Contacts of the helix formed by residues 274 - 285 (chain Z) in PDB entry 5L4K
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 ASP 274 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Z ARG* 3.1 34.7 + - - -
269Z ALA 4.2 2.0 + - - -
272Z LEU* 3.4 18.8 - - - +
273Z ASN* 1.3 78.0 - - - +
275Z MET* 1.3 55.5 + - - +
276Z GLU* 4.4 8.4 - - + +
277Z LEU* 2.8 36.2 + - + +
278Z VAL* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 275 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273Z ASN* 3.8 12.8 + - - +
274Z ASP* 1.3 72.0 - - - +
276Z GLU* 1.3 57.0 + - - +
278Z VAL* 3.3 16.9 + - + -
279Z GLU* 3.0 26.9 + - - +
314Z TYR* 5.6 5.2 - - + +
317Z LEU* 3.8 37.5 - - + -
318Z THR* 4.7 3.8 - - - +
321Z MET* 4.0 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274Z ASP* 4.6 11.3 - - + +
275Z MET* 1.3 77.0 - - - +
277Z LEU* 1.3 69.4 + - + +
279Z GLU* 4.0 11.9 - - - +
280Z ASP* 2.8 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Z ARG* 3.9 18.6 - - + -
253Z LEU* 4.2 16.2 - - + -
257Z ARG* 3.6 3.2 + - - +
269Z ALA* 3.3 25.4 - - + +
272Z LEU* 3.6 24.7 - - + -
274Z ASP* 2.8 36.5 + - + +
276Z GLU* 1.3 87.3 - - + +
278Z VAL* 1.3 62.6 + - - +
279Z GLU 3.2 1.1 - - - -
280Z ASP* 3.2 37.3 + - - +
281Z ILE* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269Z ALA* 3.7 22.2 - - - +
270Z LEU* 5.1 11.0 - - + -
273Z ASN* 4.9 6.5 - - - +
274Z ASP 2.7 25.8 + - - +
275Z MET* 3.3 21.5 + - + +
277Z LEU* 1.3 71.7 - - - +
279Z GLU* 1.3 61.5 + - - +
280Z ASP 3.0 2.6 + - - -
281Z ILE* 3.8 17.4 + - - +
282Z PHE* 4.2 2.9 + - - +
306Z GLU* 5.4 7.2 - - + -
318Z THR* 3.4 29.1 - - + +
321Z MET* 3.8 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Z MET 3.0 17.0 + - - +
276Z GLU* 4.1 11.7 - - - +
277Z LEU 3.2 0.4 - - - -
278Z VAL* 1.3 76.7 - - - +
280Z ASP* 1.3 60.4 + - - +
281Z ILE 3.5 0.4 - - - -
282Z PHE* 3.5 23.6 + - - +
283Z THR* 3.0 26.1 + - - +
321Z MET* 3.2 39.9 - - + +
325Z GLN* 5.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253Z LEU* 4.4 3.8 - - - +
257Z ARG* 3.4 31.6 + - - +
276Z GLU 2.8 22.7 - - - +
277Z LEU* 3.2 33.9 - - - +
278Z VAL 3.0 2.0 - - - -
279Z GLU* 1.3 79.7 - - - +
281Z ILE* 1.3 58.8 + - - +
283Z THR* 3.0 23.4 + - - -
284Z SER* 3.2 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257Z ARG* 3.6 20.9 - - - +
262Z PHE* 3.9 23.8 - - + +
266Z LEU* 3.7 33.4 - - + -
277Z LEU 5.5 0.4 - - - +
278Z VAL* 3.8 11.9 + - - +
280Z ASP* 1.3 80.3 - - - +
282Z PHE* 1.3 62.4 + - + +
284Z SER* 3.3 21.2 + - - +
285Z CYS* 3.4 15.6 + - + +
298Z LEU* 3.6 29.6 - - + +
299Z GLY* 4.7 2.6 - - - -
302Z GLY* 4.7 11.0 - - - -
303Z VAL* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278Z VAL 4.2 3.8 + - - +
279Z GLU* 3.5 27.5 + - - +
280Z ASP 3.3 0.6 - - - -
281Z ILE* 1.3 81.3 - - + +
283Z THR* 1.3 58.2 + - - +
284Z SER 3.4 0.2 - - - -
285Z CYS* 3.9 16.2 - - - -
286Z LYS* 3.6 42.0 - - + +
299Z GLY* 6.0 1.1 - - - -
303Z VAL* 5.0 7.6 - - + -
318Z THR* 5.8 2.0 - - + -
321Z MET* 5.4 3.4 - - + -
322Z SER* 3.4 46.2 - - - +
325Z GLN* 3.9 21.5 - - + -
326Z LEU* 4.4 13.0 - - + -
336Z GLU* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279Z GLU* 3.0 25.5 + - - +
280Z ASP* 3.0 16.7 + - - -
282Z PHE* 1.3 78.3 - - - +
284Z SER* 1.3 57.4 + - - +
285Z CYS 3.5 0.4 - - - -
286Z LYS* 5.2 1.1 - - - -
287Z ASP* 3.1 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257Z ARG* 4.1 2.4 + - - -
262Z PHE* 3.7 25.3 - - - -
280Z ASP 3.2 12.7 + - - -
281Z ILE* 3.3 22.8 + - - -
283Z THR* 1.3 77.5 - - - +
285Z CYS* 1.3 57.1 + - - +
286Z LYS 3.5 1.1 - - - -
288Z VAL* 3.1 39.6 - - - +
295Z ALA* 3.4 9.4 - - - +
298Z LEU* 6.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 285 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281Z ILE* 3.4 14.6 + - + +
282Z PHE* 3.9 27.6 - - - -
284Z SER* 1.3 77.0 - - - +
286Z LYS* 1.3 64.7 + - - +
289Z VAL* 3.0 22.8 - - - +
295Z ALA 2.9 25.1 - - - +
296Z PHE* 4.3 5.6 - - + -
299Z GLY* 3.8 24.5 - - - +
331Z LEU* 3.3 17.9 - - + +
336Z GLU* 4.6 6.7 - - - -
----------------------------------------------------------
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