Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 10KY
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 PHE 306 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE 3.7 15.3 - - - -
178A ASP* 3.6 7.9 - - - -
179A GLU* 3.4 59.5 - - + +
182A THR* 4.1 1.1 - - - -
276A VAL* 3.4 40.6 - - + -
304A LYS 3.2 10.7 + - - -
305A PHE* 1.3 72.6 - - - +
307A PRO* 1.3 64.1 - - + +
308A LYS 3.4 0.9 - - - +
309A ALA* 3.0 14.3 + - + +
310A ARG* 2.8 31.2 + - - +
341A PHE* 5.0 3.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS 5.6 0.2 - - - +
305A PHE 3.0 8.7 - - - +
306A PHE* 1.3 83.4 - - + +
308A LYS* 1.3 62.1 + - + +
310A ARG* 3.2 9.0 + - + +
311A ASP* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 5.3 8.3 - - - +
183A ARG* 6.0 1.6 - - - +
306A PHE* 3.4 1.0 - - - +
307A PRO* 1.3 78.4 - - + +
309A ALA* 1.3 61.3 + - - +
311A ASP* 3.4 6.6 + - + +
312A LEU* 3.0 22.7 + - - +
339A HIS* 3.3 13.4 - - + -
340A PRO* 4.2 27.4 - - + +
341A PHE* 3.8 23.0 - - + +
343A GLU* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.8 5.6 - - + -
276A VAL* 4.4 9.9 - - + -
305A PHE* 3.8 15.0 - - + -
306A PHE* 3.0 18.1 + - + +
308A LYS* 1.3 75.2 - - - +
310A ARG* 1.3 61.8 + - - +
312A LEU* 3.2 4.9 + - - +
313A VAL* 2.8 33.6 + - - +
341A PHE* 3.6 35.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.5 49.2 + - + +
302A PRO 5.3 1.6 + - - -
303A GLU* 6.3 0.6 - - - +
305A PHE* 3.6 24.2 - - + +
306A PHE 2.8 13.1 + - - +
307A PRO* 3.4 13.0 - - + +
309A ALA* 1.3 78.2 - - - +
311A ASP* 1.3 64.0 + - - +
313A VAL* 3.3 1.4 + - - +
314A GLU* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO 2.9 15.9 + - - +
308A LYS* 3.6 9.0 - - - +
310A ARG* 1.3 78.2 - - - +
312A LEU* 1.3 62.1 + - - +
314A GLU* 3.3 15.9 + - - +
315A LYS* 3.0 52.6 + - - +
339A HIS* 3.0 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 3.8 24.5 - - + -
308A LYS 3.0 17.2 + - - +
309A ALA* 3.5 4.3 - - - +
311A ASP* 1.3 77.4 - - - +
313A VAL* 1.3 64.0 + - - +
315A LYS* 3.0 13.1 + - - +
316A LEU* 3.3 19.7 + - + +
325A LEU* 4.1 11.9 - - + -
336A LEU* 3.8 26.7 - - + -
339A HIS* 3.6 19.9 + - + +
341A PHE* 3.8 19.1 - - + -
342A PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY 3.9 13.2 - - - +
272A ILE* 3.6 29.2 - - + -
273A TYR* 4.1 10.1 - - + +
299A TYR* 4.0 0.4 - - - +
301A PHE* 3.8 22.2 - - + -
305A PHE* 4.3 10.5 - - + -
309A ALA 2.8 22.8 + - - +
310A ARG 3.7 4.0 - - - +
312A LEU* 1.3 73.3 - - - +
314A GLU* 1.3 58.3 + - - +
316A LEU* 3.0 8.8 + - - +
317A LEU* 2.8 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR* 4.4 8.3 - - - +
301A PHE* 3.6 19.4 - - + -
310A ARG* 2.9 55.7 + - - +
311A ASP* 3.6 14.9 - - - +
312A LEU 3.2 0.4 - - - -
313A VAL* 1.3 76.1 - - - +
315A LYS* 1.3 58.8 + - + +
316A LEU 3.2 0.2 - - - -
317A LEU 4.0 6.2 - - - +
318A VAL* 3.4 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP* 3.0 36.8 + - - +
312A LEU 3.0 9.2 + - - +
314A GLU* 1.3 80.2 - - + +
316A LEU* 1.3 59.4 + - - +
318A VAL* 3.5 9.2 - - - +
323A LYS 4.0 1.6 - - - +
324A ARG* 3.5 7.3 - - - -
325A LEU* 3.1 53.2 + - + +
339A HIS* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.9 21.1 - - + +
266A TRP* 4.1 5.4 - - - -
268A LEU* 3.8 15.7 - - + -
269A GLY* 3.7 24.9 - - - +
272A ILE* 3.6 30.5 - - + -
312A LEU* 3.5 22.9 - - + +
313A VAL* 3.0 7.1 + - - +
315A LYS* 1.3 82.9 - - - +
317A LEU* 1.3 60.1 + - - +
318A VAL 2.9 10.9 + - - -
324A ARG* 3.3 24.3 + - + -
325A LEU* 3.3 31.2 - - + +
336A LEU* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TRP* 3.6 56.1 - - + +
269A GLY* 4.0 5.4 - - - +
270A CYS* 3.9 11.2 - - - +
281A PRO* 4.2 18.4 - - + -
282A PHE* 4.3 5.6 - - + -
297A LEU* 3.5 23.1 - - + +
299A TYR* 3.7 33.8 + - + +
313A VAL* 2.8 36.3 + - + +
314A GLU* 4.0 5.7 - - - +
316A LEU* 1.3 71.8 - - - +
318A VAL* 1.3 62.1 - - - +
----------------------------------------------------------
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