Contacts of the strand formed by residues 459 - 464 (chain A) in PDB entry 1ZJK
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 GLN 459 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 3.0 21.7 + - + +
457A PRO 3.3 2.5 - - - +
458A TRP* 1.3 84.4 - - - +
460A VAL* 1.3 73.7 + - - +
469A ALA* 3.6 16.1 - - - +
470A GLY 4.0 7.1 + - - +
499A MET* 3.5 21.5 - - - +
500A GLY 4.5 2.9 + - - -
501A THR 5.6 2.2 - - - +
571A SER* 2.5 41.8 + - - +
572A GLY* 4.9 0.5 - - - -
573A TRP* 3.7 32.6 - - + -
585A LEU* 4.1 15.0 - - + +
635A GLY* 5.4 0.9 - - - -
636A ALA 5.7 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TRP 3.3 16.8 - - - +
459A GLN* 1.3 86.1 - - - +
461A LEU* 1.3 66.0 + - - +
462A ILE* 4.2 5.6 - - + -
469A ALA* 3.3 6.8 - - - +
470A GLY 3.0 34.9 + - - +
471A ALA 4.1 2.5 - - - -
472A LEU* 3.7 20.4 - - + +
478A VAL* 4.2 21.5 - - + -
497A ILE* 3.7 30.5 - - + -
498A ARG 3.6 5.8 - - - +
499A MET* 4.4 11.2 - - + -
573A TRP* 4.7 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A VAL* 1.3 73.9 - - - +
462A ILE* 1.3 66.2 + - - +
463A LEU* 3.9 34.9 + - + -
467A THR* 5.2 0.4 - - + -
468A ALA 3.7 10.5 - - - +
496A ASP 3.6 4.2 - - - +
497A ILE* 3.6 1.7 - - - -
498A ARG* 2.9 48.3 + - + +
501A THR* 6.2 2.9 - - + -
504A ARG* 3.9 38.1 - - + +
573A TRP* 4.2 22.4 - - + -
575A LEU* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A VAL* 4.2 9.6 - - + -
461A LEU* 1.3 76.4 - - - +
463A LEU* 1.3 64.9 + - - +
466A THR* 3.0 32.7 - - + +
467A THR* 3.4 2.3 - - - -
468A ALA* 2.9 34.0 + - + +
469A ALA 3.4 29.2 - - - +
470A GLY 4.2 1.1 - - - +
478A VAL* 4.4 5.8 - - + -
480A THR* 3.8 13.9 - - + +
485A VAL* 4.5 6.5 - - + -
495A LEU* 3.9 23.8 - - + -
496A ASP 3.7 1.6 - - - -
497A ILE* 4.6 10.3 - - + -
536A ILE* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 4.0 24.9 - - + -
462A ILE* 1.3 80.4 - - - +
464A GLY* 1.3 63.3 + - - +
465A GLY 3.9 0.7 + - - -
466A THR 3.3 8.1 - - - +
467A THR* 4.1 22.2 - - + +
494A ALA 3.5 3.1 - - - +
495A LEU* 3.7 7.4 - - - +
496A ASP* 2.8 40.5 + - + +
498A ARG* 3.5 44.6 - - - +
504A ARG 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 1.3 76.9 - - - +
465A GLY* 1.3 67.0 + - - +
466A THR 3.2 4.2 + - - +
467A THR* 5.3 1.0 + - - -
494A ALA 3.5 8.5 - - - -
496A ASP* 4.3 5.3 - - - +
----------------------------------------------------------
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