Contacts of the strand formed by residues 360 - 366 (chain B) 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 MET 360 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 4.0 18.6 - - + -
302B THR 3.9 2.7 - - - -
304B SER* 3.5 6.1 - - - -
308B PHE* 3.6 9.4 - - + -
309B GLN 2.9 25.1 + - - +
330B ALA* 4.0 25.6 - - + +
333B ILE* 3.9 39.5 - - + -
334B VAL* 3.6 24.5 - - - -
356B VAL* 3.8 11.4 - - + +
357B LYS* 3.3 18.9 + - - +
358B ASN 3.4 0.2 - - - -
359B HIS* 1.3 80.1 - - - +
361B TRP* 1.3 59.8 + - - +
362B ILE* 3.9 6.5 - - + +
407B ILE* 4.5 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TRP* 3.8 34.1 - + - -
274B TYR* 4.1 15.9 - - + -
275B LEU* 4.4 9.4 - - + -
300B CYS 3.9 0.5 - - - +
301B LEU* 3.4 2.8 - - - +
302B THR* 2.8 69.3 + - + +
303B MET 4.5 6.1 - - - -
304B SER* 3.8 10.1 - - - -
309B GLN* 3.5 50.2 + - + +
311B ILE* 3.8 20.5 - - + +
360B MET* 1.3 73.2 - - - +
362B ILE* 1.3 65.5 + - - +
363B PHE* 3.4 29.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 3.8 9.4 - - + -
300B CYS 3.4 9.2 - - - +
301B LEU* 4.2 10.1 - - + -
308B PHE* 4.0 20.4 - - + -
309B GLN 2.9 16.9 + - - +
310B GLN* 3.2 11.6 - - + +
311B ILE 3.0 22.9 + - - -
326B VAL* 4.3 8.3 - - + +
329B VAL* 3.5 31.6 - - + -
330B ALA* 4.1 13.5 - - + +
333B ILE* 3.8 17.5 - - + -
360B MET* 4.6 3.8 - - + -
361B TRP* 1.3 75.5 - - - +
363B PHE* 1.3 69.0 + - - +
364B VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 3.7 19.0 - + + -
270B TYR* 5.4 1.1 - + - -
271B VAL* 3.7 38.8 - - + -
274B TYR* 3.9 14.6 - + + -
275B LEU* 4.1 11.0 - - + -
288B VAL* 6.2 0.2 - - + -
298B GLU 3.6 0.5 - - - +
299B VAL* 3.3 7.8 - - - +
300B CYS* 2.7 45.7 + - + +
301B LEU 5.6 0.2 - - - -
302B THR* 4.4 9.4 - - + -
311B ILE* 3.1 39.9 - - + -
361B TRP* 3.4 45.5 - + - -
362B ILE* 1.3 75.3 - - - +
364B VAL* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 3.8 4.2 - - - -
297B TRP* 3.8 35.0 - - + -
298B GLU 3.5 4.7 - - - +
299B VAL* 4.5 2.7 - - + -
311B ILE 2.9 10.5 + - - -
312B SER* 3.0 16.5 - - - -
313B PHE* 2.8 27.5 + - - +
325B HIS* 4.6 9.9 - - + +
326B VAL* 4.7 11.4 - - + -
329B VAL* 4.2 16.8 - - + -
362B ILE* 4.1 25.4 - - + -
363B PHE* 1.3 80.1 - - - +
365B ASN* 1.3 64.4 + - - +
366B ALA* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY 4.4 2.6 + - - -
249B SER* 3.0 53.1 + - - +
267B PHE* 3.8 29.8 - - + +
296B ARG 3.7 1.0 - - - +
297B TRP* 3.6 3.3 - - - -
298B GLU* 3.0 41.6 + - + +
313B PHE* 3.3 13.4 - - - +
316B SER 5.1 1.9 + - - -
364B VAL* 1.3 73.2 - - - +
366B ALA* 1.3 64.6 + - - +
367B LEU* 6.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG 3.3 5.2 - - - +
297B TRP* 3.6 31.9 - - + -
313B PHE 2.9 14.5 + - - +
314B VAL* 3.3 4.3 - - - -
315B ASN 2.8 25.1 + - - -
325B HIS* 4.9 3.1 - - + -
364B VAL* 4.3 3.8 - - + -
365B ASN* 1.3 79.6 + - - +
367B LEU* 1.3 65.8 + - - +
368B ILE* 3.3 20.0 - - + -
----------------------------------------------------------
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