Contacts of the helix formed by residues 525 - 531 (chain A) in PDB entry 3ZNS
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 ASP 525 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 1.3 87.9 - - - +
526A SER* 1.3 67.7 + - - +
527A VAL* 2.7 41.5 + - - +
528A MET* 3.3 24.5 + - - +
529A LEU 4.4 0.7 + - - -
548A ILE* 4.5 5.0 - - - +
568A ARG* 3.0 39.9 + - - +
640A TRP* 3.4 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 4.3 7.5 - - - -
525A ASP* 1.3 75.6 + - - +
527A VAL* 1.3 58.7 + - - +
528A MET 3.1 0.2 - - - -
529A LEU* 2.8 53.4 + - - +
530A LYS* 3.8 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASP* 2.7 31.6 + - - +
526A SER* 1.3 73.8 + - - +
528A MET* 1.3 58.4 + - - +
530A LYS* 3.3 28.9 + - + +
568A ARG* 5.3 3.8 - - - +
633A HIS 5.3 0.3 - - - +
636A ASN* 4.5 26.7 - - + +
637A ALA* 3.9 6.8 - - - +
640A TRP* 4.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 4.8 1.8 - - + -
524A TYR* 4.2 3.4 - - - -
525A ASP 3.3 34.0 + - - +
526A SER 3.1 1.0 - - - -
527A VAL* 1.3 72.6 - - - +
529A LEU* 1.3 61.0 + - - +
530A LYS 3.2 2.2 + - - -
531A HIS* 3.7 7.8 + - - +
548A ILE* 3.8 11.7 - - + -
637A ALA* 3.8 19.4 - - - +
640A TRP* 3.8 29.4 - - + +
641A ALA* 4.1 5.4 - - - -
663A VAL 3.8 17.0 - - - +
664A VAL* 3.7 30.7 - - + -
665A ARG* 2.8 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 3.7 18.2 - - - +
526A SER* 2.8 40.5 + - - +
528A MET* 1.3 71.4 - - - +
530A LYS* 1.3 60.9 + - + +
531A HIS 3.2 4.4 + - - -
532A GLN* 3.0 26.8 - - - +
545A ALA* 3.4 39.3 - - + +
548A ILE* 3.7 18.8 - - + -
549A GLN* 3.7 24.0 - - + +
665A ARG* 3.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A SER* 3.9 9.9 - - - +
527A VAL* 3.3 25.6 - - + +
528A MET 3.2 1.2 - - - -
529A LEU* 1.3 75.8 - - + +
531A HIS* 1.3 58.9 + - - +
532A GLN* 3.0 15.4 + - - +
630A ASN* 4.1 4.0 + - - -
633A HIS* 3.4 58.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A MET 3.7 2.1 + - - +
529A LEU 3.2 1.4 - - - -
530A LYS* 1.3 73.0 - - - +
532A GLN* 1.3 61.8 + - - +
543A GLU* 3.5 25.3 + - - -
628A ILE* 3.6 24.1 + - + +
630A ASN* 5.0 0.2 - - - -
633A HIS* 4.4 4.2 - - - +
634A SER* 2.7 35.0 + - - -
637A ALA* 3.8 22.6 - - + +
665A ARG* 2.8 45.4 + - - +
666A PRO* 3.9 14.3 - - + +
679A PHE* 5.3 0.6 + - - -
681A PHE* 3.5 35.7 - + - -
----------------------------------------------------------
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