Contacts of the helix formed by residues 262 - 284 (chain M) in PDB entry 7PRC
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 262 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 6.0 0.4 - - - -
35H GLU* 3.8 24.7 - - - -
36H ASP* 2.7 24.2 + - - -
258M ALA* 3.1 0.7 - - - +
259M THR* 2.7 41.2 + - - -
261M GLU* 1.3 75.5 - - - +
263M VAL* 1.3 54.6 + - - +
265M ARG* 2.6 38.7 + - - +
266M TRP* 2.9 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213M LEU* 5.1 6.2 - - + +
217M HIS* 4.3 14.1 - - + +
258M ALA* 4.0 12.1 - - + -
259M THR 2.9 13.6 + - - +
260M ILE* 3.4 23.6 - - - +
262M SER* 1.3 78.6 + - - +
264M HIS* 1.3 70.6 + - + +
266M TRP* 3.2 10.6 + - + +
267M GLY* 2.9 23.7 + - - -
501M MQ7 3.7 51.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU* 6.4 1.6 - - + -
190L HIS* 2.9 20.3 + + - -
191L GLY* 3.8 22.3 - - - +
194L ILE* 3.7 24.4 - - + +
195L LEU* 4.2 8.7 - - + -
217M HIS* 2.9 15.3 + + - -
232M GLU* 2.7 21.2 + - + -
260M ILE* 2.7 29.6 + - + -
261M GLU 3.0 8.3 + - - +
262M SER 3.0 1.4 + - - -
263M VAL* 1.3 72.5 - - + +
265M ARG* 1.3 59.7 + - - +
267M GLY* 3.6 1.6 - - - +
268M TRP* 2.8 30.4 + - - +
500M FE2 2.0 33.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H TYR* 3.1 32.4 + - + -
32H LEU* 3.8 15.9 - - + -
35H GLU* 4.0 24.2 + - - +
66H LYS* 3.7 3.6 - - - +
195L LEU* 3.5 32.6 - - + +
199L ASN* 3.1 14.8 + - - +
143M HIS* 4.7 1.6 + - - -
261M GLU* 2.7 35.0 + - - +
262M SER* 2.6 19.6 + - - +
264M HIS* 1.3 69.1 - - - +
266M TRP* 1.3 64.8 + - - +
268M TRP* 2.9 15.2 + - - +
269M PHE* 2.9 14.6 + - - +
802M SO4 2.8 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 266 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 3.7 28.9 - - + -
32H LEU* 3.8 40.1 - - + +
33H ARG* 4.1 12.1 - - + -
36H ASP* 3.0 37.5 + - - -
213M LEU* 4.0 10.8 - - + -
256M PHE* 5.0 2.7 - + - -
258M ALA* 4.5 0.4 - - + -
262M SER 2.9 22.7 + - - -
263M VAL* 3.4 11.4 - - + +
265M ARG* 1.3 72.4 - - - +
267M GLY* 1.3 57.1 + - - +
269M PHE* 3.8 2.4 - - - +
270M PHE* 3.0 61.1 + + - +
501M MQ7 3.8 49.1 - - + +
701M LDA 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 267 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU* 4.0 32.5 - - - +
191L GLY* 5.9 0.2 - - - -
213M LEU* 4.0 11.4 - - - +
263M VAL 2.9 13.8 + - - -
264M HIS* 3.6 3.8 - - - -
265M ARG 3.1 0.2 - - - -
266M TRP* 1.3 74.7 - - - +
268M TRP* 1.3 65.8 + - - +
270M PHE* 3.0 3.8 + - - +
271M SER* 2.8 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 268 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU 4.8 2.0 + - - -
188L GLY* 3.9 11.4 - - - -
191L GLY* 5.1 0.2 - - - -
192L GLY* 3.5 30.1 - - - +
195L LEU* 4.2 17.0 - - + -
143M HIS* 2.8 41.9 + + + -
146M TRP* 3.9 14.8 - - + -
147M ASN* 3.4 28.2 - - + +
264M HIS 2.8 20.0 + - - +
265M ARG* 2.9 4.2 + - - +
267M GLY* 1.3 71.7 - - - +
269M PHE* 1.3 62.6 + + + +
