Contacts of the strand formed by residues 355 - 360 (chain A) in PDB entry 6EJ9
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 PHE 355 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 3.7 53.2 - - + -
328A ILE 2.8 17.5 + - - +
329A ALA* 4.3 5.8 - - + -
330A PHE* 2.8 28.4 + - - +
353A ASP 3.9 2.0 - - - -
354A HIS* 1.3 78.5 - - - +
356A TYR* 1.3 67.1 + - - +
357A TYR* 5.9 0.2 - - - -
380A ASN* 3.6 10.1 - - + -
413A ASP 4.6 1.1 - - - -
414A TRP* 3.3 61.5 - + + -
415A PRO* 3.7 16.8 - - + -
416A TRP* 3.7 30.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 3.3 35.6 - + + +
332A LEU* 5.1 4.7 - - + -
346A PHE* 4.1 18.4 - + + -
349A ILE* 2.8 41.7 + - + -
350A TYR* 3.8 19.3 - + - -
351A HIS 2.9 14.4 + - - -
354A HIS* 3.5 27.4 - - + +
355A PHE* 1.3 74.2 - - - +
357A TYR* 1.3 59.1 + - - +
358A ILE* 4.2 7.0 - - + -
380A ASN* 3.0 35.4 + - - +
381A VAL* 3.3 15.8 - - + +
382A ARG 2.9 27.4 + - - +
414A TRP* 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA* 6.4 0.2 - - + -
330A PHE 2.9 12.2 + - - +
331A VAL* 3.3 14.0 - - + +
332A LEU* 3.0 21.6 + - - +
355A PHE 5.9 0.2 - - - -
356A TYR* 1.3 71.7 - - - +
358A ILE* 1.3 62.7 + - - +
359A HIS 4.0 0.2 + - - -
382A ARG* 3.3 23.6 - - + -
383A VAL 3.8 20.6 - - - -
384A THR* 3.6 19.4 - - + +
385A PRO* 3.9 15.8 - - - +
404A SER* 4.2 17.7 - - - -
407A ASP* 2.9 40.6 + - + +
408A LEU* 3.9 30.7 - - + -
411A MET* 3.7 23.5 - - + +
414A TRP* 4.6 3.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.4 38.1 - - + +
334A VAL* 4.2 11.2 - - + -
342A LEU* 5.3 3.1 - - + -
346A PHE* 5.1 6.5 - - + -
356A TYR* 4.6 3.1 - - + -
357A TYR* 1.3 79.5 - - - +
359A HIS* 1.3 60.4 + - - +
360A VAL* 3.9 13.1 + - + +
371A VAL* 3.7 37.0 - - + -
374A VAL* 5.3 5.2 - - + -
381A VAL* 3.8 25.4 - - + -
382A ARG 3.0 13.4 + - - +
383A VAL* 3.4 7.1 - - + +
384A THR* 3.1 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 5.6 3.8 - - + -
332A LEU 2.8 13.1 + - - +
333A VAL* 4.3 18.8 - - + +
334A VAL* 3.1 26.9 + - - +
357A TYR 4.0 1.6 + - - -
358A ILE* 1.3 71.2 - - - +
360A VAL* 1.3 69.1 + - - +
361A ASP* 4.2 3.3 + - - -
384A THR* 3.4 24.4 - - + +
386A TRP* 3.4 34.3 - + + -
387A ARG* 3.7 3.0 - - - -
388A MET* 3.1 41.3 + - - +
390A THR* 4.0 20.2 - - + -
400A THR* 4.0 12.3 - - + +
404A SER* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 3.7 19.1 - - + +
358A ILE* 3.9 10.2 + - + +
359A HIS* 1.3 79.9 - - - +
361A ASP* 1.3 71.8 + - - +
362A LYS 3.3 1.6 + - - -
364A SER* 3.5 31.6 - - - +
367A LEU* 4.3 7.6 - - + -
368A HIS* 3.8 37.4 - - + +
371A VAL* 4.1 23.3 - - + -
383A VAL* 6.0 0.2 - - + -
384A THR* 4.4 2.4 + - - -
387A ARG* 3.1 23.3 + - - +
----------------------------------------------------------
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