Contacts of the strand formed by residues 698 - 704 (chain A) in PDB entry 2OR4
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 ASN 698 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LYS 3.3 19.8 + - - -
208A VAL* 3.6 19.7 - - + +
209A PHE 3.0 19.6 + - - -
212A ASN* 3.4 5.8 - - - +
546A PHE* 3.5 21.8 - - - -
695A SER* 3.1 20.7 + - - +
696A SER 3.6 0.4 - - - -
697A HIS* 1.3 83.3 - - + +
699A LYS* 1.3 64.9 + - - +
700A TYR* 2.9 15.3 + - - +
701A ALA* 2.9 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 3.7 31.2 - - + +
212A ASN* 2.9 18.4 + - - +
259A LEU 5.0 1.4 + - - -
260A ASN* 6.0 1.8 - - - +
261A LEU* 4.6 22.4 - - - +
262A ASN* 4.7 6.0 - - - +
263A GLY 5.1 0.8 - - - +
427A GLY 5.6 0.6 + - - -
428A LEU* 4.9 2.8 - - - +
517A SER* 2.9 47.1 + - - +
518A GLY* 4.0 6.1 - - - +
522A GLU* 3.5 12.1 + - - -
687A TYR* 3.6 10.9 + - - +
694A PRO* 3.7 10.2 - - + +
695A SER 3.6 7.7 + - - -
698A ASN* 1.3 72.1 + - - +
700A TYR* 1.3 58.5 + - - +
701A ALA 3.3 1.1 + - - +
1801A QUS 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 4.3 1.6 - - - -
209A PHE* 3.5 49.6 - + + -
210A ARG* 3.7 10.0 + - - -
514A LYS 5.6 0.7 - - - +
516A GLY* 4.8 2.4 + - - -
517A SER 3.8 12.3 + - - +
518A GLY* 3.7 24.7 - - - -
546A PHE* 3.5 53.7 - + + -
552A TYR* 3.4 15.2 + + - -
698A ASN* 2.9 8.4 + - - +
699A LYS* 1.3 78.7 - - - +
701A ALA* 1.3 59.0 + - - +
702A GLY 4.1 1.0 + - - -
1801A QUS 2.6 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLY* 3.7 2.6 - - - -
546A PHE* 3.9 19.1 - - + -
694A PRO* 3.4 5.5 - - - +
695A SER* 2.8 37.8 + - - -
698A ASN* 2.9 27.0 + - + +
700A TYR* 1.3 79.9 - - - +
702A GLY* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LYS* 3.3 33.5 + - - +
515A LEU 3.7 7.6 - - - -
516A GLY* 3.5 25.7 - - - +
693A ALA 3.5 1.6 - - - -
695A SER* 5.2 0.3 - - - -
700A TYR 4.1 0.8 + - - -
701A ALA* 1.3 79.8 - - - +
703A GLU* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LYS* 4.3 4.2 - - - -
610A LYS* 4.0 15.4 + - - -
692A TYR* 3.2 8.0 - - - -
693A ALA 2.8 35.2 + - - +
695A SER* 4.2 23.8 + - - +
702A GLY* 1.3 75.9 - - - +
704A SER* 1.4 90.4 + - - +
706A PRO* 3.8 11.1 - - + +
709A TYR* 3.8 51.3 - - + -
710A ASP* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LYS* 4.1 9.3 - - - +
607A TYR* 3.5 51.5 + - - +
610A LYS* 4.4 15.2 + - - +
611A ILE* 5.1 2.3 - - - +
691A ILE 3.1 6.3 - - - -
692A TYR* 4.6 0.9 - - - -
703A GLU* 1.4 90.8 + - - +
705A PHE* 1.3 73.8 + - - +
706A PRO 3.1 2.6 - - - -
709A TYR* 4.0 4.9 - - - +
----------------------------------------------------------
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