Contacts of the helix formed by residues 315 - 321 (chain F) in PDB entry 3KC3
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 315 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET 5.0 3.7 + - - -
308A THR* 4.4 19.2 - - + +
309A GLU* 6.0 2.2 - - + -
312A GLN* 5.3 6.3 - - - +
246F MET* 3.9 4.5 - - - -
313F ARG 4.7 3.6 - - - +
314F MET* 1.3 77.8 - - - +
316F ILE* 1.3 68.8 + - - +
317F THR* 3.7 8.2 + - - -
318F GLU* 2.8 40.4 + - - +
319F PHE* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 5.1 7.9 - - + -
171F GLY* 3.7 15.3 - - - +
174F ILE* 3.7 26.5 - - + -
175F GLN* 3.7 27.1 - - + +
178F HIS* 2.7 41.5 - - + +
242F LYS* 6.0 0.2 - - - -
246F MET* 3.4 19.0 - - + -
249F LEU* 4.3 11.4 - - + -
315F THR* 1.3 75.8 - - - +
317F THR* 1.3 67.5 + - - +
319F PHE* 3.8 4.7 - - + -
320F MET* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 2.6 47.3 + - - +
282A GLY 3.9 14.4 - - - +
283A GLN* 4.1 24.8 + - + +
175F GLN* 4.3 9.0 + - - +
315F THR* 2.9 7.1 + - - -
316F ILE* 1.3 83.2 - - - +
318F GLU* 1.3 63.1 + - + +
320F MET* 4.0 0.7 - - - +
321F ASN* 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 3.0 38.7 + - - +
312A GLN* 5.0 2.3 + - - +
313F ARG 4.7 0.5 - - - +
314F MET* 3.3 23.9 - - + +
315F THR* 2.8 39.6 + - - +
317F THR* 1.3 77.4 - - + +
319F PHE* 1.3 65.1 + - - +
321F ASN* 3.2 7.5 + - - +
322F HIS* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F MET* 3.8 20.4 - - + -
246F MET* 4.9 2.0 - - - -
249F LEU* 3.8 30.5 - - + -
253F MET* 3.4 26.5 - - + -
301F LEU* 4.0 17.0 - - + -
305F LEU* 4.0 13.0 - - + -
314F MET* 3.5 12.6 - - + -
315F THR 2.9 16.6 + - - +
316F ILE* 3.6 10.1 - - + +
318F GLU* 1.3 76.7 - - - +
320F MET* 1.3 95.2 + - + +
322F HIS* 3.1 25.1 + - - +
325F ILE* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LYS* 3.9 12.1 - - - +
171F GLY* 3.3 36.1 - - - +
172F GLU* 4.0 16.8 - - - -
175F GLN* 3.8 26.2 - - - +
316F ILE* 2.9 22.5 + - + +
317F THR 4.0 3.1 - - - +
319F PHE* 1.3 113.4 - - + +
321F ASN* 1.3 61.5 + - - +
322F HIS 3.2 1.9 + - - -
325F ILE* 3.8 24.7 - - + +
326F MET* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F GLN* 5.3 1.4 + - - -
317F THR* 2.8 38.5 + - - +
318F GLU* 3.2 7.8 + - - +
319F PHE 3.2 0.8 - - - -
320F MET* 1.3 82.2 + - - +
322F HIS* 1.3 62.5 + - - +
323F PRO* 3.6 4.3 - - - +
326F MET* 3.5 36.2 - - + +
----------------------------------------------------------
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