Contacts of the helix formed by residues 236 - 256 (chain B) in PDB entry 4RN1
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 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 3.6 10.3 + - - +
235B ILE* 1.3 79.1 - - - +
237B ASP* 1.3 67.6 + - - +
238B GLU* 3.3 3.4 + - + +
239B LYS* 3.5 5.9 + - + +
240B TYR* 3.0 22.7 + - - +
278B ASN* 3.5 37.6 - - + +
279B MET* 3.5 6.1 - - - -
350B PRO* 4.2 17.4 - - + +
351B SER 4.7 1.8 + - - -
353B ARG 4.5 7.9 + - - -
355B ASP* 5.0 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLN* 1.3 76.6 - - - +
238B GLU* 1.3 63.4 + - - +
240B TYR* 3.7 1.4 - - - +
241B TYR* 3.0 26.3 + - - +
278B ASN 4.7 0.8 + - - -
279B MET* 3.2 19.2 - - - +
280B THR* 2.3 54.7 + - - +
282B VAL* 4.4 4.1 - - + +
283B GLY* 3.2 23.3 + - - +
286B LYS* 5.9 4.9 - - - -
350B PRO* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLN* 3.4 1.8 - - + +
237B ASP* 1.3 78.7 - - - +
239B LYS* 1.3 63.3 + - - +
241B TYR* 3.4 5.3 + - - +
242B GLN* 3.1 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 4.1 13.9 - - + -
236B GLN* 3.5 7.8 + - + +
237B ASP 3.5 0.2 - - - -
238B GLU* 1.3 76.4 - - - +
240B TYR* 1.3 64.8 + - - +
242B GLN* 3.4 17.2 + - - +
243B ILE* 3.2 30.4 + - + +
355B ASP* 2.4 32.8 + - - +
357B ASN* 3.0 32.8 + - + +
359B PRO* 5.0 10.9 - - - +
362B ILE* 4.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.6 29.6 + - + +
200B LEU* 3.6 38.6 + - + +
231B ILE* 4.1 6.3 - - + -
235B ILE* 3.7 26.8 - - + +
236B GLN 3.0 19.3 + - - +
237B ASP 3.7 0.4 - - - +
239B LYS* 1.3 77.6 - - - +
241B TYR* 1.3 57.3 + - - +
243B ILE* 3.3 4.7 + - - +
244B CYS* 2.9 25.2 + - + +
268B THR* 5.1 1.2 - - + +
277B PHE* 4.1 22.8 - + - -
279B MET* 3.5 32.5 - - + -
284B ILE* 4.2 13.9 - - + -
287B CYS* 3.9 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP 3.0 17.0 + - - +
238B GLU* 3.8 5.6 - - - +
240B TYR* 1.3 74.4 - - - +
242B GLN* 1.3 61.8 + - + +
244B CYS* 4.2 4.0 - - - -
245B GLU* 2.8 75.1 + - + +
283B GLY* 4.8 2.5 - - - +
286B LYS* 3.3 62.2 + - + -
287B CYS* 3.9 15.9 - - - -
290B TYR* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 3.1 41.0 + - + +
239B LYS* 3.6 19.0 - - - +
240B TYR 3.3 0.2 - - - -
241B TYR* 1.3 82.6 - - + +
243B ILE* 1.3 58.2 + - + +
245B GLU* 4.3 5.7 - - - +
246B SER* 2.8 34.0 + - - -
366B LEU* 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.4 9.4 - - + -
229B VAL* 3.7 29.2 - - + -
231B ILE* 4.6 7.9 - - + -
235B ILE* 3.8 21.3 - - + -
239B LYS* 3.2 18.7 + - + +
240B TYR* 3.7 5.4 - - - +
242B GLN* 1.3 75.5 - - + +
244B CYS* 1.3 64.8 + - - +
246B SER* 3.4 2.3 + - - -
247B VAL* 3.1 25.8 + - + +
362B ILE* 3.6 47.8 - - + -
366B LEU* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 4.3 14.6 - - - -
200B LEU* 3.9 25.8 - - + -
240B TYR* 2.9 17.5 + - + +
241B TYR* 3.8 2.5 - - + +
243B ILE* 1.3 77.6 - - - +
245B GLU* 1.3 58.2 + - - +
247B VAL* 3.4 4.4 + - - +
248B LEU* 2.9 57.6 + - - +
287B CYS* 3.6 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 2.8 57.5 + - + +
242B GLN* 4.3 5.0 - - - +
244B CYS* 1.3 73.4 - - - +
246B SER* 1.3 58.2 + - - +
248B LEU* 4.0 4.8 - - - +
249B LYS* 2.9 35.1 + - + +
