 28 (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 VAL* 1.3 77.6 - - - +
29B GLY* 1.3 66.1 + - - +
31B LYS* 3.1 21.4 + - + +
33B LYS* 3.6 41.8 + - + +
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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