Contacts of the helix formed by residues 312 - 319 (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 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 1.3 74.5 - - - +
313A SER* 1.3 63.5 + - - +
315A LEU* 3.2 29.1 + - + +
329A PHE* 4.1 24.9 - - + -
349A PHE* 4.1 9.2 - - + -
350A SER 3.5 31.9 - - - +
351A PRO* 3.8 6.5 - - + +
354A ILE* 3.7 33.7 - - + -
365A PRO* 3.9 8.5 - - + -
383A GLU* 3.2 6.8 + - - +
384A ASN 4.6 1.6 + - - -
386A LEU* 4.1 11.7 - - + +
389A LEU* 3.7 24.2 - - + -
393A TRP* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 3.1 4.2 - - - -
312A LEU* 1.3 73.0 - - - +
314A SER* 1.3 57.2 + - - +
315A LEU 2.9 11.2 + - - -
316A LYS* 3.0 42.0 + - - +
351A PRO 4.2 9.0 - - - -
365A PRO* 3.5 14.0 - - - +
366A ASP* 4.1 4.3 + - - +
383A GLU* 2.7 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 3.1 14.4 - - - +
311A THR* 2.7 42.8 + - - -
313A SER* 1.3 74.7 - - - +
315A LEU* 1.3 60.4 + - - +
316A LYS 3.1 2.5 + - - -
317A GLU* 3.5 36.8 + - - +
318A LYS* 5.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 4.9 1.1 - - - +
238A TYR* 3.7 44.6 - - + +
239A SER* 3.8 16.8 - - - +
310A THR* 4.5 2.0 - - + -
311A THR 4.0 9.0 - - - +
312A LEU* 3.3 26.9 - - + +
313A SER 2.9 1.4 + - - -
314A SER* 1.3 77.4 - - - +
316A LYS* 1.3 61.9 + - - +
317A GLU 2.9 6.7 + - - -
318A LYS* 3.0 20.7 + - - +
319A VAL* 3.4 8.7 - - - +
327A PRO* 5.1 2.1 - - + +
329A PHE* 4.1 26.9 - - + -
351A PRO* 3.8 15.8 - - + +
386A LEU* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 4.5 11.8 + - - +
313A SER* 3.0 32.0 + - - +
314A SER 4.8 0.2 - - - -
315A LEU* 1.3 79.0 - - - +
317A GLU* 1.3 56.0 + - + +
318A LYS 3.2 0.6 + - - -
319A VAL* 3.3 11.3 - - - +
320A ASN* 3.1 31.4 + - - +
351A PRO* 2.9 31.3 + - + +
352A TYR* 3.8 31.4 + - + +
364A ALA* 5.6 2.8 - - - +
365A PRO* 4.4 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.5 31.5 - - - +
315A LEU 2.9 0.6 - - - -
316A LYS* 1.3 78.4 - - + +
318A LYS* 1.3 71.0 + - + +
319A VAL 3.4 0.7 - - - -
320A ASN* 3.2 22.2 + - - +
323A GLN* 3.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.3 40.8 - - + +
239A SER 4.7 2.5 - - - -
240A HIS 2.6 27.1 + - - -
241A PRO* 3.3 16.7 + - - +
243A PHE* 2.6 30.1 + - + +
244A PRO* 4.4 2.5 - - + -
314A SER 5.7 1.3 - - - -
315A LEU* 3.0 14.8 + - - +
317A GLU* 1.3 90.4 - - + +
319A VAL* 1.3 59.9 + - + +
323A GLN* 3.2 26.6 - - - +
324A CYS* 3.4 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.0 37.2 - - + -
238A TYR* 6.2 0.9 - - + -
315A LEU 3.4 15.0 - - - +
316A LYS* 3.3 20.6 - - - +
318A LYS* 1.3 81.5 - - + +
320A ASN* 1.3 64.5 + - - +
321A THR 3.2 3.4 - - - -
322A ALA* 3.0 11.1 + - - +
323A GLN* 3.5 5.2 - - - +
324A CYS* 4.7 3.8 - - + +
326A LEU* 3.8 12.8 - - + -
327A PRO* 5.2 5.8 - - + -
351A PRO* 4.6 10.1 - - + -
352A TYR* 3.0 24.9 + - + +
----------------------------------------------------------
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