Contacts of the helix formed by residues 521 - 527 (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 PHE 521 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A TYR* 3.4 30.3 - - + -
451A ASN* 3.5 11.1 + - + -
515A LEU* 3.9 26.9 - - + -
516A GLY 3.1 32.5 - - - -
517A SER* 3.6 19.1 - - - -
519A ASN* 3.7 19.7 - - + -
520A ASP* 1.3 76.8 - - - +
522A GLU* 1.3 70.6 + - - +
523A VAL 3.3 0.4 - - - -
524A PHE* 3.1 5.4 + - - +
525A PHE* 3.0 30.2 + - + +
526A GLN* 4.9 1.1 - - - -
532A SER* 4.4 8.5 - - - -
533A GLY 5.4 2.0 - - - +
534A ARG* 3.4 41.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY* 3.2 21.5 + - - +
428A LEU* 3.6 16.6 - - + +
432A THR* 4.9 4.7 + - - -
517A SER* 2.4 34.6 + - - +
519A ASN 3.1 16.2 + - - +
520A ASP 3.1 1.0 - - - -
521A PHE* 1.3 88.1 - - - +
523A VAL* 1.3 61.6 + - - +
526A GLN* 2.8 44.1 + - + +
687A TYR* 2.7 40.1 + - + -
699A LYS* 3.5 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 5.4 1.3 - - - +
428A LEU* 5.5 0.2 - - - +
431A SER* 4.0 10.1 - - - +
432A THR* 4.0 29.3 + - + +
435A ALA* 3.5 35.7 - - + -
436A GLU* 5.4 0.2 - - + -
520A ASP 4.2 3.3 + - - +
522A GLU* 1.3 83.0 + - - +
524A PHE* 1.3 82.4 + - + +
527A ARG* 3.2 40.0 + - + +
528A LEU* 3.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 4.2 11.0 - - + -
421A TRP* 3.6 31.2 - + - -
431A SER* 4.2 4.3 - - - -
434A TRP* 3.9 12.1 - + - -
435A ALA* 4.2 4.9 - - + -
442A LEU* 3.9 24.5 - - + -
449A TYR* 3.6 44.0 - + + -
520A ASP 3.4 24.7 - - - -
521A PHE 3.1 5.7 + - - +
523A VAL* 1.3 90.8 - - + +
525A PHE* 1.3 52.4 + - - +
528A LEU* 3.5 9.0 - - + +
529A GLY 3.1 8.0 + - - -
530A ILE* 2.8 52.4 + - + +
532A SER* 4.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A THR* 4.0 15.0 - - - -
515A LEU* 3.9 27.6 - - + -
521A PHE* 3.0 19.3 + - + +
522A GLU 4.3 0.2 - - - +
524A PHE* 1.3 76.6 - - - +
526A GLN* 1.4 82.3 + - + +
529A GLY* 3.1 23.9 + - - -
530A ILE 3.3 17.7 - - - -
532A SER* 3.7 19.1 - - - +
672A GLU* 3.5 35.2 - - + -
676A ILE* 4.2 0.3 - - - +
689A HIS* 3.8 16.3 - + - -
692A TYR* 3.7 44.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU 3.0 21.4 + - - -
516A GLY* 2.9 31.0 + - - +
522A GLU* 2.8 31.2 + - + +
525A PHE* 1.4 93.2 - - + +
527A ARG* 1.4 55.5 + - - +
676A ILE* 3.9 0.6 - - - +
686A PHE 4.1 0.9 - - - -
687A TYR* 3.9 20.0 - - + +
688A ARG 2.8 30.7 + - - -
689A HIS* 3.3 15.8 + - - +
692A TYR* 3.1 23.1 - - - +
693A ALA* 3.6 5.0 - - - +
694A PRO* 3.8 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 2.8 28.3 + - - +
264A ALA 3.5 9.9 + - - -
271A GLY* 4.2 4.6 + - - -
432A THR* 3.5 9.3 - - - +
436A GLU* 2.7 43.5 + - - +
522A GLU 3.6 1.0 + - - -
523A VAL* 3.2 31.2 + - + +
526A GLN* 1.4 80.8 - - - +
528A LEU* 1.3 72.8 + - + +
529A GLY 3.7 0.2 - - - -
676A ILE* 3.6 6.1 - - - +
686A PHE* 3.4 49.1 - - - +
688A ARG* 2.9 42.0 + - - +
----------------------------------------------------------
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