Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 1ZHH
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 TYR 200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A HIS* 3.4 17.3 - - + -
199A THR* 1.3 80.2 - - - +
201A TYR* 1.3 62.1 + - - +
230A GLU* 3.4 29.2 + - + -
232A GLN* 3.3 35.0 - - + -
257A ASP* 3.2 45.5 - - + +
258A VAL* 4.2 2.2 - - - -
259A ASP* 3.0 30.0 + - - +
260A PHE 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR 4.0 1.6 - - - -
200A TYR* 1.3 75.6 - - - +
202A SER* 1.3 71.1 + - - +
203A VAL* 3.6 24.0 - - + -
219A PHE* 3.9 12.8 - + - -
220A ILE* 3.5 19.6 - - - +
223A VAL* 3.4 11.4 - - + +
224A ASN* 2.9 19.8 + - - -
229A PHE* 3.6 28.7 - - + -
230A GLU 3.2 11.3 + - - -
231A LEU* 3.5 27.1 - - + +
232A GLN* 2.8 26.5 + - - +
258A VAL* 3.8 6.0 - - - +
260A PHE* 3.3 48.7 - + + +
262A TYR* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 1.3 75.3 + - - +
203A VAL* 1.3 67.7 + - - +
204A LEU* 5.9 1.1 - - - -
231A LEU* 4.1 0.4 - - - -
232A GLN* 4.0 0.7 - - - +
233A SER* 2.7 35.5 + - - -
235A TYR* 6.1 0.2 - - - -
251A SER* 3.5 12.4 + - - -
255A HIS* 4.6 1.6 - - - +
258A VAL* 3.5 21.2 - - - +
260A PHE 3.2 6.1 + - - -
261A ILE* 3.3 18.0 - - - -
262A TYR 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 3.6 25.6 - - + -
202A SER* 1.3 79.3 - - - +
204A LEU* 1.3 77.9 + - - +
205A TYR* 3.9 26.9 - - + +
216A GLY* 4.9 0.7 - - - -
219A PHE* 4.9 0.2 - - + -
220A ILE* 3.8 16.6 - - + -
231A LEU* 3.6 7.6 - - + -
233A SER 3.0 6.9 + - - -
234A ALA* 3.2 11.8 - - + -
235A TYR* 3.0 25.8 + - - -
262A TYR* 3.3 28.3 - - + +
264A CYS* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 5.9 1.1 - - - -
203A VAL* 1.3 79.3 - - - +
205A TYR* 1.3 63.5 + - - +
235A TYR* 3.7 13.5 - - + -
237A THR* 4.6 2.7 - - + -
244A GLY* 3.9 13.5 - - - +
247A ALA* 3.8 31.4 - - + +
248A ALA* 4.2 7.4 - - + +
251A SER* 4.9 4.9 - - - +
261A ILE* 3.8 20.9 - - + -
262A TYR 2.8 11.5 + - - +
263A ALA* 3.5 4.8 - - + -
264A CYS* 3.0 27.2 + - - -
268A VAL* 3.7 22.0 - - + +
272A ALA* 3.8 29.4 - - + -
----------------------------------------------------------
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