290B TYR* 3.7 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLN 2.8 21.9 + - - -
243B ILE 3.7 3.6 - - - -
245B GLU* 1.3 80.2 + - - +
247B VAL* 1.3 62.0 + - - +
249B LYS* 3.8 5.2 - - - +
250B GLU* 3.3 29.6 + - - +
366B LEU* 4.2 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B VAL* 3.9 27.6 - - + -
200B LEU* 5.2 2.9 - - + -
227B VAL* 4.1 12.8 - - + -
229B VAL* 4.0 21.3 - - + -
243B ILE* 3.1 21.4 + - + +
244B CYS* 3.8 4.9 - - - +
246B SER* 1.3 77.3 - - - +
248B LEU* 1.3 59.4 + - + +
250B GLU* 3.3 6.2 + - - +
251B VAL* 2.9 37.2 + - + +
366B LEU* 3.8 19.3 - - + -
369B ILE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.7 4.5 - - + -
175B VAL* 3.9 31.0 - - + -
198B VAL* 4.7 13.5 - - + -
200B LEU* 6.2 1.6 - - + -
244B CYS* 2.9 41.5 + - - +
245B GLU 4.0 0.4 - - - +
247B VAL* 1.3 80.3 - - + +
249B LYS* 1.3 57.7 + - - +
251B VAL* 3.9 4.8 - - + +
252B TYR* 2.9 32.7 + - - +
287B CYS* 4.7 3.1 - - - +
290B TYR* 4.0 22.4 - - + -
291B ILE* 3.8 30.3 - - + -
294B TRP* 3.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU* 2.9 20.8 + - + +
246B SER* 3.8 6.5 - - - +
248B LEU* 1.3 78.2 - - - +
250B GLU* 1.3 66.3 + - + +
252B TYR* 3.9 3.4 - - - +
253B GLN* 3.3 37.3 + - - +
290B TYR* 3.4 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 3.3 15.6 + - - +
247B VAL* 3.3 7.0 + - - +
249B LYS* 1.3 76.9 - - - +
251B VAL* 1.3 65.7 + - - +
253B GLN* 3.5 14.3 + - - +
254B ALA* 3.1 26.9 + - - +
369B ILE* 5.8 1.3 - - + -
370B LYS* 3.3 51.2 + - + +
373B LEU* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 3.6 39.9 - - + -
196B MET* 3.6 17.3 - - - -
198B VAL* 3.8 20.2 - - + -
227B VAL* 4.3 4.0 - - + -
247B VAL* 2.9 28.5 + - + +
248B LEU* 3.9 7.0 - - + +
250B GLU* 1.3 77.6 - - - +
252B TYR* 1.3 58.1 + - - +
254B ALA* 4.8 0.2 - - - -
255B PHE* 2.8 33.4 + - + +
373B LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 2.9 19.5 + - - +
249B LYS* 3.9 5.2 - - - +
251B VAL* 1.3 78.4 - - - +
253B GLN* 1.3 66.7 + - + +
256B ASN* 2.9 43.7 + - - +
257B PRO* 3.8 21.8 - - + -
294B TRP* 3.4 66.5 + + + +
296B LEU* 4.2 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 3.3 23.8 + - - +
250B GLU* 4.0 14.0 - - - +
251B VAL 3.3 0.2 - - - -
252B TYR* 1.3 85.8 - - + +
254B ALA* 1.3 62.5 + - - +
256B ASN* 4.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLU 3.1 18.5 + - - +
251B VAL 4.1 1.1 - - - +
253B GLN* 1.3 80.9 - - - +
255B PHE* 1.3 60.5 + - + +
256B ASN* 5.0 0.9 - - - +
373B LEU* 3.7 32.5 - - + +
376B VAL* 3.7 28.1 - - + +
377B VAL* 4.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.0 51.8 + - + -
172B ILE 3.5 22.9 - - - -
173B LEU* 4.7 4.3 - - + -
193B SER 3.2 21.3 - - - -
194B LYS 3.8 13.7 - - - -
196B MET* 3.6 48.5 - - + -
225B TYR* 3.9 16.2 - + - -
251B VAL* 2.8 18.6 + - + +
254B ALA* 1.3 74.0 - - - +
256B ASN* 1.3 70.5 + - - +
257B PRO* 3.9 17.3 - - + -
376B VAL* 4.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 2.3 43.5 + - - +
252B TYR* 2.9 30.2 + - - +
253B GLN 4.8 6.3 - - - +
254B ALA 5.0 0.7 - - - +
255B PHE* 1.3 77.7 - - - +
257B PRO* 1.3 74.2 - - - +
258B LYS* 4.6 11.3 - - - +
----------------------------------------------------------
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