Contacts of the strand formed by residues 383 - 392 (chain A) in PDB entry 2Y33
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 ARG 383 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA 3.6 1.4 - - - +
302A SNC 3.3 4.6 - - - -
303A TYR* 2.9 65.1 + - + -
329A TYR* 3.8 12.9 - - - -
331A ASN* 3.6 15.7 - - - +
334A TRP* 3.8 14.8 - - + -
341A GLY* 2.7 41.5 + - - -
343A LEU* 4.1 10.5 - - - +
358A PRO* 3.8 13.3 - - + +
376A VAL* 3.9 12.3 - - - +
379A ALA* 4.2 6.3 - - + -
381A ALA 3.9 3.6 - - - +
382A THR* 1.3 73.5 - - - +
384A TYR* 1.3 63.0 + - - +
385A ALA* 4.4 5.9 - - - +
901A UN9 2.7 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLY 6.0 0.2 - - - -
226A VAL* 3.2 31.6 - - + -
227A ARG* 4.0 29.3 - - + +
230A HIS* 3.4 30.2 + - + +
235A PHE* 4.2 9.6 - + - -
301A ALA 3.4 3.8 - - - -
302A SNC 3.1 33.6 - - + -
329A TYR* 4.0 1.4 - - - -
330A LEU* 3.6 28.9 + - + -
331A ASN* 2.9 36.7 + - - +
382A THR* 3.3 24.6 - - + +
383A ARG* 1.3 73.5 - - - +
385A ALA* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET 3.9 0.7 - - - +
300A VAL* 3.5 4.0 - - - +
301A ALA* 2.8 41.3 + - + +
303A TYR* 6.0 0.4 - - + -
327A ILE* 4.0 9.2 - - + -
328A TYR 3.4 8.1 - - - -
329A TYR* 3.8 26.2 - - + -
330A LEU* 4.0 1.3 - - - +
383A ARG* 4.4 4.7 - - - +
384A TYR* 1.3 78.1 - - - +
386A ILE* 1.3 63.3 + - - +
387A THR* 4.2 2.9 - - - +
901A UN9 4.1 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 3.7 24.5 - - + -
226A VAL* 4.1 11.2 - - + -
269A ILE* 4.3 14.1 - - + -
272A LEU* 3.6 33.4 - - + -
273A MET* 5.7 0.7 - - + -
276A MET* 4.2 3.8 - - + +
298A ALA* 4.0 25.8 - - + -
299A MET 3.6 2.7 - - - +
300A VAL* 4.2 19.3 - - + -
326A CYS 3.6 1.0 - - - +
327A ILE* 3.4 2.3 - - - -
328A TYR* 2.9 35.1 + - - +
330A LEU* 4.1 12.1 - - + -
385A ALA* 1.3 78.5 - - - +
387A THR* 1.3 63.7 + - - +
388A VAL* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS 3.9 1.0 - - - +
298A ALA* 3.4 0.5 - - - -
299A MET* 2.7 54.1 + - - +
301A ALA* 5.9 1.4 - - - +
325A THR* 4.0 13.2 - - + -
326A CYS 3.2 9.4 - - - +
327A ILE* 3.5 21.1 - - + +
385A ALA* 5.2 2.4 - - - +
386A ILE* 1.3 74.6 + - - +
388A VAL* 1.3 71.5 + - - +
389A TRP* 3.7 44.2 - - + -
901A UN9 5.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A MET* 4.6 11.4 - - + -
276A MET* 4.0 26.5 - - + -
295A ARG* 3.4 34.8 - - + -
296A THR* 4.1 8.1 - - - +
297A LYS 4.3 0.7 - - - +
298A ALA* 3.8 25.6 - - + +
324A VAL 4.1 0.3 - - - +
325A THR* 4.0 0.5 - - - -
326A CYS* 2.9 34.8 + - + +
386A ILE* 5.1 1.8 - - + -
387A THR* 1.3 80.2 - - - +
389A TRP* 1.3 65.7 + - - +
390A TYR* 3.9 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TRP* 4.0 22.9 - + - -
295A ARG* 3.2 4.9 - - - +
296A THR* 3.0 55.4 + - + +
299A MET* 3.9 28.0 - - + -
315A ASP* 3.0 28.8 + - - -
322A ARG* 3.4 48.5 - - + +
324A VAL 3.4 4.3 - - - +
325A THR* 3.1 21.9 + - - +
368A SER* 3.8 12.1 - - - -
387A THR* 3.7 25.1 - - + -
388A VAL* 1.3 74.8 - - - +
390A TYR* 1.3 61.7 + - - +
391A PHE* 4.0 0.5 + - - -
901A UN9 4.2 22.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A MET* 3.2 23.9 - - + +
277A ASP* 2.5 33.4 + - - -
280A ILE* 3.5 38.6 - - + -
292A ILE* 3.8 35.2 - - + -
294A GLY 3.5 1.8 - - - -
295A ARG* 3.6 19.8 - - + -
322A ARG* 3.6 3.0 - - - -
323A CYS* 2.9 26.9 + - - -
324A VAL* 2.9 25.4 + - + +
326A CYS* 4.1 19.7 - - + -
388A VAL* 3.9 18.1 - - + +
389A TRP* 1.3 74.8 - - - +
391A PHE* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.1 24.3 - - - +
293A ASN* 3.2 19.2 + - - +
294A GLY* 2.8 13.8 + - - +
295A ARG* 3.6 38.4 - - - -
296A THR* 3.7 22.2 - - + -
320A ASP* 4.0 5.4 - - - -
321A GLY 3.3 14.6 - - - +
322A ARG* 3.7 19.1 - - + -
323A CYS* 4.2 2.2 - - - -
389A TRP 4.6 0.2 - - - -
390A TYR* 1.3 73.4 - - - +
392A ASP* 1.3 57.9 - - - +
396A ARG* 3.5 54.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER 4.9 0.2 - - - +
290A TYR* 3.3 23.6 - - + -
291A LYS* 3.0 32.9 + - - +
293A ASN* 4.2 0.4 - - - -
321A GLY 2.9 14.3 + - - +
323A CYS* 3.9 20.5 - - + -
391A PHE* 1.3 72.7 - - - +
393A ALA* 1.3 64.6 + - - +
394A ASP* 3.4 10.8 + - - +
395A GLU* 2.9 33.8 + - + +
396A ARG* 3.0 26.2 + - - +
----------------------------------------------------------
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