Contacts of the strand formed by residues 732 - 741 (chain A) in PDB entry 3RLN
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 732 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A VAL* 4.1 23.6 - - + -
691A PHE 3.3 6.5 - - - +
692A GLU* 3.9 30.3 - - + +
693A VAL 4.6 0.2 - - - +
731A ASP* 1.3 82.8 - - - +
733A LEU* 1.3 63.5 + - - +
734A LYS 4.0 0.2 - - - -
760A VAL* 3.6 6.2 - - - +
761A ILE* 2.8 49.7 + - + +
763A THR* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A GLY 3.4 3.1 - - - +
690A VAL* 3.3 3.2 - - - -
691A PHE* 2.7 39.4 + - + +
693A VAL* 3.7 15.5 - - + -
705A TYR* 3.8 35.7 - - + -
707A ILE* 4.6 8.3 - - + -
716A VAL* 4.6 7.6 - - + -
725A ILE* 3.8 13.2 - - + -
727A CYS* 3.3 24.0 - - + -
732A LYS* 1.3 71.7 - - - +
734A LYS* 1.3 60.1 + - - +
735A LEU* 3.5 24.5 + - + +
758A ILE* 3.8 24.7 - - + -
759A LYS 4.0 1.1 - - - -
760A VAL* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ASN* 6.3 1.0 - - - +
689A GLY* 3.4 7.1 + - - +
690A VAL* 4.0 26.1 - - + +
732A LYS 3.9 1.0 + - - -
733A LEU* 1.3 70.6 - - - +
735A LEU* 1.3 64.6 + - - +
736A THR* 4.9 6.0 + - - +
757A HIS* 3.7 2.3 + - - +
758A ILE* 3.5 4.2 - - - -
759A LYS* 2.8 76.3 + - + +
761A ILE* 4.4 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 4.8 3.4 - - + +
688A ASN* 3.3 6.3 - - - +
689A GLY 2.7 35.4 + - - +
691A PHE* 3.9 20.4 - - + -
716A VAL* 4.3 13.2 - - + -
733A LEU* 3.7 35.2 - - + +
734A LYS* 1.3 77.0 + - - +
736A THR* 1.3 65.2 + - - +
738A PHE* 3.7 42.4 - - + -
750A LEU* 4.0 21.5 - - + -
757A HIS 3.6 2.2 - - - -
758A ILE* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.4 8.3 - - + +
601A HIS* 3.5 39.7 - - + +
641A PHE* 5.9 1.6 - - + -
688A ASN* 3.5 20.1 + - - +
734A LYS* 4.9 8.0 + - - +
735A LEU* 1.3 76.1 + - - +
737A CYS* 1.3 71.9 + - + +
738A PHE* 3.4 3.3 + - - -
756A SER* 3.4 0.7 - - - -
757A HIS* 2.8 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A HIS* 3.7 20.4 - - + -
614A LYS* 3.6 22.4 - - - -
641A PHE* 3.6 32.1 - - + -
686A PHE* 4.2 12.6 - - - -
687A VAL 3.3 4.9 + - - +
688A ASN* 3.0 15.1 + - - -
736A THR* 1.3 74.7 - - + +
738A PHE* 1.3 57.1 + - - +
753A VAL* 3.3 10.5 - - - +
755A HIS* 4.1 11.9 - - - +
756A SER* 2.8 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 3.3 4.0 - - - -
687A VAL* 2.8 40.2 + - - +
716A VAL* 3.7 28.3 - - + -
718A VAL* 4.1 4.0 - - + -
722A LEU* 4.0 2.9 - - + -
735A LEU* 3.7 28.9 - - + -
736A THR 3.7 8.3 - - - -
737A CYS* 1.3 76.9 - - - +
739A GLU* 1.3 60.3 + - - +
740A LEU 3.7 0.5 + - - -
750A LEU* 4.4 15.7 - - + -
751A ARG 3.6 20.6 - - - +
752A SER* 3.6 27.6 - - - -
756A SER* 3.7 13.9 - - - -
757A HIS 3.7 17.7 - - - -
758A ILE* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLY* 5.2 6.2 - - - -
685A SER 3.5 9.4 + - - +
686A PHE* 3.7 26.8 - - + -
737A CYS 4.2 1.0 + - - -
738A PHE* 1.3 71.9 - - - +
740A LEU* 1.3 73.9 + - - +
741A ALA* 3.5 7.0 + - + +
750A LEU* 3.3 3.3 - - - -
751A ARG* 2.7 44.2 + - + +
753A VAL* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A LEU* 3.1 60.3 - - + +
679A CYS* 4.9 0.4 - - - -
681A GLN* 3.7 29.6 - - + +
683A LYS 4.1 0.2 - - - +
684A GLY* 3.4 13.2 - - - -
685A SER* 3.0 18.8 + - - +
687A VAL* 4.5 2.5 - - + -
714A MET* 4.4 6.5 - - + -
738A PHE 3.7 1.6 + - - -
739A GLU* 1.3 77.3 - - - +
741A ALA* 1.3 62.3 + - - +
742A PRO* 3.1 33.1 - - + +
748A GLY* 5.1 2.0 - - - -
749A GLU 3.5 7.9 - - - +
750A LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A GLU* 3.5 6.8 + - + +
740A LEU* 1.3 71.9 - - - +
742A PRO* 1.3 69.9 - - - +
743A LYS* 3.4 4.3 + - - +
748A GLY* 3.3 0.5 - - - -
749A GLU* 2.7 30.8 + - - +
751A ARG* 3.3 50.5 - - - +
----------------------------------------------------------
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