Contacts of the strand formed by residues 370 - 374 (chain A) in PDB entry 2BV5
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 ILE 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A THR* 3.1 17.7 - - - +
369A PRO* 1.3 94.4 - - + +
371A ILE* 1.3 69.0 + - - +
372A VAL* 4.2 5.6 - - + -
428A LYS* 3.2 14.1 - - + -
430A TYR* 3.8 26.9 - - + -
454A VAL* 4.2 7.4 - - + +
457A ALA* 3.8 15.5 - - + +
458A ALA* 3.6 40.2 - - + +
461A GLU* 4.7 4.5 - - + +
468A ILE* 3.6 26.4 - - + +
469A ILE 3.1 12.8 + - - -
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.8 24.7 - - + -
360A TRP* 4.5 4.7 - - + -
363A VAL* 4.1 8.1 - - + -
368A THR* 4.3 3.4 - - + -
370A ILE* 1.3 78.8 - - - +
372A VAL* 1.3 63.9 + - - +
387A TYR* 3.6 18.8 - - - +
427A LEU* 4.0 30.7 - - + -
428A LYS 2.9 8.3 + - - +
429A HIS* 3.8 19.7 - - + -
430A TYR* 2.8 34.5 + - - +
469A ILE* 3.2 22.7 - - + +
471A HIS* 4.0 15.9 - - + -
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 4.2 1.8 - - + -
371A ILE* 1.3 78.3 - - - +
373A MET* 1.3 60.2 + - - +
374A ILE* 4.1 13.2 - - + -
430A TYR* 3.5 7.2 - - + +
432A PHE* 5.5 0.2 - - + -
450A LEU* 3.9 31.4 - - + -
454A VAL* 3.9 30.3 - - + -
468A ILE* 4.1 14.1 - - + -
469A ILE 2.7 11.3 + - - +
470A VAL* 3.3 8.7 - - + +
471A HIS* 2.9 28.9 + - - +
482A PHE* 4.0 22.2 - - + -
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Residues in contact with MET 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ILE 4.0 0.2 - - - -
372A VAL* 1.3 72.9 - - - +
374A ILE* 1.3 61.9 + - - +
375A THR* 3.8 9.4 - - - +
380A MET* 3.5 33.2 - - - -
384A CYS* 3.7 18.6 - - - -
387A TYR* 3.8 0.7 - - - -
388A TRP* 3.6 30.3 - - + -
429A HIS* 3.8 19.3 - - + +
430A TYR 2.8 15.2 + - - +
431A TRP* 3.7 20.0 - - + +
432A PHE* 2.9 30.1 + - - +
471A HIS* 3.4 29.8 - - + +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL* 4.1 12.1 - - + -
373A MET* 1.3 75.8 - - - +
375A THR* 1.3 62.9 + - - +
432A PHE* 3.9 22.2 - - + -
435A TRP* 3.7 32.5 - - + -
447A LEU* 5.6 1.8 - - + -
450A LEU* 4.9 2.0 - - + -
470A VAL* 3.9 16.2 - - + -
471A HIS 2.8 15.0 + - - +
472A SCY 3.7 7.4 - - + +
478A ARG* 3.3 45.6 + - + +
479A THR* 4.2 1.6 - - - +
482A PHE* 3.6 34.1 - - + -
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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