Contacts of the helix formed by residues 235 - 247 (chain A) in PDB entry 3KQG
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 SER 235 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 3.6 4.7 - - - +
234A THR* 1.3 83.9 + - - +
236A GLU* 1.3 64.8 + - - +
237A SER* 2.9 24.2 + - - -
238A GLU* 3.1 12.4 + - - +
239A GLN* 3.0 21.8 + - - +
276A GLN* 3.7 8.2 - - - +
280A PHE* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 1.3 71.6 - - - +
237A SER* 1.3 61.5 + - - +
239A GLN* 3.1 3.1 + - - +
240A GLU* 2.8 31.9 + - - +
276A GLN* 4.4 1.2 - - - +
279A ARG* 3.0 48.7 + - - +
280A PHE* 3.8 20.3 - - + -
303A LEU* 3.9 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.8 9.6 - - - -
203A LYS* 3.8 31.7 + - - +
235A SER* 2.9 20.7 + - - -
236A GLU* 1.3 80.3 - - - +
238A GLU* 1.3 56.0 + - - +
240A GLU* 3.4 8.7 + - - +
241A PHE* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 4.0 12.3 - - + -
205A ASN* 4.7 2.0 + - - -
207A TYR* 2.5 32.4 + - + +
232A SER 3.4 10.3 - - - +
233A VAL* 4.6 0.4 - - - -
234A THR* 2.8 40.6 + - - +
235A SER* 3.1 16.6 + - - +
237A SER* 1.3 79.5 + - - +
239A GLN* 1.3 60.0 + - - +
241A PHE* 3.3 2.7 + - + +
242A LEU* 2.9 46.5 + - + +
320A LYS* 2.7 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 3.3 21.4 - - + +
235A SER 3.0 14.5 + - - +
236A GLU 3.4 7.9 - - - +
238A GLU* 1.3 75.0 - - - +
240A GLU* 1.3 58.1 + - - +
242A LEU* 3.2 7.2 + - - +
243A TYR* 2.9 30.0 + - + +
280A PHE* 3.5 33.6 + - + +
298A ILE* 4.7 4.3 - - - +
303A LEU* 3.0 35.2 + - + +
305A ALA* 3.9 9.9 - - - +
306A TRP* 3.1 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU 2.8 17.2 + - - +
237A SER* 3.7 7.7 - - - +
239A GLN* 1.3 73.2 - - - +
241A PHE* 1.3 65.9 + - - +
243A TYR* 3.5 19.1 - - + -
244A LYS* 3.0 64.1 + - + +
303A LEU* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 4.4 9.0 - - + -
201A TYR 4.6 0.9 - - - -
202A PHE* 3.7 50.3 - + + -
207A TYR* 3.6 42.4 - + - -
209A PHE* 4.2 13.7 - + - -
237A SER 2.9 17.3 + - - +
238A GLU 3.6 4.9 - - - +
240A GLU* 1.3 77.5 - - - +
242A LEU* 1.3 71.6 + - + +
244A LYS* 4.9 2.5 - - - -
245A THR* 2.7 53.5 + - + -
197C GLN* 3.8 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.9 29.6 - - + -
209A PHE* 4.2 10.3 - - + -
231A THR* 4.1 15.0 - - + +
232A SER 4.3 1.6 - - - +
233A VAL* 3.7 30.3 - - + -
238A GLU* 2.9 33.7 + - + +
239A GLN* 3.2 4.2 + - - +
241A PHE* 1.3 84.2 - - + +
243A TYR* 1.3 61.2 + - - +
245A THR* 3.4 1.2 + - - -
246A ALA* 2.9 29.3 + - - +
253A ILE* 5.2 0.2 - - + -
298A ILE* 3.4 21.2 - - + +
318A ILE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 2.9 28.8 + - + +
240A GLU* 3.5 22.6 - - + +
242A LEU* 1.3 73.5 - - - +
244A LYS* 1.3 96.8 + - + +
246A ALA* 3.2 18.5 + - - +
247A GLY 3.7 3.3 + - - -
248A GLY 4.7 2.3 + - - -
298A ILE* 3.8 8.9 - - + +
300A ALA 4.1 9.6 - - - +
301A PRO* 3.4 25.4 - - + +
302A SER* 3.2 37.8 - - - +
303A LEU* 3.5 25.6 + - + +
305A ALA* 4.2 8.3 - - + -
226C ARG* 4.6 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 3.0 48.8 + - + +
241A PHE* 4.3 2.7 - - - +
243A TYR* 1.3 108.6 - - + +
245A THR* 1.3 61.6 + - - +
247A GLY* 3.3 12.0 + - - -
208C TYR* 4.4 8.0 + - - -
225C SER 4.4 12.1 + - - -
226C ARG* 3.6 53.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 3.5 33.7 - - + -
209A PHE* 3.5 23.6 - - + -
241A PHE* 2.7 41.8 + - + -
244A LYS* 1.3 73.7 - - - +
246A ALA* 1.3 61.5 + - - +
247A GLY* 3.0 7.9 + - - -
251A TYR* 5.2 0.7 + - - -
197C GLN* 3.9 18.9 + - - +
198C GLY* 5.1 1.8 - - - -
208C TYR* 4.9 5.6 + - - -
211C LEU* 4.5 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.0 4.0 - - + -
242A LEU 2.9 19.3 + - - +
243A TYR 3.2 9.8 + - - +
245A THR* 1.3 76.9 - - - +
247A GLY* 1.3 57.4 + - - +
248A GLY 3.1 1.8 - - - +
249A LEU* 3.0 39.1 + - - +
251A TYR* 3.4 28.1 + - + -
298A ILE* 3.8 18.4 - - + -
318A ILE* 5.3 0.7 - - + -
211C LEU* 4.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR 3.7 2.2 + - - -
244A LYS 3.3 8.9 + - - -
245A THR 3.0 4.7 - - - -
246A ALA* 1.3 77.4 - - - +
248A GLY* 1.3 56.9 + - - +
249A LEU* 3.3 2.5 + - - -
208C TYR* 3.4 25.3 + - - -
211C LEU* 4.2 9.7 + - - +
212C ILE* 3.1 29.3 + - - +
222C PHE* 5.3 10.9 - - - -
226C ARG* 5.4 0.9 - - - -
----------------------------------------------------------
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