Contacts of the helix formed by residues 257 - 265 (chain C) in PDB entry 3KYS
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 GLY 257 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C PRO* 3.3 20.0 - - - -
253C GLU* 4.0 1.1 - - - -
254C LYS 3.0 14.9 + - - -
256C GLY* 1.3 78.4 - - - +
258C LEU* 1.3 58.4 + - - -
259C LYS 3.0 4.5 + - - -
260C GLU* 3.1 6.3 + - - +
261C LEU* 2.8 36.7 + - - +
373C LEU* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 4.1 16.4 - - + -
247C ILE* 3.8 28.0 - - + -
248C TYR* 3.8 24.1 - - + -
251C PHE* 3.8 24.9 - - + -
252C PRO 3.2 6.9 + - - -
253C GLU* 3.3 11.7 - - - +
257C GLY* 1.3 70.7 - - - -
259C LYS* 1.3 59.8 + - - +
261C LEU* 4.1 9.1 - - - +
262C PHE* 3.3 23.0 + - - +
270C PHE* 4.6 4.7 - - + -
373C LEU* 4.1 28.6 - - + +
387C CYS* 4.3 13.5 - - - -
389C ALA* 4.7 7.4 - - + -
408C LEU* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C TYR* 3.4 44.6 + - + +
253C GLU* 2.7 31.3 + - + +
258C LEU* 1.3 71.2 - - - +
260C GLU* 1.3 69.2 + - - +
262C PHE* 3.4 4.0 + - - +
263C GLY* 3.3 15.2 + - - -
410C LYS* 5.3 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLU* 4.5 0.2 + - - -
254C LYS 4.7 3.8 + - - +
255C LYS* 4.0 14.0 - - - +
256C GLY* 2.6 35.6 + - - +
257C GLY* 3.1 12.6 + - - +
259C LYS* 1.3 76.8 - - - +
261C LEU* 1.3 66.4 + - - +
263C GLY* 3.0 13.7 + - - -
264C LYS* 3.2 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLY* 4.5 12.1 - - - +
257C GLY 2.8 29.3 + - - +
258C LEU* 4.1 6.5 - - - +
260C GLU* 1.3 79.0 - - - +
262C PHE* 1.3 55.2 + - - +
264C LYS* 3.2 17.0 + - - +
265C GLY* 2.7 32.2 + - - -
270C PHE* 3.4 16.3 - - + -
373C LEU* 4.8 3.8 - - + -
375C VAL* 4.0 35.4 - - + -
384C THR* 3.5 23.3 + - - +
387C CYS* 4.7 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 3.6 22.7 - - + -
248C TYR* 3.6 17.0 - - - +
258C LEU 3.3 18.1 + - - +
259C LYS 3.7 4.7 - - - +
260C GLU 3.2 0.8 - - - -
261C LEU* 1.3 78.6 - - - +
263C GLY* 1.3 64.6 + - - +
265C GLY 3.4 13.2 - - - +
267C GLN* 3.6 57.5 + - + +
270C PHE* 3.6 29.3 - + + -
408C LEU 3.8 22.7 - - - -
409C VAL 4.1 11.7 - - - -
410C LYS* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LYS 3.3 6.3 + - - -
260C GLU 3.0 8.8 + - - -
262C PHE* 1.3 81.2 - - - +
264C LYS* 1.3 60.4 + - - +
265C GLY 4.3 1.0 - - - +
267C GLN* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLU* 3.2 9.8 + - + +
261C LEU* 3.2 22.3 + - - +
263C GLY* 1.3 76.8 - - - +
265C GLY* 1.3 73.6 + - - +
266C PRO* 3.9 0.9 - - - +
382C GLN 3.8 21.7 + - - -
383C GLU* 5.0 2.0 - - - +
384C THR* 3.7 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU 2.7 19.5 + - - -
262C PHE 3.4 12.6 - - - +
263C GLY 4.3 1.2 - - - +
264C LYS* 1.3 85.0 - - - +
266C PRO* 1.3 78.9 - - - +
267C GLN* 3.3 3.5 + - - +
270C PHE* 4.2 6.7 - - - -
384C THR* 4.5 13.0 - - - -
----------------------------------------------------------
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