Contacts of the strand formed by residues 605 - 612 (chain V) in PDB entry 3RWR
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 SER 605 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598V GLU* 5.1 9.6 - - - -
599V LYS 4.2 8.3 - - - -
600V ASN* 4.8 12.1 - - - -
601V LEU 5.0 0.4 - - - +
603V ASP 4.1 5.3 + - - -
604V VAL* 1.3 85.7 - - - +
606V PHE* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 606 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561V MET* 4.9 19.7 - - + -
598V GLU* 3.3 10.2 - - - +
599V LYS* 2.7 76.9 + - + -
601V LEU* 4.4 15.5 - - + -
604V VAL* 4.4 13.9 - - + -
605V SER* 1.3 80.5 - - - +
607V ARG* 1.3 78.0 + - - +
608V LEU* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561V MET* 6.1 0.2 - - - +
596V PHE* 3.3 51.4 - - + -
598V GLU* 3.4 26.3 + - + +
606V PHE* 1.3 95.6 - - - +
608V LEU* 1.3 70.7 + - - +
609V GLY 4.5 9.2 - - - +
610V SER* 4.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555V GLU* 3.4 13.7 - - - +
561V MET* 5.9 7.6 - - + -
566V TYR* 2.5 40.5 + - + +
569V GLU* 5.3 9.2 - - + +
570V LEU* 4.2 8.5 - - + -
584V TYR* 4.3 12.6 - - + -
597V PHE* 3.0 55.1 + - + +
598V GLU 4.1 0.2 - - - -
599V LYS* 3.6 34.1 - - + +
606V PHE* 5.1 5.4 - - + -
607V ARG* 1.3 79.0 - - - +
609V GLY* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 609 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555V GLU* 3.4 7.9 - - - -
566V TYR* 3.4 9.2 - - - -
595V PHE 4.0 0.3 - - - +
596V PHE* 3.6 2.1 - - - +
597V PHE* 3.0 46.9 + - - -
607V ARG* 4.5 2.7 - - - +
608V LEU* 1.3 87.1 - - - +
610V SER* 1.3 60.3 + - - -
611V PHE* 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555V GLU* 2.9 20.1 + - - +
594V TYR* 4.2 18.7 - - - -
595V PHE 3.7 3.6 - - - -
596V PHE* 4.3 12.1 - - - +
607V ARG* 4.8 9.4 - - - -
609V GLY* 1.3 73.7 - - - -
611V PHE* 1.3 71.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 611 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532V PHE* 4.4 13.5 - + - -
534V ILE* 4.2 18.4 - - + -
545V GLY* 5.3 0.2 - - - -
546V THR 4.1 13.9 - - - -
547V VAL* 3.3 45.3 - - + -
551V GLU* 4.3 4.7 - - - -
552V ILE* 5.6 2.7 - - + -
555V GLU* 4.6 16.8 - - + -
570V LEU* 6.4 1.6 - - + -
594V TYR* 3.1 12.4 - - - -
595V PHE* 2.6 51.5 + + + +
597V PHE* 5.5 5.4 - + - -
609V GLY* 4.5 4.5 - - - -
610V SER* 1.3 103.9 - - - +
612V ASN* 1.3 58.1 + - - +
613V LEU* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 612 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544V THR 4.3 1.7 - - - +
545V GLY* 4.6 4.3 - - - -
592V SER 3.7 4.4 + - - -
593V CYS* 3.0 12.5 + - + +
594V TYR* 3.0 58.9 + - - -
611V PHE* 1.3 72.7 - - - +
613V LEU* 1.3 64.9 + - - +
614V GLU* 4.0 6.9 + - - +
----------------------------------------------------------
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