Contacts of the helix formed by residues 236 - 258 (chain B) in PDB entry 1RRM
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 ASP 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 5.6 0.7 + - - -
231B GLY* 2.9 24.7 + - - +
232B SER* 4.2 2.8 - - - +
234B ALA* 3.6 2.5 - - + +
235B GLY* 1.3 75.4 - - - +
237B LYS* 1.3 77.5 + - - +
238B ASP* 3.5 12.6 + - - +
239B ALA* 2.9 28.1 + - + +
240B GLY* 3.2 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.9 42.6 + - - +
183B ASP* 5.3 6.1 - - - +
235B GLY 3.3 10.0 + - - +
236B ASP* 1.3 85.4 + - - +
238B ASP* 1.3 67.7 + - - +
240B GLY 3.1 7.4 + - - -
241B GLU 3.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 5.5 1.4 + - - +
236B ASP* 3.5 10.9 + - - +
237B LYS* 1.3 77.6 - - - +
239B ALA* 1.3 64.9 + - - +
241B GLU* 3.2 17.2 + - - +
242B GLU* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA* 3.5 13.8 - - + +
231B GLY* 3.7 7.6 - - - -
232B SER* 3.4 29.6 - - - +
236B ASP* 2.9 20.3 + - + +
238B ASP* 1.3 76.1 - - - +
240B GLY* 1.3 57.5 + - - +
242B GLU* 3.2 14.8 + - - +
243B MSE 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.5 4.9 - - - -
142B ALA* 5.4 0.5 - - - +
179B ALA* 4.0 8.8 - - - +
182B MSE 4.8 4.2 - - - +
183B ASP* 5.3 2.5 - - - -
190B LYS* 6.2 0.7 - - - -
232B SER* 3.6 17.2 + - - -
236B ASP 3.2 9.0 + - - -
237B LYS 3.1 9.0 + - - -
239B ALA* 1.3 78.3 - - - +
241B GLU* 1.3 59.9 + - - +
243B MSE 3.4 4.1 + - - +
244B ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MSE 5.8 3.6 - - - +
15B GLY* 3.6 11.4 - - - -
16B ARG* 3.1 40.8 + - - +
179B ALA* 3.8 19.2 - - + +
237B LYS 3.3 10.2 + - - +
238B ASP* 3.2 19.1 + - - +
240B GLY* 1.3 73.9 - - - +
242B GLU* 1.3 66.9 + - + +
244B ALA* 3.2 5.8 + - + +
245B LEU* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ILE* 3.2 20.3 - - + +
227B GLY 4.9 2.8 - - - +
228B ALA* 3.4 23.4 + - + +
236B ASP* 5.5 0.2 - - - +
238B ASP* 3.0 29.6 + - - +
239B ALA* 3.2 11.9 + - - +
241B GLU* 1.3 77.8 - - - +
243B MSE 1.3 57.8 + - - +
245B LEU* 3.2 6.8 + - - +
246B GLY 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 3.7 22.9 - - + +
190B LYS 5.3 0.2 - - - +
194B GLY* 3.6 31.4 - - - +
197B ALA* 4.7 2.7 - - + -
224B ILE* 5.1 0.2 - - - -
225B ILE* 3.8 36.8 - - + +
228B ALA* 4.1 6.7 - - + -
229B LEU* 3.7 29.4 - - + -
232B SER* 3.8 21.5 - - - +
239B ALA 2.8 19.2 + - - +
240B GLY* 3.7 7.4 - - - +
242B GLU* 1.3 75.6 - - - +
244B ALA* 1.3 63.8 + - - +
246B GLY* 4.4 1.8 - - - +
247B GLN* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 4.4 0.4 - - - +
177B ILE* 3.4 23.0 - - + +
179B ALA* 4.5 9.0 - - + +
182B MSE 3.6 29.2 - - + -
240B GLY 3.1 11.5 + - - +
