Contacts of the helix formed by residues 314 - 321 (chain C) in PDB entry 1KKQ
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 TYR 314 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C VAL* 5.7 2.2 - - + -
311C TYR 4.2 3.5 + - - +
313C VAL* 1.3 92.9 - - + +
315C GLU* 1.3 64.1 + - - +
316C ALA 3.2 0.4 - - - -
317C ILE* 3.7 11.9 - - + +
318C PHE* 3.1 40.8 + + + -
437C VAL* 3.7 22.7 - - + -
440C HIS* 6.0 6.1 - + - -
441C ALA* 6.3 0.7 - - + -
777C 471 3.6 52.8 + - + +
682G ASN* 4.2 32.5 - - + -
683G MET* 4.4 15.4 - - + +
685G LEU* 3.5 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C TYR 4.6 4.3 - - - +
312C GLY* 4.0 9.4 - - - -
313C VAL 3.4 0.2 - - - -
314C TYR* 1.3 76.7 - - - +
316C ALA* 1.3 58.0 + - - +
318C PHE* 3.4 1.3 + - - -
319C ALA* 3.0 29.1 + - - +
382C ILE* 3.5 20.4 - - + +
388C ARG* 3.0 32.5 + - - -
430C MET 5.0 2.0 - - - +
433C LEU* 3.5 29.1 - - + +
434C ARG* 3.0 41.6 + - - +
437C VAL* 3.8 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 4.0 14.1 - - + -
312C GLY 3.9 4.5 - - - +
313C VAL 3.6 8.9 + - - +
314C TYR 3.2 0.2 - - - -
315C GLU* 1.3 80.4 - - - +
317C ILE* 1.3 57.2 + - - +
319C ALA* 3.9 7.0 - - - -
320C MET* 3.1 34.2 + - - +
379C VAL* 3.7 27.8 - - + -
382C ILE* 3.5 18.6 - - + +
383C ILE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C SER* 5.3 1.3 - - - +
283C THR* 3.6 30.1 - - + -
284C VAL* 4.5 18.6 - - + -
287C LEU* 3.9 11.2 - - + -
313C VAL* 2.8 27.1 - - + +
314C TYR* 3.2 17.9 + - + +
315C GLU 3.2 0.4 - - - -
316C ALA* 1.3 78.1 - - - +
318C PHE* 1.3 54.1 - - + +
319C ALA 3.2 4.5 - - - -
320C MET* 4.5 3.5 - - - +
321C LEU* 2.6 45.8 + - + +
777C 471 4.1 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TYR* 3.1 36.8 + + + +
315C GLU* 3.8 2.9 - - - +
317C ILE* 1.3 78.6 - - + +
319C ALA* 1.3 64.4 + - - +
321C LEU* 3.7 22.0 - - + +
322C SER* 3.6 12.5 + - - -
355C MET* 5.3 1.3 - - + -
358C LYS* 3.5 46.6 - - + +
361C PHE* 4.0 10.2 - - - -
433C LEU* 4.2 7.2 - - + -
436C LEU* 4.1 21.3 - - + +
437C VAL* 4.4 13.2 - - + -
440C HIS* 4.1 29.6 - + + -
777C 471 4.0 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU 3.0 17.8 + - - +
316C ALA* 3.9 9.0 - - - +
317C ILE 3.2 0.2 - - - -
318C PHE* 1.3 75.0 - - - +
320C MET* 1.3 68.7 + - + +
321C LEU 3.0 0.7 - - - -
322C SER* 3.1 21.8 + - - -
323C SER* 4.3 1.9 + - - -
361C PHE* 4.6 6.3 - - - -
365C PHE* 4.4 11.9 - - + -
375C ILE* 5.4 2.0 - - + -
378C PHE* 4.1 20.4 - - + -
379C VAL* 4.6 4.3 - - + -
382C ILE* 6.1 0.9 - - + -
433C LEU* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TYR* 4.1 19.5 - - - +
218C PHE* 3.5 40.6 - - + -
283C THR* 5.1 7.0 - - + -
287C LEU* 3.7 22.0 - - + -
316C ALA 3.1 22.7 + - - +
317C ILE* 4.5 4.5 - - - +
319C ALA* 1.3 75.2 - - - +
321C LEU* 1.3 61.3 + - - +
322C SER 2.9 7.7 + - - -
323C SER* 3.1 26.6 + - - +
324C VAL* 4.3 5.0 + - - +
375C ILE* 4.4 8.1 - - + -
379C VAL* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 2.6 28.9 + - + +
318C PHE* 3.7 32.3 - - + +
319C ALA 3.0 0.6 - - - -
320C MET* 1.3 76.1 - - - +
322C SER* 1.3 57.2 + - - +
323C SER 3.4 0.4 - - - -
324C VAL* 3.0 25.8 - - + +
325C MET* 3.1 20.7 - - - +
330C MET* 4.0 15.7 - - + -
355C MET* 3.7 28.7 - - + -
358C LYS* 4.6 5.2 - - + -
777C 471 3.7 25.4 - - + +
----------------------------------------------------------
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