Contacts of the strand formed by residues 289 - 294 (chain B) in PDB entry 2ZL6
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 LYS 289 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 2.8 33.3 + - - +
248A LEU* 4.8 4.9 - - - +
249A PRO* 4.7 5.1 - - - +
247B PRO* 6.3 0.4 - - - -
284B LEU 5.1 1.1 - - - -
285B SER* 2.8 27.8 + - - +
286B HIS 3.9 9.4 - - - +
287B VAL 3.3 9.4 - - - +
288B ALA* 1.3 81.8 - - - +
290B ILE* 1.3 70.8 + - - +
304B LEU* 4.2 24.8 - - + +
318B ILE 4.7 2.8 - - - +
319B GLY 3.1 4.8 + - - +
320B PHE* 3.4 19.6 + - - -
370B VAL* 4.7 6.3 - - + +
371B GLY 3.1 14.6 - - - +
372B VAL* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS* 1.3 82.1 - - - +
291B ARG* 1.3 64.3 + - - +
292B GLY 6.0 0.2 - - - +
299B ILE* 5.0 3.8 - - + -
301B LEU* 4.4 12.1 - - + -
304B LEU* 4.9 2.0 - - - -
320B PHE* 3.5 30.3 - - + -
321B PRO* 3.7 10.8 - - + -
330B ILE* 4.2 15.3 - - + -
332B MET* 3.9 15.5 - - + -
343B TYR* 3.8 35.2 - - + -
359B ILE* 4.4 8.7 - - + -
369B TYR 5.6 0.4 - - - +
370B VAL* 3.4 7.4 - - - +
371B GLY* 2.8 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 1.3 75.9 - - - +
292B GLY* 1.3 61.2 + - - +
299B ILE* 5.3 0.2 - - - -
301B LEU* 3.4 11.7 - - - +
302B THR* 2.9 41.0 + - - +
303B GLU 3.5 13.9 - - - +
304B LEU* 2.9 37.3 + - + +
305B ASP* 3.8 5.3 + - - +
306B GLY* 3.8 15.4 - - - +
335B PHE* 4.0 27.7 - - - -
368B ASN* 2.9 33.2 + - - +
369B TYR 3.3 14.1 + - - -
370B VAL* 3.9 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 5.5 0.8 - - - +
291B ARG* 1.3 79.1 - - - +
293B THR* 1.3 64.3 + - - -
294B SER 4.1 0.5 + - - -
299B ILE* 4.0 13.7 - - - +
300B ASN 3.1 13.5 - - - -
301B LEU* 4.1 0.4 - - - -
302B THR* 4.3 5.2 - - - -
367B GLY 3.9 0.7 - - - +
368B ASN* 3.4 6.5 + - - -
369B TYR* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY* 1.3 72.0 - - - -
294B SER* 1.3 71.1 + - - +
295B ASN* 3.9 0.6 + - + -
298B VAL 3.7 1.0 - - - +
299B ILE* 3.4 1.9 - - - -
300B ASN* 2.9 39.5 + - - +
302B THR* 6.0 1.2 - - - +
367B GLY* 3.3 17.0 - - - +
368B ASN* 3.0 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY 4.1 1.0 + - - -
293B THR* 1.3 83.4 - - - +
295B ASN* 1.3 57.7 + - - +
296B GLY* 2.8 12.2 + - - -
298B VAL 3.3 5.8 - - - -
299B ILE* 3.9 16.7 - - - +
361B ALA* 3.7 6.6 - - - +
364B ILE* 2.7 30.9 + - - -
365B GLY 3.4 17.2 + - - -
366B SER* 3.1 4.2 - - - -
367B GLY 2.8 27.5 + - - -
369B TYR* 4.1 1.7 - - - -
----------------------------------------------------------
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