241B GLU* 3.3 14.4 - - + +
242B GLU 3.2 0.2 - - - -
243B MSE 1.3 77.7 - - - +
245B LEU* 1.3 61.6 + - - +
247B GLN* 3.0 29.9 + - - +
248B TYR* 3.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TRP* 4.1 18.8 - - + -
212A ALA* 3.7 29.8 - - + -
213A LEU* 4.3 13.2 - - + +
14B PHE* 4.1 27.8 - - + -
177B ILE* 5.0 2.9 - - - -
224B ILE* 4.4 15.5 - - + -
241B GLU 3.2 7.9 + - - +
242B GLU* 3.2 9.9 + - - +
244B ALA* 1.3 78.1 - - - +
246B GLY* 1.3 59.4 + - - +
248B TYR* 3.1 6.1 + - - +
249B VAL* 2.9 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA* 3.7 8.2 - - - +
224B ILE* 3.7 30.7 - - - +
225B ILE* 4.0 13.8 - - - +
242B GLU 2.9 11.8 + - - -
243B MSE 3.3 1.1 + - - -
245B LEU* 1.3 78.0 - - - +
247B GLN* 1.3 60.8 + - - +
249B VAL* 3.3 2.3 + - - -
250B ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PRO* 4.8 0.4 - - - +
141B THR 4.1 4.3 - - - +
142B ALA* 3.7 18.8 - - - +
143B GLY* 3.4 24.0 + - - +
144B THR 3.8 0.2 + - - -
145B ALA* 3.2 37.4 + - - +
147B GLU* 2.9 24.4 + - - +
177B ILE* 4.2 6.3 - - - +
182B MSE 4.5 5.1 - - - +
197B ALA* 3.7 24.4 - - + +
200B HIS* 5.4 0.2 + - - -
225B ILE* 4.4 1.8 - - - +
243B MSE 3.0 22.3 + - + +
244B ALA* 3.0 19.6 + - - +
246B GLY* 1.3 75.7 - - - +
248B TYR* 1.3 67.9 + - - +
250B ALA* 3.5 5.4 - - - +
251B GLY 3.4 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 6.0 1.9 - - - +
213A LEU* 5.6 0.2 - - + -
8B LEU* 5.9 0.2 - - - +
9B ASN* 2.6 37.8 + - - +
12B ALA* 3.7 11.3 - - + +
14B PHE* 3.3 32.9 - + + -
145B ALA* 4.5 3.4 - - - -
147B GLU* 3.5 21.5 - - + -
148B VAL* 3.5 20.2 - - + +
177B ILE* 3.7 22.4 - - + -
244B ALA 3.6 4.9 - - - +
245B LEU 3.1 9.5 + - - +
247B GLN* 1.3 92.4 - - - +
249B VAL* 1.3 69.7 + - + +
251B GLY* 2.9 12.5 + - - -
252B MSE 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.1 19.3 - - + -
217B LEU* 3.4 45.9 - - + +
220B LYS* 4.8 8.1 - - + -
221B ALA* 4.1 9.0 - - + +
224B ILE* 4.9 5.4 - - + -
245B LEU* 2.9 42.1 + - + +
246B GLY* 3.8 6.3 - - - +
248B TYR* 1.3 76.1 - - + +
250B ALA* 1.3 63.4 + - - +
252B MSE 3.2 26.1 + - - +
253B GLY 3.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 4.0 20.6 - - - +
200B HIS* 4.2 6.3 - - + -
201B ALA* 4.1 11.4 - - + +
218B HIS* 3.4 10.1 + - - -
221B ALA* 3.7 16.3 - - + +
225B ILE* 4.7 1.1 - - + -
246B GLY 3.0 13.3 + - - +
247B GLN* 3.5 12.6 - - - +
249B VAL* 1.3 76.2 - - - +
251B GLY* 1.3 63.3 + - - +
253B GLY 3.1 3.3 + - - -
254B PHE* 3.1 26.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 3.6 14.1 - - - -
148B VAL* 3.9 9.1 - - - +
149B THR* 4.0 1.6 - - - +
247B GLN 3.4 4.2 + - - -
248B TYR 2.9 8.4 + - - -
250B ALA* 1.3 75.9 - - - +
