Contacts of the strand formed by residues 666 - 672 (chain B) in PDB entry 1VDV
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 666 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 3.9 31.0 - - + -
608B VAL 3.8 4.9 - - - +
609B THR* 4.2 9.6 - - + -
654B VAL 4.2 7.2 - - - +
655B PHE* 3.5 25.1 - - + -
656B ALA* 2.8 30.2 + - - +
664B GLY 3.8 6.5 - - - +
665B HIS* 1.3 72.7 - - - +
667B ILE* 1.3 53.7 + - - +
668B GLY 3.7 19.5 - - - +
807B LEU* 4.1 31.4 - - + +
811B ALA* 5.6 0.2 - - + -
835B ILE* 4.1 6.1 - - + -
5015B GOL 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B VAL* 2.9 15.5 + - + +
609B THR 4.1 3.1 - - - -
610B SER* 3.8 20.0 - - - +
617B ILE* 4.1 13.7 - - + -
620B ILE* 3.7 30.1 - - + -
634B PHE* 4.9 4.0 - - + -
636B SER* 4.2 9.4 - - - -
655B PHE* 3.5 17.7 - - - +
656B ALA* 3.8 14.5 + - + +
660B VAL* 3.8 23.8 - - + -
665B HIS 3.7 9.6 - - - +
666B ILE* 1.3 74.4 - - - +
668B GLY* 1.3 59.3 + - - +
687B VAL* 4.4 15.5 - - + -
689B TYR* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 3.7 0.9 - - - -
608B VAL* 2.8 26.7 + - - +
634B PHE* 4.2 6.7 - - - -
635B LEU 3.1 15.0 - - - -
655B PHE* 3.8 13.2 - - - -
666B ILE* 3.6 10.7 - - - +
667B ILE* 1.3 81.5 - - - +
669B ALA* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU* 3.7 33.7 - - + -
606B ARG 3.3 13.0 - - - +
607B LEU* 4.3 3.6 - - + -
608B VAL* 3.9 2.2 - - - -
633B CYS 3.9 0.3 - - - +
634B PHE* 3.3 7.0 - - - -
635B LEU* 2.7 44.1 + - + +
655B PHE* 4.3 11.9 - - + -
668B GLY* 1.3 77.0 - - - +
670B VAL* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B PHE 3.6 0.5 - - - +
605B LEU* 3.3 5.2 - - - +
606B ARG* 2.9 33.7 + - - +
608B VAL* 4.0 3.3 - - + +
631B PHE* 3.8 18.6 - - + -
633B CYS 3.4 2.7 - - - +
634B PHE* 4.0 16.4 - - + -
669B ALA* 1.3 77.0 - - - +
671B VAL* 1.3 76.8 + - - +
672B ALA* 4.8 0.9 - - + -
678B ALA* 4.0 18.4 - - - +
681B ALA* 3.8 23.3 - - + -
682B ALA* 3.8 24.9 - - + +
685B VAL* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 3.6 39.5 - - + -
604B PHE 3.1 9.4 - - - +
605B LEU* 4.6 5.4 - - + -
632B VAL* 2.8 29.5 + - + +
633B CYS* 2.9 34.1 + - - +
635B LEU* 4.0 9.4 - - + -
670B VAL* 1.3 81.2 - - - +
672B ALA* 1.3 64.6 + - - +
815B ALA* 3.9 25.6 - - + -
819B THR* 4.5 4.9 - - + -
823B VAL* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 3.7 5.1 - - - +
604B PHE* 3.0 31.5 + - - +
630B GLY 3.2 17.0 - - - +
631B PHE* 4.3 3.8 - - - -
632B VAL* 3.9 7.2 - - - -
670B VAL* 4.8 1.6 - - + -
671B VAL* 1.3 75.8 - - - +
673B ASP* 1.3 62.2 + - - +
674B THR 3.3 3.9 + - - +
677B HIS* 3.9 9.9 - - + +
678B ALA* 3.5 33.4 - - + +
----------------------------------------------------------
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