271M SER* 3.1 4.9 + - - -
272M LEU* 2.8 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H VAL* 6.2 1.8 - - + -
24H ILE* 5.0 9.6 - - + -
27H VAL* 3.9 32.5 - - + -
28H VAL* 4.1 17.7 - - + -
32H LEU* 3.5 30.7 - - + -
206M PHE* 4.4 9.0 - + - -
265M ARG 2.9 15.5 + - - +
266M TRP 3.8 1.6 - - - +
268M TRP* 1.3 88.8 - + + +
270M PHE* 1.3 82.9 + + - +
271M SER 3.2 0.2 + - - -
272M LEU* 3.3 10.8 + - + +
273M MET* 2.9 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 5.5 0.2 - - + -
304L BCB 3.9 22.7 - - + -
206M PHE* 3.6 30.6 - + - +
209M GLY* 4.0 25.8 - - - -
210M CYS* 3.7 11.7 - - - -
213M LEU* 4.0 13.7 - - + -
266M TRP* 3.0 52.0 + + - +
267M GLY* 3.5 3.6 - - - +
269M PHE* 1.3 95.3 - + - +
271M SER* 1.3 62.2 + - - +
273M MET* 3.3 6.8 + - - +
274M VAL* 3.4 15.8 + - - +
501M MQ7 3.7 23.6 - - + -
701M LDA 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA 3.2 18.8 + - - -
187L LEU* 4.4 1.1 - - - -
188L GLY* 3.4 24.5 - - - -
401L BPB 3.1 33.7 - - - +
147M ASN* 3.1 10.8 + - - -
210M CYS* 3.7 13.0 - - - -
267M GLY 2.8 16.1 + - - -
268M TRP 3.5 6.1 - - - -
270M PHE* 1.3 70.9 - - - +
272M LEU* 1.3 67.2 + - - +
273M MET 3.2 0.7 + - - -
274M VAL* 3.2 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 5.3 0.2 - - - -
146M TRP 4.1 14.4 - - - +
147M ASN* 3.3 17.5 + - - +
150M ALA* 3.7 25.6 - - + -
268M TRP* 2.8 46.3 + - + +
269M PHE* 3.3 12.1 - - + +
271M SER* 1.3 73.3 - - - +
273M MET* 1.3 65.6 + - - +
275M MET* 3.1 10.4 + - - +
276M VAL* 3.0 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 273 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 3.5 29.4 - - - +
23H VAL* 5.2 11.0 - - + -
24H ILE* 4.4 14.8 - - + -
206M PHE* 3.6 28.5 - - + -
269M PHE* 2.9 53.2 + - + +
270M PHE 3.3 0.4 + - - +
271M SER 3.2 0.6 + - - -
272M LEU* 1.3 76.5 - - - +
274M VAL* 1.3 66.3 + - - +
275M MET 3.1 0.2 - - - -
276M VAL* 3.8 27.1 - - + -
277M SER* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA* 5.0 3.8 - - + -
401L BPB 4.2 10.8 - - + -
203M SER* 2.8 37.5 + - - +
206M PHE* 3.5 14.1 - - + +
207M ALA* 3.5 38.1 - - + +
210M CYS* 4.2 7.2 - - - -
270M PHE 3.4 8.3 + - - +
271M SER* 3.6 8.5 - - - +
272M LEU 3.2 0.4 - - - -
273M MET* 1.3 76.1 - - - +
275M MET* 1.3 75.0 + - + +
278M ALA* 3.1 16.6 + - - +
806M BCB 4.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 275 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 3.5 28.9 - - + -
147M ASN 5.6 0.7 - - - +
150M ALA* 3.8 22.4 - - + +
151M ALA* 3.7 26.2 - - - +
154M PHE* 3.9 22.7 - - + +
271M SER 4.5 0.2 - - - +
272M LEU* 3.1 7.6 + - - +
274M VAL* 1.3 82.8 - - + +
276M VAL* 1.3 65.6 + - - +
278M ALA* 3.3 3.1 + - + +
279M SER* 2.9 28.5 + - - -
806M BCB 3.3 57.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 5.7 1.8 - - - +
150M ALA* 4.5 10.5 - - + -
153M PHE* 6.5 0.2 - - - -
272M LEU* 3.0 40.0 + - + +
273M MET* 4.1 25.4 - - + -
