Contacts of the strand formed by residues 468 - 471 (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 468 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 3.0 21.6 + - + +
345A TYR* 3.1 26.9 - - + +
346A ILE 2.9 21.2 + - - -
369A PRO* 5.0 1.3 - - + -
370A ILE* 3.6 40.8 - - + +
372A VAL* 4.1 11.4 - - + -
454A VAL* 4.5 10.5 - - + -
458A ALA* 3.8 28.0 - - + -
465A CYS* 4.8 6.1 - - + -
466A ALA 4.2 6.7 - - - +
467A PRO* 1.3 71.0 - - - +
469A ILE* 1.3 69.1 + - - +
470A VAL* 3.6 8.0 + - + +
482A PHE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.4 24.0 - - + +
348A THR* 3.8 26.7 - - + -
359A PHE* 3.9 16.2 - - + -
362A MET* 4.0 18.2 - - + -
363A VAL* 3.7 33.7 - - + +
368A THR* 3.5 29.4 - - + +
370A ILE 3.1 6.9 + - - +
371A ILE* 3.2 11.7 - - + -
372A VAL* 2.7 31.9 + - - +
467A PRO 3.7 0.4 + - - -
468A ILE* 1.3 72.5 - - - +
470A VAL* 1.3 59.8 + - - +
471A HIS* 4.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 4.2 13.0 - - + -
346A ILE 2.8 9.8 + - - +
347A ALA* 3.5 2.9 - - - -
348A THR* 3.1 24.6 + - - +
372A VAL* 3.3 12.3 - - + +
374A ILE* 3.9 21.8 - - + -
468A ILE* 3.8 15.3 - - + +
469A ILE* 1.3 80.1 - - - +
471A HIS* 1.3 64.4 + - - +
479A THR* 3.6 26.0 - - + +
482A PHE* 4.0 32.3 - - + -
483A ILE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 3.1 27.1 - - + +
349A GLN 4.0 3.1 - - - +
350A GLY* 3.7 5.4 - - - -
351A PRO* 4.3 1.3 - - + -
359A PHE* 4.3 14.6 - + - -
371A ILE* 4.0 16.2 - - + -
372A VAL 2.9 10.7 + - - +
373A MET* 3.4 29.0 - - + +
374A ILE* 2.8 32.9 + - - +
384A CYS* 3.5 25.8 - - + -
387A TYR* 2.7 28.8 + + - -
469A ILE* 4.6 1.1 - - + -
470A VAL* 1.3 76.1 - - - +
472A SCY 1.6 61.7 + - - +
479A THR* 3.3 8.1 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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