Contacts of the strand formed by residues 338 - 345 (chain A) in PDB entry 1YCH
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 VAL 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG 2.9 16.6 + - - +
306A ALA* 3.1 7.7 - - + -
307A VAL* 2.9 24.8 + - - +
336A ASN* 5.8 1.1 - - - +
337A LYS* 1.3 77.9 - - - +
339A GLY* 1.3 63.1 + - - +
364A ILE* 4.4 2.0 - - - -
365A GLU* 3.5 24.5 - - - +
367A ILE* 3.7 30.1 - - + -
393A ILE* 4.9 11.9 - - + -
396A ARG* 3.9 32.5 - - + +
397A ILE* 5.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA* 5.5 0.2 - - - -
307A VAL 3.2 14.4 - - - -
308A LEU* 5.3 1.1 - - - -
338A VAL* 1.3 76.1 - - - +
340A LEU* 1.3 64.1 + - - +
364A ILE* 3.9 12.5 - - - +
365A GLU 2.9 12.5 + - - -
366A LEU* 3.5 6.7 - - - -
367A ILE* 2.7 33.5 + - - +
393A ILE* 5.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.7 24.7 - - + -
307A VAL 3.4 5.9 + - - +
308A LEU* 3.3 30.2 - - + +
309A VAL 3.0 24.3 + - - -
339A GLY* 1.3 74.9 - - - +
341A ALA* 1.3 70.0 + - - +
342A PHE* 4.5 1.0 - - + -
359A LEU* 4.0 7.1 - - - +
366A LEU* 4.3 7.1 - - - +
367A ILE* 4.3 4.9 - - + -
368A ALA* 4.1 24.0 - - + +
371A GLY* 3.8 9.6 - - - -
372A PRO* 3.5 30.7 - - + -
389A LEU* 4.3 8.5 - - + -
393A ILE* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL 3.3 6.7 - - - +
340A LEU* 1.3 76.6 - - - +
342A PHE* 1.3 60.7 + - - +
352A GLN* 2.7 26.3 + - - +
355A LEU* 3.6 28.0 - - + -
356A GLU* 3.9 16.9 + - + +
359A LEU* 4.0 9.4 - - + +
366A LEU* 5.0 2.0 - - - +
371A GLY* 3.5 2.8 - - - -
372A PRO* 3.2 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.1 7.2 - - + -
259A TYR* 4.0 6.7 - - + -
266A THR* 3.4 34.3 - - + -
269A MET* 4.0 16.6 - - + -
270A ALA* 3.7 26.9 - - + -
273A LEU* 3.6 21.8 - - + -
308A LEU* 4.2 11.2 - - + -
309A VAL 3.2 18.2 + - - -
310A GLY* 3.1 23.0 - - - -
311A SER 3.0 23.4 + - - +
340A LEU* 4.5 3.4 - - + -
341A ALA* 1.3 80.5 - - - +
343A GLY* 1.3 60.6 + - - +
352A GLN* 3.3 8.0 - - - +
355A LEU* 3.8 4.8 - - - +
372A PRO* 3.3 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR* 3.8 11.2 - - - -
269A MET* 3.4 10.8 - - - -
311A SER 3.2 15.5 - - - -
342A PHE* 1.3 80.2 - - - +
344A ALA* 1.3 62.7 + - - -
352A GLN* 3.9 1.9 + - - -
372A PRO 3.4 4.4 + - - -
373A THR* 3.3 14.3 + - - -
374A VAL 3.3 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER* 4.0 12.8 - - - -
266A THR* 3.3 12.4 + - - +
269A MET* 3.4 13.9 - - + +
311A SER 4.0 0.8 + - - +
312A PRO* 3.3 19.5 - - - +
313A THR* 3.4 7.3 + - - +
343A GLY* 1.3 75.1 - - - -
345A TYR* 1.3 66.4 + - - +
373A THR* 5.4 0.2 + - - -
374A VAL* 3.2 14.4 - - + +
376A TRP 4.4 3.4 - - - +
701A FMN 3.7 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 3.8 16.8 - - + -
344A ALA* 1.3 78.8 - - - +
346A GLY* 1.3 60.2 + - - +
347A TRP 3.6 26.5 - - - -
348A GLY 5.1 0.9 - - - -
349A GLY* 3.8 15.5 - - - -
373A THR* 3.4 41.3 - - + +
374A VAL 3.1 13.8 + - - -
375A GLN* 3.3 43.0 + - + +
376A TRP 2.9 24.4 + - - -
701A FMN 3.4 18.1 - - - +
----------------------------------------------------------
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