Contacts of the strand formed by residues 301 - 307 (chain A) in PDB entry 2XYN
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 GLU 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLY* 1.3 72.4 - - - +
302A VAL* 1.3 60.8 + - - +
303A TYR* 5.7 0.2 - - - -
317A LYS* 3.5 1.7 - - - +
318A THR* 2.8 66.3 + - + +
319A LEU* 5.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS* 3.8 3.1 - - - +
294A LEU* 2.8 44.4 + - + +
299A TYR* 3.5 31.0 - - + +
300A GLY 3.2 9.3 + - - +
301A GLU* 1.3 75.9 - - - +
303A TYR* 1.3 62.0 + - - +
315A ALA* 4.9 1.8 - - + -
316A VAL 3.4 22.2 - - - +
317A LYS* 3.9 6.1 - - + -
547A VX6 3.2 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A MET* 4.1 28.3 - - + -
292A HIS 3.2 19.7 - - - +
293A LYS* 4.2 3.4 - - - -
294A LEU* 3.9 6.1 - - - +
301A GLU 4.2 0.6 - - - -
302A VAL* 1.3 75.0 - - - +
304A VAL* 1.3 67.3 + - - +
305A GLY 3.7 0.2 + - - -
315A ALA* 3.7 1.0 - - - -
316A VAL* 2.9 32.7 + - - +
318A THR* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A MET* 3.8 4.4 - - - -
291A LYS* 3.2 25.4 + - + -
292A HIS* 3.0 58.0 + - + +
294A LEU* 3.9 18.0 - - + +
303A TYR* 1.3 74.2 - - - +
305A GLY* 1.3 63.0 + - - +
306A VAL* 6.0 1.6 - - + -
313A THR* 3.8 22.9 - - + -
314A VAL 3.6 9.6 - - - +
315A ALA* 4.6 0.2 - - - +
363A TYR* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 4.0 13.5 - - - -
289A THR 3.4 8.7 - - - -
290A MET* 4.5 0.7 - - - -
303A TYR 3.7 1.6 + - - -
304A VAL* 1.3 76.2 - - - +
306A VAL* 1.3 62.8 + - - +
313A THR* 3.4 5.2 - - - +
314A VAL* 2.5 53.0 + - - -
315A ALA* 4.5 0.2 - - - +
316A VAL* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 4.1 2.0 - - - +
289A THR* 2.7 52.2 + - + +
291A LYS* 5.2 10.8 - - + -
304A VAL* 6.0 2.0 - - + -
305A GLY* 1.3 77.2 - - - +
307A TRP* 1.3 72.4 + - - +
308A LYS* 3.2 7.8 + - - +
311A SER* 4.9 3.8 - - - -
312A LEU 3.6 12.8 - - - +
313A THR* 4.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 4.3 19.3 - - + -
287A ASP* 3.8 43.0 + - + +
288A ILE* 4.4 18.8 - - + +
305A GLY 4.0 1.0 - - - -
306A VAL* 1.3 70.0 - - - +
308A LYS* 1.3 62.8 + - - +
309A LYS* 3.9 8.8 - - + +
310A TYR* 3.7 25.8 - - + +
311A SER* 2.9 26.5 + - - -
312A LEU* 2.9 35.6 + - + +
314A VAL* 4.7 18.6 - - + +
348A LEU* 4.5 30.5 - - + -
349A GLY* 5.4 0.7 - - - -
360A VAL* 4.9 7.2 - - + -
----------------------------------------------------------
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