Contacts of the strand formed by residues 31 - 39 (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 LYS 31 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.4 5.9 - - - +
28F GLU* 3.1 30.8 + - + +
29F GLY* 3.1 11.1 - - - +
30F GLY* 1.3 84.1 - - - +
32F ILE* 1.3 69.3 + - - +
33F LYS* 3.2 1.7 + - - +
508F GLY* 3.3 30.1 - - - +
509F THR 3.2 3.6 - - - +
510F PRO* 4.1 9.2 - - + -
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Residues in contact with ILE 32 (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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25F VAL* 4.1 15.0 - - + -
26F GLU 3.5 5.4 - - - -
27F VAL* 4.5 3.1 - - + -
31F LYS* 1.3 74.2 - - - +
33F LYS* 1.3 56.4 + - - +
34F ASN 3.4 24.9 - - - +
506F LEU* 3.1 40.8 - - + +
507F ILE* 3.7 5.3 - - - +
508F GLY* 2.8 24.4 + - - -
509F THR* 2.8 40.7 + - - +
511F ILE* 3.5 25.4 - - + -
520F ILE* 3.7 20.4 - - + -
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F GLU* 2.7 49.2 + - + +
27F VAL 4.8 0.2 - - - -
28F GLU* 3.6 46.9 + - + +
31F LYS 3.2 1.3 + - - +
32F ILE* 1.3 73.0 - - - +
34F ASN* 1.3 61.7 + - + +
507F ILE* 3.9 16.6 - - - +
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Residues in contact with ASN 34 (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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25F VAL* 3.5 1.0 - - - -
26F GLU* 3.2 35.8 + - - +
32F ILE* 3.4 8.0 - - - +
33F LYS* 1.3 81.8 - - + +
35F ALA* 1.3 83.2 + - - +
36F TRP* 3.7 30.1 - - + -
493F ARG* 2.8 27.9 + - - +
499F LEU* 4.2 8.5 - - - +
507F ILE* 4.0 6.3 - - - -
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Residues in contact with ALA 35 (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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24F GLU 3.6 2.2 - - - -
25F VAL* 4.0 5.2 - - + -
32F ILE* 4.3 0.7 - - + -
34F ASN* 1.3 93.6 + - - +
36F TRP* 1.3 61.7 + - - +
493F ARG* 2.7 31.4 + - - -
503F GLU* 3.6 22.2 - - - +
506F LEU* 3.8 40.4 - - + -
507F ILE* 4.0 3.8 - - + +
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Residues in contact with TRP 36 (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 12.8 - - + -
22F ARG 4.1 0.2 - - - +
23F ILE* 3.8 7.7 - - - +
24F GLU* 3.0 62.9 + - + +
25F VAL* 4.2 1.8 - - - -
26F GLU* 3.7 38.4 - - + -
34F ASN* 3.7 24.0 - - + -
35F ALA* 1.3 83.8 - - - +
37F SER* 1.3 60.4 + - - +
38F MET* 3.8 9.0 + - + +
349F HIS* 3.8 28.9 + + + -
354F TYR* 4.0 22.6 - + + -
493F ARG* 3.1 26.9 - - - +
503F GLU* 3.5 6.3 - - - -
506F LEU* 6.2 0.4 - - - -
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Residues in contact with SER 37 (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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21F LEU* 3.7 14.2 - - - +
22F ARG 4.2 1.6 - - - -
23F ILE* 4.3 8.5 - - - +
36F TRP* 1.3 70.9 - - - +
38F MET* 1.3 61.1 + - - +
39F SER 4.0 0.2 - - - -
354F TYR* 3.4 16.3 - - - -
355F SER* 3.9 9.4 + - - -
490F LEU* 2.8 32.9 + - - +
491F GLY 4.5 0.4 - - - -
492F PRO* 4.7 1.4 - - - +
502F VAL* 3.7 26.0 - - - +
503F GLU* 2.9 17.6 + - - +
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Residues in contact with MET 38 (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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21F LEU* 3.4 4.8 - - - +
22F ARG* 2.7 63.3 + - + +
24F GLU* 3.4 33.9 - - - +
36F TRP* 4.1 8.1 - - + +
37F SER* 1.3 75.5 + - - +
39F SER* 1.3 60.6 - - - +
40F THR* 3.7 4.5 - - + +
327F TRP* 4.6 1.1 - - + -
348F PHE* 3.6 44.0 - - + -
349F HIS* 3.9 16.2 - - + +
354F TYR* 3.4 33.4 - - + +
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Residues in contact with SER 39 (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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20F HIS 3.7 5.8 - - - -
21F LEU* 4.1 8.3 - - - +
37F SER 4.0 0.2 + - - -
38F MET* 1.3 70.5 - - - +
40F THR* 1.3 58.8 + - - +
41F LEU 3.8 1.8 - - - -
327F TRP* 3.6 5.9 - - - -
354F TYR 4.2 0.2 + - - -
355F SER* 3.3 16.9 + - - -
356F TRP* 3.3 26.5 + - - -
357F MET* 3.4 27.3 - - - +
490F LEU 4.3 3.8 + - - -
531F ILE* 3.7 18.6 - - - +
535F VAL* 3.7 17.3 - - - -
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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