Contacts of the strand formed by residues 302 - 310 (chain A) in PDB entry 3ZJU
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 GLY 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 5.3 0.2 - - - +
281A PHE* 3.8 7.2 - - - -
301A LYS* 1.3 79.3 - - - +
303A VAL* 1.3 69.8 + - - +
321A TRP* 4.1 6.6 - - - -
322A ALA 3.1 14.4 - - - -
348A PHE* 3.8 11.4 - - - -
352A TYR* 2.9 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASN* 4.6 0.9 - - - +
277A GLU* 3.7 39.0 - - + +
278A LEU* 3.9 34.4 - - + +
281A PHE* 3.8 27.7 - - + -
301A LYS* 6.6 0.4 - - - -
302A GLY* 1.3 79.4 - - - +
304A ASP* 1.3 76.9 + - - +
321A TRP* 3.4 9.8 - - - -
322A ALA* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASN* 3.5 12.8 + - - -
277A GLU* 5.1 0.8 + - - -
278A LEU* 5.0 0.2 - - - +
303A VAL* 1.3 88.3 - - - +
305A THR* 1.3 78.7 + - - +
306A GLY* 2.9 19.2 + - - -
307A PHE 4.8 1.6 - - - +
308A LYS* 5.5 5.5 + - - -
319A PRO* 4.6 7.6 - - - +
320A VAL 3.2 10.9 + - - +
321A TRP* 3.5 41.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 5.0 0.2 - - + -
267A LEU* 3.6 24.5 - - + -
268A ALA* 4.3 6.5 - - + -
271A ALA* 3.6 26.7 - - - +
275A ASN* 4.3 8.3 + - - +
278A LEU* 4.1 20.2 - - + -
303A VAL 4.6 0.2 - - - +
304A ASP* 1.3 78.5 + - - +
306A GLY* 1.3 54.8 + - - -
307A PHE* 3.1 26.4 + - - +
320A VAL* 2.8 25.8 + - - +
321A TRP 4.3 1.6 - - - -
322A ALA* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASN* 5.0 1.1 - - - +
304A ASP* 2.9 17.1 + - - -
305A THR* 1.3 76.6 - - - +
307A PHE* 1.3 64.5 + - - +
308A LYS* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.7 25.4 - - + -
238A ASP* 3.3 43.5 - - + -
239A TYR* 3.7 23.6 - + + -
267A LEU* 4.0 20.2 - - + -
270A LYS* 4.3 11.2 - - + -
271A ALA* 3.8 31.4 - - + -
304A ASP* 4.8 0.9 - - - +
305A THR* 3.1 20.0 + - - +
306A GLY* 1.3 80.1 - - - +
308A LYS* 1.3 64.9 + - - +
309A ALA 4.1 0.2 - - - -
319A PRO* 3.8 0.9 - - - +
320A VAL* 3.1 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.3 4.8 - - - +
237A ASN* 3.1 43.4 + - + +
304A ASP* 5.5 4.9 + - - -
306A GLY* 3.6 13.6 + - - +
307A PHE* 1.3 82.2 - - - +
309A ALA* 1.3 59.7 + - - +
317A GLU* 3.9 31.4 + - + +
318A ILE 3.3 10.1 - - - +
319A PRO* 4.2 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 4.1 11.9 - - + -
235A ASN 3.4 9.6 - - - +
236A VAL* 4.4 5.6 - - + +
259A LEU* 3.8 29.4 - - + -
308A LYS* 1.3 74.2 - - - +
310A VAL* 1.3 62.6 + - - +
311A HIS 3.8 0.6 + - - -
317A GLU* 3.4 3.6 - - - -
318A ILE* 2.6 48.7 + - + +
320A VAL* 4.1 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 3.5 12.7 - - - +
235A ASN* 2.9 30.5 + - + +
237A ASN* 4.2 20.0 - - - +
309A ALA* 1.3 73.7 - - - +
311A HIS* 1.3 75.6 + - - +
312A PRO* 3.2 10.8 - - + +
315A GLY* 4.0 20.4 - - - +
316A GLU 3.9 2.5 - - - -
317A GLU* 4.3 15.7 - - + +
----------------------------------------------------------
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