Contacts of the strand formed by residues 634 - 639 (chain F) in PDB entry 6V3O
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 634 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F ASN 5.6 3.2 + - - -
593F GLY 2.8 17.0 + - - +
594F LYS* 3.6 22.8 - - + +
595F GLN 3.1 23.4 + - - +
632F GLY 4.3 0.2 + - - -
633F VAL* 1.3 70.4 - - - +
635F LEU* 1.3 63.6 + - - +
636F THR* 3.7 6.1 + - - +
664F ILE 4.4 3.2 + - - -
665F ASN* 3.1 31.5 + - + +
666F GLY 4.8 0.4 - - - -
667F SER* 3.6 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 635 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578F VAL* 5.4 3.4 - - + -
582F PHE* 5.2 4.0 - - + -
595F GLN* 3.3 23.6 - - + +
597F VAL* 3.7 28.7 - - + -
621F GLN* 5.3 0.9 - - - +
624F MET* 3.7 43.5 - - + +
625F ALA* 4.1 8.5 - - + +
628F ALA* 4.0 17.0 - - + -
633F VAL* 3.3 5.1 + - + -
634F LYS* 1.3 74.3 - - - +
636F THR* 1.3 63.2 + - - +
637F LEU* 4.5 17.5 - - + -
663F THR* 4.2 15.2 - - - +
664F ILE 4.4 9.0 - - - +
665F ASN* 5.5 2.8 + - - -
667F SER* 4.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 636 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595F GLN 2.9 11.2 + - - -
596F GLN* 3.1 18.6 - - + +
597F VAL 2.9 25.3 + - - -
634F LYS* 4.4 9.0 + - - -
635F LEU* 1.3 74.0 - - - +
637F LEU* 1.3 74.6 + - - +
667F SER* 2.6 38.3 + - - +
668F ILE 4.3 0.2 - - - +
669F ARG* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 637 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597F VAL* 3.3 17.9 - - + +
599F VAL* 4.9 8.5 - - + -
621F GLN* 3.2 47.8 - - + +
624F MET* 4.2 22.4 - - + -
635F LEU* 4.2 14.1 + - + -
636F THR* 1.3 82.1 - - - +
638F PHE* 1.3 60.5 + - - +
639F HIS* 4.0 18.0 - - + +
659F GLN* 5.1 0.2 - - - +
663F THR* 4.5 23.5 + - + +
667F SER 4.8 3.0 + - - -
668F ILE* 3.9 4.3 - - + +
669F ARG 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 638 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F VAL* 3.5 30.5 - - + -
288F TRP* 3.6 28.9 - + - -
533F ILE* 3.8 10.1 - - + -
596F GLN* 3.5 18.4 - - - +
597F VAL 2.9 12.3 + - - +
598F MET* 3.3 40.5 - - + +
599F VAL* 3.0 25.8 + - - -
636F THR 4.0 0.2 + - - -
637F LEU* 1.3 71.9 - - - +
639F HIS* 1.3 63.4 + - - +
669F ARG* 3.5 37.5 - - + -
671F THR* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 639 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599F VAL* 4.0 9.8 - - + +
601F TYR* 2.6 34.7 + - + -
621F GLN* 3.5 12.8 - - - -
637F LEU* 4.0 16.6 - - + +
638F PHE* 1.3 74.6 - - - +
640F GLY* 1.3 56.6 + - - +
643F GLY* 5.9 0.2 - - - -
645F VAL* 3.9 18.7 - - + +
659F GLN* 3.3 29.6 + - - +
664F ILE* 6.1 1.0 - - - +
668F ILE* 4.0 26.2 - - + +
669F ARG 2.9 21.7 + - - +
670F VAL* 4.6 7.6 - - + +
671F THR* 2.3 35.6 + - - -
----------------------------------------------------------
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