Contacts of the helix formed by residues 282 - 293 (chain F) in PDB entry 1P3K
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 THR 282 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685E GLN* 3.3 31.0 - - + +
688E ALA* 3.6 7.4 - - - +
278F ARG* 3.3 31.1 + - - +
280F THR* 3.6 7.2 - - - +
281F VAL* 1.3 76.3 - - - +
283F ALA* 1.3 64.7 + - - +
284F MET* 3.5 9.9 + - - +
285F ASP* 3.0 39.6 + - - +
286F VAL* 3.4 5.2 + - - +
101I C 5.7 3.1 - - - +
102I A 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685E GLN* 3.0 8.8 + - - +
687E SER* 3.3 35.7 - - - +
688E ALA* 3.7 12.3 - - - +
691E ALA* 5.1 1.4 - - + +
282F THR* 1.3 73.9 - - - +
284F MET* 1.3 59.3 + - + +
286F VAL* 3.2 4.7 + - - +
287F VAL* 2.7 31.6 + - - +
300F PHE* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 284 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F THR* 3.2 9.2 + - - +
283F ALA* 1.3 76.0 - - + +
285F ASP* 1.3 56.0 + - - +
287F VAL* 3.7 13.0 - - + +
288F TYR* 2.7 91.0 + - + +
300F PHE 3.8 4.9 - - - +
301F GLY* 3.3 44.9 - - - +
302F GLY* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F ALA* 3.7 18.2 - - - +
272F TYR* 3.4 23.5 - - - +
273F THR* 3.3 14.4 + - - -
278F ARG* 2.7 44.9 + - - -
281F VAL* 4.0 8.3 - - + -
282F THR* 3.0 25.1 + - - +
284F MET* 1.3 76.3 - - - +
286F VAL* 1.3 58.9 + - - +
288F TYR* 3.3 5.7 + - - -
289F ALA* 3.0 29.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
688E ALA* 3.9 17.3 - - + +
691E ALA* 3.8 21.3 - - + -
692E LEU* 3.7 36.6 - - + +
265F VAL* 4.7 0.4 - - + -
269F ALA* 4.1 13.0 - - + -
281F VAL* 4.1 16.8 - - + -
282F THR 3.4 10.5 + - - +
283F ALA* 3.2 9.6 + - - +
284F MET 3.2 0.4 - - - -
285F ASP* 1.3 78.6 - - - +
287F VAL* 1.3 60.9 - - - +
289F ALA* 3.2 2.4 + - - +
290F LEU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691E ALA* 5.1 1.8 - - + -
283F ALA 2.7 22.9 + - - +
284F MET* 3.1 23.1 + - + +
286F VAL* 1.3 74.2 - - - +
288F TYR* 1.3 63.8 + - + +
290F LEU* 3.8 7.7 - - - +
291F LYS* 3.1 29.2 + - - +
296F THR* 6.3 0.4 - - + -
297F LEU* 4.4 24.6 + - + +
300F PHE* 4.1 31.9 - - + +
302F GLY* 3.9 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR* 3.7 22.8 + + + -
284F MET* 2.7 67.0 + - + +
285F ASP* 3.9 6.7 - - - +
287F VAL* 1.3 73.9 - - + +
289F ALA* 1.3 66.5 + - - +
291F LYS* 3.3 20.6 + - - +
292F ARG* 2.9 25.6 + - - +
1480H TYR* 3.3 73.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F VAL* 3.5 17.0 - - + +
268F ASP* 3.6 9.9 - - + -
269F ALA* 3.4 30.7 - - + +
272F TYR* 3.9 8.2 - - + -
285F ASP 3.0 15.1 + - - +
286F VAL 3.2 4.2 + - - +
288F TYR* 1.3 76.0 - - - +
290F LEU* 1.3 62.3 + - - +
292F ARG* 3.1 5.2 + - - +
293F GLN* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691E ALA 4.4 0.4 - - - +
695E ALA* 3.5 34.8 - - + -
261F PHE* 4.4 2.2 - - + -
265F VAL* 3.5 32.5 - - + -
286F VAL* 2.9 32.0 + - + +
287F VAL* 3.8 6.1 - - - +
289F ALA* 1.3 75.3 - - - +
291F LYS* 1.3 65.4 + - - +
293F GLN* 3.1 9.1 + - + -
295F ARG* 2.8 52.9 + - + +
296F THR 4.8 0.2 - - - +
297F LEU* 3.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265D ASP* 5.4 4.7 - - - +
1268D GLU* 3.4 33.0 + - - +
287F VAL* 3.1 25.5 + - - +
288F TYR* 3.3 25.7 + - - +
290F LEU* 1.3 76.0 - - - +
292F ARG* 1.3 63.9 + - - +
294F GLY* 3.0 13.2 + - - -
296F THR* 3.8 34.6 + - + +
302F GLY* 5.3 5.1 - - - -
1480H TYR* 4.6 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ASP* 2.6 34.8 + - - +
272F TYR* 3.3 26.2 - - + +
288F TYR 2.9 11.5 + - - +
289F ALA 3.1 11.0 + - - +
291F LYS* 1.3 77.7 - - - +
293F GLN* 1.3 63.6 + - - +
294F GLY 3.1 4.6 + - - -
1473H GLU* 2.8 25.1 + - - +
1497H LEU* 3.0 37.2 + - - +
1498H LEU* 3.6 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 5.7 1.4 - - - -
264F ASN* 3.6 41.8 + - - +
265F VAL* 3.6 19.3 - - + +
268F ASP* 3.6 16.9 + - - +
289F ALA 2.9 20.8 + - - +
290F LEU* 3.1 7.5 + - - +
292F ARG* 1.3 80.4 - - + +
294F GLY* 1.3 62.5 + - - +
295F ARG* 3.3 17.6 + - + +
----------------------------------------------------------
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