Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 1P9W
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 LEU 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU 4.3 2.9 - - - +
253A ILE 3.5 20.6 - - - +
255A ARG 3.4 20.0 - - - +
256A PRO 3.6 10.6 + - - +
257A HIS* 4.1 2.7 - - - +
258A GLY 3.5 3.8 - - - +
260A ILE* 3.6 25.4 - - + -
281A LEU* 4.3 4.0 - - + -
328A ASP 3.1 13.6 + - - +
329A VAL* 3.3 32.2 - - + +
330A VAL* 2.9 27.5 + - - +
352A HIS* 1.3 72.1 - - - +
354A VAL* 1.3 61.9 + - - +
355A MSE 4.2 13.9 - - + -
385A LEU* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY 2.9 9.2 + - - +
259A ILE* 3.4 18.8 - - + -
260A ILE* 2.8 27.6 + - - +
319A LEU* 5.7 0.4 - - + -
330A VAL* 3.3 18.2 - - + +
332A VAL* 4.2 20.6 - - + -
344A ALA* 3.8 20.4 - - + +
347A ALA* 3.8 13.5 - - + -
348A SER* 3.8 29.4 - - - +
352A HIS* 4.4 1.6 - - + +
353A LEU* 1.3 78.2 - - - +
355A MSE 1.3 67.9 + - - +
356A SER* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.2 14.6 - - + -
253A ILE* 3.8 30.7 - - + -
260A ILE* 3.3 19.1 - - + +
262A VAL* 5.1 1.1 - - + -
274A LEU* 4.0 35.4 - - + +
277A GLY* 4.6 4.7 - - - -
278A LEU* 4.2 22.7 - - - -
281A LEU* 4.6 7.0 - - - -
329A VAL* 4.7 2.0 - - + -
330A VAL 2.9 13.9 + - - +
331A MSE 3.3 12.8 - - + +
332A VAL* 2.9 28.4 + - - +
353A LEU* 4.2 20.4 - - + -
354A VAL* 1.3 79.2 - - - +
356A SER* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 5.5 0.9 - - - +
260A ILE 3.0 6.9 + - - +
261A LEU* 3.3 19.5 - - - +
262A VAL* 2.8 32.1 + - - +
274A LEU* 4.2 4.8 - - - +
332A VAL* 2.6 35.2 + - - +
334A GLU* 3.6 4.0 - - - -
335A ILE* 3.5 23.7 - - - +
354A VAL* 5.3 3.1 - - - -
355A MSE 1.3 77.1 - - - +
357A THR* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.3 2.7 - - - -
262A VAL* 3.0 16.8 - - + +
270A LYS* 3.9 32.8 - - + -
271A SER 5.4 0.2 - - - +
274A LEU* 3.6 26.9 - - + -
333A GLY 3.1 20.2 + - - +
334A GLU* 3.2 11.4 + - - +
335A ILE* 3.3 22.3 + - - +
356A SER* 1.3 84.2 + - - +
358A LEU* 1.3 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.5 30.5 - - + -
262A VAL 3.5 3.2 + - - -
263A THR* 3.4 26.8 - - + +
264A GLY 3.5 3.3 + - - +
270A LYS* 3.7 7.9 - - - +
334A GLU* 5.7 1.3 - - - -
335A ILE* 3.5 39.9 - - + +
357A THR* 1.3 78.8 - - - +
359A HIS* 1.3 58.7 + - - +
360A THR* 3.3 16.8 + - + -
366A ALA* 3.9 31.9 - - + +
369A ARG* 4.4 17.5 - - + +
370A LEU* 4.4 10.1 - - + -
373A MSE 5.2 1.1 - - + -
----------------------------------------------------------
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