Contacts of the strand formed by residues 335 - 339 (chain A) in PDB entry 1Y57
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 TYR 335 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.3 44.4 + - + -
267A LEU* 3.5 28.7 - - + -
269A LEU* 4.1 25.1 - - + +
294A ILE* 3.7 15.7 - - + -
295A LYS 3.2 3.6 - - - +
296A THR* 3.5 28.5 - - + -
307A PHE* 4.4 0.2 - - - -
328A VAL* 3.4 7.7 - - - +
329A VAL* 3.0 41.6 + - + +
333A PRO* 3.4 19.9 + - + +
334A ILE* 1.3 81.1 - - - +
336A ILE* 1.3 64.4 + - - +
337A VAL* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA 3.7 1.6 - - - +
294A ILE* 3.5 2.5 - - - -
295A LYS* 2.8 46.9 + - + +
307A PHE* 3.7 45.1 - - + +
308A LEU* 3.9 14.1 - - + -
310A GLU* 4.2 27.1 - - + +
311A ALA* 4.3 9.4 - - + +
314A MET* 4.9 6.1 - - - -
325A LEU* 3.6 24.5 - - + -
327A ALA 4.0 2.7 - - - -
328A VAL* 4.5 0.7 - - + -
335A TYR* 1.3 77.1 - - - +
337A VAL* 1.3 62.7 + - - +
338A THR* 4.0 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 4.4 8.3 - - + -
267A LEU* 3.9 33.2 - - + -
286A TRP* 5.0 3.6 - - + -
292A VAL* 3.7 37.0 - - + -
293A ALA 3.4 3.6 - - - +
294A ILE* 4.3 7.2 - - + -
325A LEU* 3.6 1.6 - - - +
326A TYR* 2.8 30.5 + - + -
327A ALA* 2.8 31.1 + - + +
328A VAL* 5.2 0.7 - - - -
329A VAL* 5.3 0.2 - - + -
335A TYR* 4.5 9.9 - - + -
336A ILE* 1.3 75.1 - - - +
338A THR* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL* 3.4 9.5 - - - +
293A ALA* 2.9 36.0 + - - +
295A LYS* 6.5 0.4 - - + -
310A GLU* 5.9 1.1 - - - +
314A MET* 3.8 25.8 - - + -
323A VAL* 3.9 8.8 - - + +
324A GLN 3.2 12.3 - - - +
325A LEU* 4.3 1.6 - - - -
326A TYR* 3.7 7.8 - - - +
336A ILE* 4.0 18.4 - - + +
337A VAL* 1.3 79.3 - - - +
339A GLU* 1.3 75.7 + - - +
600A MPZ 3.9 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 3.9 0.2 - - - +
322A LEU 3.8 1.6 - - - +
323A VAL* 3.5 12.9 - - + +
324A GLN* 2.8 44.0 + - - +
326A TYR* 3.3 35.5 - - + +
338A THR* 1.3 90.1 + - - +
340A TYR* 1.3 60.8 + - - +
341A MET* 3.7 20.5 - - - +
401A LYS* 3.0 30.4 + - - -
600A MPZ 3.2 11.6 - - - -
----------------------------------------------------------
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