Contacts of the helix formed by residues 235 - 247 (chain D) in PDB entry 4N36
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D PHE* 5.5 0.2 - - - -
203D LYS* 5.8 0.3 - - - +
233D VAL* 3.8 2.2 - - - +
234D THR* 1.3 81.6 + - - +
236D GLU* 1.3 63.8 + - - +
237D SER* 3.2 11.5 + - - -
238D GLU* 3.1 24.9 + - - +
239D GLN* 3.1 22.5 + - - +
279D ARG* 5.1 1.8 - - - +
280D PHE* 3.8 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D SER* 1.3 74.1 - - - +
237D SER* 1.3 57.7 + - - +
239D GLN* 3.3 2.4 + - - +
240D GLU* 2.9 33.4 + - + +
279D ARG* 3.8 23.6 + - - +
280D PHE* 3.8 14.4 - - + -
303D LEU* 3.7 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D PHE* 3.4 18.1 - - - -
203D LYS* 2.9 34.3 + - - +
235D SER* 3.2 11.2 + - - -
236D GLU* 1.3 79.6 - - - +
238D GLU* 1.3 60.0 + - - +
240D GLU* 3.5 12.8 + - - +
241D PHE* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D PHE* 3.7 14.8 - - + -
205D ASN* 5.8 0.2 - - - -
207D TYR* 2.4 32.2 + - + +
232D SER 3.2 14.8 - - - +
233D VAL* 3.4 4.0 - - + -
234D THR* 3.0 31.2 + - - -
235D SER* 3.1 20.3 + - - +
237D SER* 1.3 77.1 + - - +
239D GLN* 1.3 64.6 + - - +
241D PHE* 3.3 2.3 + - - +
242D LEU* 2.9 41.6 + - + +
320D LYS* 2.8 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D VAL* 3.4 18.9 - - + +
235D SER 3.1 13.4 + - - +
236D GLU 3.6 7.2 - - - +
238D GLU* 1.3 76.2 - - - +
240D GLU* 1.3 56.4 + - - +
242D LEU* 3.2 3.4 + - - +
243D TYR* 2.9 32.3 + - + +
280D PHE* 3.4 30.5 + - + +
298D ILE* 4.3 7.1 - - - +
303D LEU* 2.8 43.5 + - + +
305D ALA* 3.7 10.8 - - - +
306D TRP* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D GLU* 2.9 22.3 + - + +
237D SER* 3.6 11.3 - - - +
239D GLN* 1.3 74.4 - - - +
241D PHE* 1.3 67.2 + - - +
243D TYR* 3.7 17.4 + - + -
244D LYS* 2.9 68.6 + - + +
303D LEU* 4.2 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D LYS* 4.1 29.2 - - + -
201D TYR 4.5 5.4 - - - -
202D PHE* 3.7 47.3 - + + -
207D TYR* 3.6 32.3 - + + -
209D PHE* 4.5 2.5 - + - -
237D SER 3.0 18.2 + - - +
238D GLU 3.5 4.0 - - - +
240D GLU* 1.3 75.1 - - - +
242D LEU* 1.3 74.9 + - + +
244D LYS* 4.2 3.7 - - - +
245D THR* 2.7 51.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D TYR* 3.7 26.9 - - + -
209D PHE* 3.8 23.1 - - + -
231D THR* 3.9 16.8 - - + +
233D VAL* 3.6 31.0 - - + -
238D GLU* 2.9 32.2 + - + +
239D GLN* 3.8 2.9 - - - +
240D GLU 3.2 0.2 - - - -
241D PHE* 1.3 83.2 - - + +
243D TYR* 1.3 61.1 + - - +
245D THR* 3.3 1.7 + - - -
246D ALA* 2.8 31.5 + - - +
298D ILE* 3.6 19.0 - - + +
318D ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D GLN* 2.9 30.1 + - + +
240D GLU* 3.7 20.7 + - + +
242D LEU* 1.3 73.9 - - - +
244D LYS* 1.3 91.7 + - + +
246D ALA* 3.3 8.9 + - - +
247D GLY* 3.2 17.8 + - - -
248D GLY 4.4 2.4 + - - -
298D ILE* 4.4 12.7 - - + +
300D ALA 4.2 10.1 - - - +
301D PRO* 3.4 24.7 - - + +
302D SER* 3.3 43.4 - - - +
303D LEU* 3.6 14.7 + - + +
305D ALA* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D GLU* 2.9 55.7 + - + +
241D PHE* 4.2 3.6 - - - +
243D TYR* 1.3 101.4 - - + +
245D THR* 1.3 63.3 + - - +
247D GLY* 3.2 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D LYS* 3.6 25.8 - - + +
209D PHE* 3.5 35.2 - - + -
241D PHE* 2.7 40.6 + - - -
244D LYS* 1.3 79.0 - - - +
246D ALA* 1.3 62.2 + - - +
247D GLY* 3.2 1.7 + - - -
251D TYR* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PHE* 3.8 6.0 - - + -
242D LEU 2.8 17.9 + - - +
243D TYR* 3.6 10.1 - - - +
244D LYS 3.2 0.2 - - - -
245D THR* 1.3 76.7 - - - +
247D GLY* 1.3 65.0 + - - +
248D GLY 3.2 2.7 + - - +
249D LEU* 3.3 21.7 + - - +
251D TYR* 3.6 41.4 + - + -
298D ILE* 4.4 10.1 - - + -
318D ILE* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D TYR 3.2 8.9 + - - -
244D LYS 3.2 9.6 + - - -
245D THR 3.1 4.8 - - - -
246D ALA* 1.3 78.3 - - - +
248D GLY* 1.3 58.8 + - - +
249D LEU* 3.5 7.4 + - - +
301D PRO* 5.1 2.0 - - - -
----------------------------------------------------------
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