Contacts of the helix formed by residues 282 - 296 (chain F) in PDB entry 1XSK
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 282 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F TYR* 1.3 77.6 + - - +
283F GLU* 1.3 67.3 + - - +
284F ALA* 3.0 34.7 + - - +
285F THR* 3.0 17.6 + - - -
286F VAL* 3.0 23.1 + - - +
324F THR* 3.7 20.0 - - + +
325F PHE* 3.7 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F ASP* 1.3 74.1 + - - +
284F ALA* 1.3 65.7 + - - +
286F VAL* 2.8 16.0 + - + +
287F ASN* 2.9 33.7 + - - +
324F THR 4.5 1.7 + - - +
325F PHE* 3.8 8.7 - - + -
327F ASP* 5.1 1.6 - - - +
331F MET* 3.6 40.5 - - + +
334F ARG* 2.8 42.1 + - - +
335F LEU* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F ASP* 3.0 16.4 + - - +
283F GLU* 1.3 77.9 - - - +
285F THR* 1.3 61.3 + - - +
287F ASN* 3.4 6.7 + - - +
288F SER* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 285 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F ASN* 3.9 18.6 + - - +
281F TYR* 3.9 9.4 - - + -
282F ASP* 3.0 32.8 + - - -
284F ALA* 1.3 78.1 - - - +
286F VAL* 1.3 65.6 + - + +
288F SER* 3.3 9.4 + - - -
289F PHE* 3.2 44.5 + - + -
545F TYR* 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F THR* 4.7 4.9 - - + -
281F TYR* 5.2 3.6 - - + -
282F ASP 3.0 20.5 + - - +
283F GLU* 2.8 16.4 + - + +
285F THR* 1.3 71.0 - - + +
287F ASN* 1.3 65.3 + - - +
289F PHE* 2.8 21.0 + - + +
290F ILE* 2.9 35.8 + - + +
303F PHE* 3.7 40.2 - - + -
305F PHE* 3.9 17.7 - - + -
325F PHE* 5.3 0.4 - - + -
331F MET* 5.5 0.2 - - - -
335F LEU* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F GLU* 2.9 32.4 + - - +
284F ALA* 3.9 8.5 - - - +
286F VAL* 1.3 74.6 - - - +
288F SER* 1.3 54.6 + - - +
290F ILE* 4.1 8.1 - - - -
291F ASP* 2.7 48.6 + - - +
334F ARG* 5.5 8.1 - - - +
335F LEU* 3.8 16.7 - - - +
338F LYS* 3.3 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 288 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F ALA 3.0 14.8 + - - -
285F THR* 3.3 15.5 - - - -
287F ASN* 1.3 77.2 - - - +
289F PHE* 1.3 62.4 - - - +
291F ASP* 4.5 4.1 - - - +
292F GLY* 3.1 21.5 + - - -
549F TRP* 4.7 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F LEU* 4.9 19.5 - - + -
274F THR 5.6 1.6 - - - -
275F THR* 5.3 5.8 - - - -
281F TYR* 5.9 0.2 - - + -
285F THR* 3.2 37.4 + - + -
286F VAL* 2.8 10.0 + - - +
288F SER* 1.3 82.8 - - - +
290F ILE* 1.3 65.1 + - + +
292F GLY* 3.2 0.9 + - - -
293F MET* 3.1 29.4 + - + +
303F PHE* 5.3 7.0 - + + -
545F TYR* 3.5 46.9 - + + -
547F VAL* 3.4 40.4 - - + -
549F TRP* 3.8 13.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F VAL* 2.9 26.1 + - + +
287F ASN* 3.6 8.5 - - - +
289F PHE* 1.3 79.8 - - + +
291F ASP* 1.3 61.4 + - - +
293F MET* 3.4 6.4 + - - +
294F ALA* 3.2 22.4 + - + +
300F LEU* 5.9 8.9 - - + +
303F PHE* 5.1 10.1 - - + -
335F LEU* 3.1 35.4 - - + -
338F LYS* 3.6 30.5 - - + +
340F LEU* 3.4 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ASN* 2.7 33.5 + - - +
288F SER* 4.5 3.7 - - - +
290F ILE* 1.3 71.7 - - - +
292F GLY* 1.3 64.9 + - - +
294F ALA* 3.9 7.0 - - - +
295F GLU* 2.9 44.9 + - + +
338F LYS* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F SER 3.1 19.7 + - - -
289F PHE 3.2 2.4 + - - -
290F ILE 3.2 0.8 - - - -
291F ASP* 1.3 78.2 - - - +
293F MET* 1.3 59.1 + - - +
295F GLU* 3.8 5.4 + - - +
296F ARG* 3.0 45.7 + - - +
549F TRP* 3.9 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 3.9 20.0 - - + -
273F LEU* 5.5 5.8 - - + -
289F PHE* 3.1 19.1 + - + +
290F ILE* 3.7 6.7 - - - +
292F GLY* 1.3 74.4 - - - +
294F ALA* 1.3 65.7 + - - +
296F ARG* 2.9 9.9 + - - -
298F LEU* 2.9 65.5 + - + +
299F PRO 4.1 0.2 - - - +
300F LEU* 3.4 40.4 - - + -
539F LEU* 4.7 8.5 - - + -
547F VAL* 5.4 2.5 - - + -
548F PRO* 4.1 9.4 - - - -
549F TRP* 3.6 22.2 - - + -
559F VAL* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F ILE* 3.2 15.1 + - + +
291F ASP* 3.5 7.8 + - - +
293F MET* 1.3 79.3 - - - +
295F GLU* 1.3 54.8 + - + +
297F ASN* 2.8 29.7 + - - +
298F LEU 4.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ASP* 2.9 43.6 + - + +
292F GLY* 3.9 8.2 + - - +
294F ALA* 1.3 78.5 - - + +
296F ARG* 1.3 66.7 + - + +
297F ASN* 3.4 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F GLY* 3.0 30.8 + - - +
293F MET 2.9 8.3 + - - +
295F GLU* 1.3 82.9 + - + +
297F ASN* 1.3 66.9 + - - +
298F LEU* 3.2 10.7 + - + -
549F TRP* 3.4 59.0 - - - +
556F CYS* 3.6 17.8 - - + -
560F ARG* 2.3 39.0 + - - +
----------------------------------------------------------
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