275M MET* 1.3 79.8 - - - +
277M SER* 1.3 64.2 + - - +
279M SER* 3.2 12.7 + - - -
280M VAL* 3.2 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 3.3 23.7 + - - -
199M TRP* 3.3 20.8 - - - +
202M PHE* 3.6 13.5 - - - +
203M SER 3.8 22.0 - - - -
206M PHE* 3.8 5.9 - - - -
273M MET* 2.9 26.2 + - - +
274M VAL 4.1 0.4 - - - -
276M VAL* 1.3 74.5 - - - +
278M ALA* 1.3 63.4 + - - +
280M VAL* 3.4 1.6 + - - +
281M GLY 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M PHE* 3.6 25.1 - - + -
203M SER* 3.5 5.1 + - - +
274M VAL 3.1 19.3 + - - +
275M MET* 3.6 5.8 - - - +
276M VAL 3.2 0.4 - - - -
277M SER* 1.3 74.7 - - - +
279M SER* 1.3 57.8 + - - +
281M GLY* 2.9 5.4 + - - -
282M ILE* 2.8 26.0 + - - +
806M BCB 3.1 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M ALA 4.7 0.5 + - - -
153M PHE* 3.7 18.2 - - - -
154M PHE* 3.4 24.9 + - - -
157M CYS* 3.7 21.8 - - - -
275M MET 2.9 15.9 + - - -
276M VAL* 3.5 9.0 - - - -
278M ALA* 1.3 76.3 - - - +
280M VAL* 1.3 57.1 + - - +
282M ILE* 3.0 5.3 + - - +
283M LEU* 2.7 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL* 3.9 18.2 - - + -
20H GLN* 4.7 8.1 - - - +
199M TRP* 3.7 33.2 - - + +
276M VAL* 3.2 19.6 + - + +
277M SER 3.9 1.6 - - - +
279M SER* 1.3 74.9 - - - +
281M GLY* 1.3 64.9 + - - +
283M LEU* 3.1 12.4 + - + -
284M LEU* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194M PHE* 5.5 0.4 - - - -
197M CYS* 4.3 5.2 - - - -
199M TRP* 3.4 28.1 - - - +
277M SER 3.0 7.3 + - - -
278M ALA 2.9 8.9 + - - -
280M VAL* 1.3 78.2 - - - +
282M ILE* 1.3 60.0 + - - +
284M LEU* 3.6 3.2 + - - +
285M THR* 2.9 25.4 + - - -
292M TRP* 4.1 2.6 - - - -
806M BCB 4.0 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M PHE* 4.0 6.7 - - + -
157M CYS* 4.2 19.1 - - + +
158M ILE* 3.8 20.9 - - + -
162M HIS* 3.5 33.7 + - + +
187M PHE* 3.9 24.0 - - + -
194M PHE* 4.0 11.4 - - + -
278M ALA 2.8 19.6 + - - +
279M SER 3.0 5.6 + - - +
281M GLY* 1.3 70.1 - - - +
283M LEU* 1.3 66.5 + - + +
284M LEU 3.0 2.0 - - - -
285M THR* 2.9 22.2 + - - +
806M BCB 3.2 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M PHE* 4.3 23.3 - - + -
157M CYS* 4.4 12.1 - - + -
161M ILE* 3.9 18.6 - - + -
162M HIS* 5.3 2.2 - - - +
165M LEU* 3.7 28.7 - - + +
279M SER* 2.7 29.3 + - - +
280M VAL* 3.1 12.5 + - + +
282M ILE* 1.3 71.8 - - + +
284M LEU* 1.3 61.3 + - + +
287M THR* 2.9 27.7 + - - +
288M PHE* 4.8 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ILE* 4.3 7.9 - - + -
13H ALA* 4.0 24.2 - - + -
16H VAL* 4.4 10.1 - - + -
199M TRP* 3.4 44.4 - - + -
280M VAL* 2.9 30.1 + - + +
281M GLY 4.1 3.6 - - - +
282M ILE 3.0 0.2 - - - -
283M LEU* 1.3 82.1 - - + +
285M THR* 1.3 56.4 + - - +
288M PHE* 3.0 47.9 + - + -
289M VAL* 3.1 10.2 + - + +
292M TRP* 4.2 11.0 - - + -
----------------------------------------------------------
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