Contacts of the strand formed by residues 626 - 632 (chain A) in PDB entry 3OJX
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 HIS 626 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ARG 5.5 1.1 - - - -
521A PRO* 3.6 22.8 - - + +
522A PHE 5.2 1.2 + - - -
526A THR* 3.2 29.6 - - + +
527A PRO 2.9 11.6 + - - +
528A VAL* 3.7 0.2 - - - -
529A ILE* 2.8 26.5 + - - +
624A GLY 4.3 0.7 - - - -
625A ALA* 1.3 73.8 - - - +
627A ILE* 1.3 63.3 + - - +
628A TYR* 3.4 30.6 + - + +
670A GLY 3.2 28.0 + - - -
671A ARG* 3.5 24.0 - - + +
673A SER* 5.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ILE* 3.4 19.5 - - + +
531A VAL* 5.2 0.9 - - + -
620A ILE* 3.4 37.2 - - + -
625A ALA 5.0 2.0 - - - +
626A HIS* 1.3 79.0 - - - +
628A TYR* 1.3 66.0 + - - +
629A VAL* 4.3 6.5 - - + -
644A PHE* 3.9 34.3 - - + -
666A LEU* 4.8 9.4 - - + -
671A ARG 2.8 15.5 + - - +
672A TYR* 3.4 31.1 - - + -
673A SER* 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 3.5 19.7 - + + -
519A ARG 2.7 32.8 + - - -
520A LEU* 3.3 0.6 - - - -
521A PRO* 3.2 22.4 - - + +
528A VAL* 4.0 22.2 - - + -
529A ILE 2.8 15.0 + - - +
530A MET* 3.5 1.1 - - - -
531A VAL* 2.8 32.7 + - - +
540A PHE* 3.6 11.9 - - + -
543A PHE* 3.4 26.5 - + - -
626A HIS* 3.4 35.8 + - + -
627A ILE* 1.3 79.0 - - - +
629A VAL* 1.3 61.0 + - - +
673A SER* 3.2 28.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 3.9 2.0 - - - -
531A VAL* 3.2 16.4 - - + +
540A PHE* 4.3 1.1 - - - -
627A ILE* 4.3 5.6 - - + -
628A TYR* 1.3 80.1 - - - +
630A CYS* 1.3 62.7 + - - +
631A GLY 4.3 0.2 - - - -
636A MET* 3.9 28.5 - - + -
637A ALA* 4.2 16.4 - - + +
640A VAL* 4.1 14.6 - - + -
672A TYR* 3.8 35.4 - - + +
673A SER 3.0 6.7 + - - +
674A LEU* 3.5 11.0 - - + +
675A ASP 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 4.6 0.7 - - + -
531A VAL 3.0 8.7 + - - -
532A GLY* 4.0 7.4 - - - -
533A PRO* 4.0 2.3 - - - +
536A GLY* 3.2 33.0 - - - +
539A PRO* 3.8 21.1 - - + -
540A PHE* 4.0 7.2 - - + -
629A VAL* 1.3 76.0 - - - +
631A GLY* 1.3 58.7 + - - +
636A MET* 3.4 14.4 - - - +
675A ASP* 3.5 11.2 - - + +
677A TRP* 3.2 45.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A PRO 6.0 0.2 - - - -
536A GLY* 5.2 1.8 - - - -
629A VAL 4.3 0.2 - - - -
630A CYS* 1.3 77.8 - - - +
632A ASP* 1.3 62.7 + - - -
633A ALA 3.5 0.2 + - - -
636A MET* 3.9 4.2 - - - +
637A ALA* 5.5 0.4 - - - -
674A LEU* 5.0 1.9 - - - +
675A ASP 3.0 8.5 + - - -
676A VAL* 3.1 9.5 - - - +
677A TRP* 2.8 45.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A GLY* 1.3 70.1 - - - -
633A ALA* 1.3 55.9 + - - +
634A ARG* 3.6 7.8 + - - -
635A ASN* 2.9 43.3 + - - +
636A MET* 3.7 6.9 + - + +
637A ALA* 2.8 33.6 + - - +
678A SER* 2.9 35.9 + - - +
753A NAP 3.1 41.0 + - + +
----------------------------------------------------------
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