Contacts of the strand formed by residues 361 - 366 (chain A) in PDB entry 1ZXN
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 TRP 361 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 3.7 38.1 - + - -
274A TYR* 4.1 20.6 - + + -
275A LEU* 5.8 2.9 - - + -
300A CYS 3.6 1.0 - - - +
301A LEU* 3.9 1.8 - - - +
302A THR* 2.9 51.4 + - + +
303A MET 4.0 12.1 - - - +
304A SER* 4.1 1.6 - - - -
309A GLN* 3.0 47.2 + - + +
310A GLN 4.3 0.2 - - - -
311A ILE* 3.3 16.8 - - + +
360A MET* 1.3 74.6 - - - +
362A ILE* 1.3 63.0 + - - +
363A PHE* 3.2 41.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 5.6 4.0 - - + -
300A CYS 3.6 5.2 - - - +
301A LEU* 4.3 9.4 - - + -
308A PHE* 4.2 22.4 - - + -
309A GLN 2.7 9.2 + - - +
310A GLN* 3.2 6.5 - - + +
311A ILE 3.0 24.6 + - - +
326A VAL* 4.9 3.1 - - + +
329A VAL* 6.2 1.6 - - + -
330A ALA* 5.4 6.7 - - + +
333A ILE* 6.2 2.0 - - + -
360A MET* 3.8 5.8 - - + -
361A TRP* 1.3 74.3 - - - +
363A PHE* 1.3 62.4 + - - +
364A VAL* 4.0 12.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.5 10.4 - + + -
270A TYR* 5.4 1.8 - + - -
271A VAL* 3.6 44.4 - - + -
274A TYR* 4.1 18.4 - + + -
275A LEU* 6.2 1.6 - - + -
299A VAL* 3.3 6.5 - - - +
300A CYS* 2.8 47.6 + - + +
302A THR* 4.3 8.1 - - + -
311A ILE* 3.3 36.1 - - + +
361A TRP* 3.2 61.0 - + - -
362A ILE* 1.3 73.6 - - - +
364A VAL* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.9 3.8 - - - -
297A TRP* 3.9 32.5 - - + -
298A GLU 3.8 2.0 - - - -
299A VAL* 4.2 11.0 - - + -
311A ILE 3.0 7.0 + - - +
312A SER* 3.0 34.5 - - - -
313A PHE* 3.2 3.7 + - - -
325A HIS* 4.2 16.8 - - + +
326A VAL* 4.0 23.5 - - + +
329A VAL* 4.2 21.5 - - + -
362A ILE* 4.0 4.7 - - + -
363A PHE* 1.3 81.5 - - - +
365A ASN* 1.3 66.1 + - - +
366A ALA 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY 4.3 3.8 + - - -
249A SER* 3.2 50.3 + - - +
267A PHE* 3.5 34.4 - - + +
296A ARG 3.9 0.5 - - - +
297A TRP* 3.6 4.5 - - - -
298A GLU* 3.2 32.0 + - + +
313A PHE* 3.3 14.3 - - - +
316A SER 5.3 1.2 + - - -
364A VAL* 1.3 79.0 - - - +
366A ALA* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG 3.3 6.7 - - - +
297A TRP* 3.4 37.5 - - + -
313A PHE 3.1 13.2 + - - +
314A VAL* 3.6 1.2 - - - -
315A ASN 3.1 22.7 + - - -
316A SER 5.0 0.2 + - - -
325A HIS* 4.7 2.7 - - + -
364A VAL* 4.2 2.7 - - + -
365A ASN* 1.3 77.4 - - - +
367A LEU* 1.3 65.9 + - - +
368A ILE* 3.4 20.2 - - + -
----------------------------------------------------------
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