Contacts of the strand formed by residues 630 - 636 (chain B) in PDB entry 4RS6
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 THR 630 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B PHE* 2.8 33.0 + - - +
628B ASP* 2.7 34.5 + - - +
629B HIS* 1.3 76.8 - - - +
631B LYS* 1.3 64.5 + - - +
645B TYR* 3.7 17.3 - - - +
646B ILE 3.1 9.0 - - - -
647B ASN 3.8 0.4 - - - -
648B GLU* 3.6 34.1 - - + +
672B ARG* 2.7 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B TRP* 4.2 26.2 - - + -
504B VAL 4.4 2.9 - - - -
505B THR 5.3 4.3 - - - -
622B GLN* 4.0 9.9 - - - +
623B VAL 3.2 9.0 - - - +
624B ASN* 3.4 38.4 - - - +
625B PHE* 4.6 1.3 - - - -
626B TYR* 6.0 1.0 - - - +
629B HIS* 3.8 26.8 + - - +
630B THR* 1.3 79.8 - - - +
632B ILE* 1.3 66.0 + - - +
633B ILE* 5.0 2.5 - - + -
644B THR 4.5 0.2 - - - -
645B TYR* 3.3 8.8 - - - -
646B ILE* 2.8 51.9 + - + -
650B ARG* 5.8 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 3.8 3.0 - - + +
622B GLN* 3.2 3.3 - - - +
623B VAL* 2.8 41.9 + - + +
625B PHE* 4.1 6.5 - - + -
631B LYS* 1.3 77.9 - - - +
633B ILE* 1.3 65.9 + - - +
634B ILE* 4.2 12.6 - - + -
643B LEU* 3.8 26.9 - - + -
644B THR 3.4 4.7 - - - +
645B TYR* 4.3 3.4 - - + -
669B LEU* 4.1 22.2 - - + -
672B ARG* 3.5 47.6 - - + +
673B MET* 3.6 9.2 - - + +
676B ALA* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B PHE* 4.5 10.3 - - + -
502B GLN 4.1 18.2 - - - +
503B TRP* 3.8 22.0 - - + -
620B THR* 4.3 9.6 - - + -
621B PHE 3.3 8.3 - - - +
622B GLN* 3.6 24.5 - - + +
631B LYS* 5.0 3.1 - - + -
632B ILE* 1.3 79.2 - - - +
634B ILE* 1.3 73.0 + - - +
635B CYS* 4.9 6.1 - - + +
642B LEU 3.9 0.5 - - - +
643B LEU* 3.2 3.6 - - - +
644B THR* 2.7 57.2 + - + +
646B ILE* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B VAL* 4.7 15.0 - - + -
478B VAL* 5.7 1.8 - - + -
479B LEU* 4.1 26.2 - - + -
619B GLY 4.1 1.2 - - - +
620B THR* 3.5 2.9 - - - +
621B PHE* 2.8 58.9 + - + +
632B ILE* 4.2 7.0 - - + -
633B ILE* 1.3 78.4 - - - +
635B CYS* 1.3 67.1 + - - +
641B TYR* 4.1 22.9 - - + -
642B LEU 3.2 11.2 - - - +
643B LEU* 3.6 29.8 - - + -
657B LEU* 5.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B PHE* 4.5 17.3 - - + -
502B GLN 5.8 1.6 - - - +
619B GLY 5.3 2.0 - - - -
620B THR* 4.3 23.8 - - + +
633B ILE* 5.0 6.1 - - + -
634B ILE* 1.3 78.0 - - - +
636B SER* 1.3 60.7 + - - +
637B GLN* 4.2 20.9 - - - -
641B TYR* 3.5 8.8 - - - -
642B LEU* 2.7 52.5 + - - +
644B THR* 5.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ASP 5.7 2.2 + - - -
619B GLY 6.1 0.6 - - - -
635B CYS* 1.3 79.1 - - - +
637B GLN* 1.3 63.1 + - - +
639B GLU* 4.7 10.7 + - - -
640B GLU 3.3 14.4 - - - -
641B TYR* 3.9 27.3 - - - -
----------------------------------------------------------
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