Contacts of the helix formed by residues 234 - 248 (chain D) in PDB entry 2CNW
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 GLN 234 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET 4.8 7.0 - - - +
40A ASP* 4.3 26.5 - - - +
42A ASP* 2.9 22.3 + - - +
43D ASP* 2.6 38.6 + - - +
44D VAL 4.3 2.6 - - - +
45D GLY* 3.6 23.7 - - - +
233D GLY* 1.3 73.9 - - - -
235D ASN* 1.3 61.9 + - - +
236D GLY 3.1 1.0 + - - -
237D LEU* 3.4 23.5 + - - +
238D GLU* 4.0 2.6 + - - +
265D VAL* 4.2 10.3 - - - +
268D PRO* 4.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 4.3 5.6 + - - +
221A MET* 4.2 15.9 - - + +
250A ASP* 2.8 28.5 + - - -
251A ALA* 3.3 34.9 + - + +
197D HIS* 3.3 14.4 + - - -
232D THR* 4.4 1.3 - - + -
233D GLY 3.1 1.0 + - - -
234D GLN* 1.3 74.8 - - - +
236D GLY* 1.3 59.3 + - - +
237D LEU 3.2 0.2 - - - -
238D GLU* 3.1 10.9 + - - +
239D GLN* 2.8 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 3.8 17.1 - - - +
232D THR* 3.5 17.4 - - - +
233D GLY 3.1 10.9 + - - -
235D ASN* 1.3 77.2 - - - +
237D LEU* 1.3 56.1 + - - +
239D GLN* 3.4 8.5 + - - +
240D ALA* 3.0 22.7 + - - +
265D VAL* 4.2 4.0 - - - -
269D ILE* 3.5 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D GLN* 3.4 15.7 + - - +
235D ASN 3.2 0.4 - - - -
236D GLY* 1.3 74.5 - - - +
238D GLU* 1.3 60.3 + - - +
240D ALA* 3.2 2.6 + - + +
241D LYS* 3.0 59.5 + - + +
265D VAL* 3.7 14.3 - - + +
268D PRO* 3.7 39.9 - - + +
269D ILE* 3.9 14.4 - - + +
271D ARG* 4.5 10.3 - - - +
272D THR* 4.3 10.1 - - + +
273D LEU* 5.3 1.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
250A ASP* 3.8 14.6 - - - +
197D HIS* 3.8 22.3 - - + +
234D GLN 4.0 1.7 + - - +
235D ASN* 3.1 19.0 + - - +
237D LEU* 1.3 75.3 - - - +
239D GLN* 1.3 64.6 + - - +
241D LYS* 3.5 24.1 + - - +
242D LYS* 2.8 56.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
221A MET* 3.5 24.4 - - - +
110D VAL* 3.5 40.7 + - + +
113D VAL* 4.8 4.5 - - - +
197D HIS* 3.7 13.7 - - + +
226D LEU* 4.8 6.7 - - + +
227D VAL 4.8 4.7 - - - +
228D LEU* 4.2 15.3 - - + +
229D ASP 5.6 0.2 + - - -
232D THR* 4.0 6.5 + - - +
235D ASN* 2.8 38.2 + - - +
236D GLY* 3.4 10.8 - - - +
237D LEU 3.2 0.2 - - - -
238D GLU* 1.3 75.8 - - - +
240D ALA* 1.3 63.2 + - - +
243D PHE* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LEU* 3.9 22.6 - - + +
236D GLY 3.0 17.6 + - - +
237D LEU* 3.2 4.9 + - + +
239D GLN* 1.3 76.8 - - - +
241D LYS* 1.3 57.0 + - - +
244D HIS* 3.0 31.5 + - - +
249D LEU* 3.6 5.8 - - + +
269D ILE* 3.7 24.7 - - + -
273D LEU* 3.5 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D LEU* 3.0 46.7 + - + +
238D GLU* 3.5 27.0 + - - +
240D ALA* 1.3 75.8 - - - +
242D LYS* 1.3 63.0 + - + +
244D HIS* 3.4 3.6 + - - +
245D GLU* 3.0 29.3 + - - +
272D THR* 5.1 7.8 - - + +
273D LEU* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D HIS* 3.8 39.5 - - + +
198D THR* 6.4 0.2 - - - +
203D MET* 3.5 12.9 - - + +
238D GLU* 2.8 49.4 + - - +
239D GLN 4.2 0.2 - - - +
241D LYS* 1.3 84.6 - - + +
243D PHE* 1.3 59.8 + - - +
245D GLU* 3.7 8.1 + - + +
246D ALA* 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D VAL* 3.9 12.3 - - + -
109D GLY* 3.8 22.7 - - - -
110D VAL* 3.9 21.3 - - + -
195D ARG* 3.8 26.2 - - + -
197D HIS* 3.9 16.4 - - + -
203D MET* 3.6 24.7 - - + -
206D LEU* 3.6 28.5 - - + -
226D LEU* 4.2 17.9 - - + -
239D GLN* 3.0 30.9 + - + +
240D ALA 4.3 1.1 - - - +
242D LYS* 1.3 73.3 - - - +
244D HIS* 1.3 66.1 + - - +
246D ALA* 3.3 0.7 + - - -
247D VAL* 3.1 31.1 + - - +
249D LEU* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ALA 3.0 21.3 + - - +
241D LYS* 3.4 5.4 - - - +
242D LYS 3.3 0.2 - - - -
243D PHE* 1.3 76.9 - - - +
245D GLU* 1.3 59.3 + - - +
248D GLY* 2.8 34.9 + - - -
249D LEU* 2.9 54.7 + - + +
273D LEU* 4.2 37.0 + - + -
275D VAL* 4.6 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LYS* 4.5 10.6 + - - -
241D LYS 3.0 17.2 + - - +
242D LYS* 3.9 10.5 - - + +
244D HIS* 1.3 77.5 - - - +
246D ALA* 1.3 66.1 + - - +
248D GLY 4.9 0.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
203D MET* 3.8 26.9 - - + +
206D LEU* 5.2 0.4 - - + -
207D LYS* 3.4 43.3 - - + +
242D LYS 3.4 14.8 + - - +
243D PHE 3.3 4.1 + - - +
244D HIS 3.2 0.8 - - - -
245D GLU* 1.3 83.2 - - - +
247D VAL* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 5.1 2.2 - - + -
108D VAL* 4.7 8.7 - - + -
206D LEU* 4.0 38.1 - - + +
207D LYS* 4.1 18.8 - - - +
210D LYS* 2.7 46.9 + - + +
224D VAL* 3.7 24.2 - - + +
243D PHE* 3.1 18.1 + - - +
244D HIS 3.4 0.2 + - - -
246D ALA* 1.3 83.2 - - + +
248D GLY* 1.3 67.1 + - - +
249D LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LYS* 4.8 2.5 + - - -
224D VAL* 3.3 15.2 - - - +
244D HIS* 2.8 23.6 + - - -
245D GLU 4.8 0.2 - - - -
247D VAL* 1.3 83.5 - - - +
249D LEU* 1.3 68.0 + - - +
250D THR* 3.5 5.4 + - - +
----------------------------------------------------------
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