Contacts of the strand formed by residues 326 - 333 (chain A) in PDB entry 1CJY
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 326 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 3.7 37.0 - - + +
157A PHE* 3.3 23.1 - - + -
222A THR 3.0 12.2 + - - +
223A TYR* 3.5 15.5 - - + -
224A VAL 3.1 21.6 + - - +
238A TYR* 4.8 0.2 - - - -
319A VAL* 3.8 13.2 - - + -
325A PRO* 1.3 70.5 - - - +
327A PRO* 1.4 83.3 - - + +
328A LEU* 3.6 13.7 + - + +
350A SER* 4.7 3.6 - - - -
351A PRO* 4.0 13.2 - - + -
352A TYR* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 3.4 9.2 - - + +
234A MET* 4.0 6.5 - - + -
238A TYR* 3.0 42.2 - - + -
315A LEU* 5.1 2.2 - - + +
319A VAL* 5.2 5.6 - - + -
325A PRO 3.3 4.3 - - - +
326A LEU* 1.4 93.2 - - + +
328A LEU* 1.3 68.8 + - - +
329A PHE* 3.8 25.2 - - + -
349A PHE 3.9 0.2 - - - +
350A SER* 3.6 2.6 - - - -
351A PRO* 3.5 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 3.8 26.9 - - + -
224A VAL 2.7 13.3 + - - +
225A ALA* 4.0 9.2 - - + -
226A GLY 3.0 24.1 + - - -
234A MET* 3.2 8.7 - - - +
326A LEU* 3.9 20.0 - - + +
327A PRO* 1.3 84.1 - - - +
329A PHE* 1.3 61.7 + - - +
348A GLU* 5.4 1.1 - - + +
349A PHE 3.4 3.8 - - - +
350A SER* 3.7 20.2 - - - -
560A LEU* 4.1 25.1 - - + +
561A ILE* 4.5 8.7 - - + -
566A ARG* 3.8 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY 3.6 5.8 - - - -
231A THR* 3.4 20.2 - - - +
234A MET* 3.7 28.9 - - + -
235A SER* 3.8 20.4 - - - -
238A TYR* 5.8 0.2 - + - -
312A LEU* 4.1 17.5 - - + -
315A LEU* 4.1 16.2 - - + -
327A PRO* 3.8 32.5 - - + -
328A LEU* 1.3 77.3 - - - +
330A THR* 1.3 64.4 + - - +
349A PHE* 2.9 43.1 + - + -
350A SER* 5.1 0.7 - - - -
351A PRO* 5.2 0.2 - - + -
386A LEU* 5.5 0.4 - - + -
393A TRP* 3.4 41.7 - + + -
560A LEU* 3.5 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY 3.5 7.6 + - - +
227A LEU* 3.5 31.4 - - + +
231A THR* 4.9 0.6 + - - -
329A PHE* 1.3 78.7 - - - +
331A CYS* 1.3 71.7 + - - +
346A TRP* 3.2 31.3 - - + +
347A VAL 3.1 15.0 + - - -
349A PHE* 4.1 1.6 - - - -
393A TRP* 3.1 25.8 - - - +
550A SER* 3.7 10.1 + - - +
557A PRO* 4.0 2.0 - - + -
560A LEU* 3.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A THR* 1.3 80.9 + - - +
332A LEU* 1.3 62.9 + - - +
346A TRP* 3.7 2.6 - - - -
347A VAL* 2.9 33.6 + - - -
349A PHE* 3.6 24.5 - - - -
392A VAL* 4.1 12.1 - - + +
393A TRP* 3.9 13.7 - - + -
547A VAL* 3.7 29.6 - - - -
548A VAL 3.6 10.8 - - - +
550A SER* 3.3 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A CYS* 1.3 77.7 - - - +
333A HIS* 1.3 60.4 + - - +
334A VAL* 3.8 7.1 + - + -
341A LEU* 4.7 4.0 - - + +
344A ALA* 4.3 16.2 - - + -
345A ASP 3.4 7.6 - - - +
346A TRP* 3.4 48.7 - - + +
347A VAL* 4.4 0.4 - - - -
546A HIS 3.5 0.5 - - - +
547A VAL* 3.0 28.2 - - - +
548A VAL* 2.8 26.4 + - + +
549A ASP 4.0 14.1 - - - +
550A SER* 3.7 16.4 - - - +
552A LEU* 4.7 5.8 - - + -
553A THR* 3.3 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 1.3 71.6 - - - +
334A VAL* 1.3 65.2 + - - +
335A LYS* 3.7 29.4 + - + +
336A PRO* 6.0 0.7 - - + -
344A ALA* 3.7 4.0 - - - +
345A ASP* 2.8 46.2 + - + +
347A VAL* 3.9 17.4 - - + +
356A MET* 3.7 31.6 - - + +
493A MET* 6.1 1.8 - - - +
539A ASP* 4.3 11.7 + - - +
545A ILE* 3.7 38.5 - - + +
546A HIS 3.4 10.3 + - - -
547A VAL* 4.7 3.6 - - + -
----------------------------------------------------------
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