252B MSE 1.3 63.5 + - - +
253B GLY 3.0 3.2 + - - -
254B PHE* 3.4 20.6 - - - -
255B SER* 3.2 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MSE 5.9 0.9 - - + -
8A LEU* 4.1 16.4 - - + -
213A LEU* 4.6 16.4 - - + -
217A LEU* 5.8 2.0 - - + -
252A MSE 4.2 11.9 - - + -
6B MSE 3.4 11.4 - - - +
8B LEU* 3.9 38.9 - - + +
148B VAL* 4.4 5.4 - - + -
217B LEU* 3.9 26.7 - - + -
248B TYR* 3.1 42.0 + - + +
249B VAL* 3.2 22.4 + - - +
251B GLY* 1.3 76.2 - - - +
253B GLY* 1.3 57.5 + - - +
256B ASN* 2.9 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 3.8 13.8 - - - +
217B LEU* 4.1 8.0 - - - +
218B HIS* 3.2 23.6 - - - -
249B VAL 3.5 3.0 + - - -
250B ALA 3.1 4.0 + - - -
251B GLY 3.0 1.6 - - - -
252B MSE 1.3 79.6 - - - +
254B PHE* 1.3 62.9 + - - +
255B SER 3.2 2.0 - - - -
256B ASN* 3.0 16.6 + - - +
257B VAL* 3.3 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR 3.8 7.4 - - - -
145B ALA* 4.2 2.5 - - + -
149B THR* 3.5 21.1 - - + -
151B ASN* 4.2 5.4 + - - -
200B HIS* 3.4 46.0 - + + +
218B HIS* 2.7 19.3 + - + +
250B ALA 3.1 20.9 + - - -
251B GLY* 3.4 18.8 - - - -
253B GLY* 1.3 70.7 - - - +
255B SER* 1.3 62.8 + - - +
257B VAL* 4.0 1.3 - - - -
258B GLY* 2.8 34.2 + - - +
259B LEU* 3.5 40.4 - - + -
390B PGO 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE 4.8 1.1 + - - -
148B VAL 4.2 3.1 + - - -
149B THR* 3.3 20.8 - - - -
150B ILE* 2.9 47.8 + - - +
151B ASN* 4.2 11.1 + - - +
166B VAL* 5.4 1.2 - - - +
251B GLY 3.2 17.3 + - - -
253B GLY 3.2 0.6 + - - -
254B PHE* 1.3 87.3 - - - +
256B ASN* 1.3 68.8 + - - +
257B VAL 3.9 0.3 + - - -
258B GLY 4.9 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
5B ARG* 3.7 15.7 + - - +
6B MSE 3.6 29.9 - - - +
7B ILE* 2.7 55.1 + - - +
150B ILE* 5.2 2.6 - - - +
211B TRP* 5.3 0.2 + - - -
214B THR* 4.8 0.9 - - + -
252B MSE 2.9 22.3 - - - +
253B GLY 3.0 6.9 + - - +
255B SER* 1.3 86.3 + - - +
257B VAL* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASN* 5.8 0.7 - - - +
204B GLY 4.1 0.7 - - - +
207B THR* 3.7 29.0 + - + +
209B GLY* 3.4 32.4 + - - +
210B ALA* 4.7 0.2 - - - -
211B TRP* 3.6 12.3 - - + +
214B THR* 3.5 26.9 - - + +
218B HIS* 3.9 18.8 - - + -
253B GLY 3.3 16.4 - - - +
254B PHE* 4.0 1.3 - - - -
255B SER 3.6 0.2 - - - -
256B ASN* 1.3 84.4 - - - +
258B GLY* 1.3 62.3 + - - +
365B GLY* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY* 3.5 22.0 - - - -
207B THR* 3.5 10.5 - - - +
254B PHE* 2.8 17.0 + - - +
255B SER 4.8 0.6 + - - -
257B VAL* 1.3 79.3 - - - +
259B LEU* 1.3 67.0 + - - +
365B GLY* 5.8 1.8 - - - -
----------------------------------------------------------
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