Contacts of the strand formed by residues 688 - 693 (chain A) in PDB entry 1R4X
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 GLU 688 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A PRO* 5.3 0.2 - - - -
686A ALA 3.9 3.1 + - - +
687A TYR* 1.3 75.4 - - - +
689A VAL* 1.3 72.3 + - - +
690A LEU* 3.4 19.6 + - + +
710A VAL* 3.2 3.5 - - - +
711A ALA* 2.8 45.3 + - + +
714A LYS* 5.1 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A MET* 3.4 32.8 - - + +
683A PRO* 4.8 11.1 - - + +
687A TYR 4.2 0.6 + - - -
688A GLU* 1.3 79.3 - - - +
690A LEU* 1.3 64.2 + - - +
691A CAS 4.1 6.1 - - - +
692A TYR* 3.6 34.5 - - + +
708A THR* 3.8 9.2 - - + -
709A LEU 3.6 10.8 - - - +
710A VAL* 4.1 14.4 - - + -
724A PHE* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A HIS* 3.7 33.9 - - + +
688A GLU* 3.7 40.6 - - - +
689A VAL* 1.3 75.9 - - - +
691A CAS 1.3 83.6 + - + +
709A LEU* 2.7 31.9 + - + +
711A ALA* 4.0 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CAS 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A GLU* 4.0 39.7 - - + +
689A VAL* 3.9 1.6 - - - +
690A LEU* 1.3 109.4 + - + +
692A TYR* 1.3 71.9 + - - +
693A VAL* 5.0 3.1 - - + +
707A TYR 4.2 0.2 - - - +
708A THR* 3.6 4.0 - - - +
709A LEU* 2.9 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A GLU* 4.9 3.3 - - - +
678A THR* 3.8 28.0 - - + -
679A VAL 3.2 23.3 - - - -
680A GLN* 3.5 17.5 - - + +
681A MET 3.1 27.3 + - - -
689A VAL* 3.6 20.7 - - + +
690A LEU 6.0 0.2 - - - -
691A CAS 1.3 77.2 - - - +
693A VAL* 1.3 62.4 + - - +
694A PRO* 3.6 8.7 - - + +
707A TYR 3.5 2.7 - - - -
708A THR* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A VAL* 4.2 11.4 - - + -
622A GLU* 3.8 35.0 - - + +
623A PHE* 4.1 24.9 - - + -
678A THR* 4.5 1.3 - - - -
691A CAS 5.0 2.5 - - + -
692A TYR* 1.3 74.4 - - - +
694A PRO* 1.3 75.3 - - + +
705A THR 6.0 0.4 - - - +
706A CYS* 3.3 4.6 - - - +
707A TYR* 2.9 56.6 + - + +
----------------------------------------------------------
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