Contacts of the helix formed by residues 185 - 203 (chain B) in PDB entry 4X5O
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 MET 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PRO* 1.3 92.6 - - + +
186B ILE* 1.3 58.4 + - - +
187B PRO 3.5 1.3 - - - -
188B ASP* 3.3 36.6 - - + +
189B ALA* 3.1 25.8 + - - +
215B ARG* 5.1 3.8 - - - +
301B ASP* 3.2 57.7 - - + +
304B LEU* 4.9 3.1 - - + +
305B LEU* 4.2 21.4 - - + +
308B TYR* 3.6 13.8 - - + -
334B VAL* 5.3 8.5 - - + -
362B ARG* 4.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 3.8 27.8 - - + -
425A LEU* 4.2 24.5 - - + -
440A LEU* 4.2 5.2 - - + -
441A LEU 4.9 0.4 - - - +
442A TYR* 3.7 44.2 - - + +
443A LYS* 4.0 2.2 - - - +
444A LYS* 5.2 0.2 - - + -
183B ASP* 3.4 24.0 - - + +
184B PRO* 5.6 0.2 - - + -
185B MET* 1.3 71.9 - - - +
187B PRO* 1.4 74.3 - - + +
189B ALA* 3.3 4.8 + - + +
190B GLU* 3.0 21.6 + - - +
308B TYR* 4.2 22.0 - - + +
312B PHE* 5.2 4.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 4.2 10.3 - - + -
178B ILE* 3.8 30.4 - - + +
182B PHE* 3.7 33.0 - - + -
183B ASP 4.0 4.3 - - - +
184B PRO 3.6 13.5 - - - +
186B ILE* 1.4 94.1 - - + +
188B ASP* 1.3 59.8 + - - +
190B GLU* 2.9 20.2 + - + +
191B CYS* 3.2 17.5 + - - -
362B ARG* 4.0 6.3 - - - +
380B VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PRO 3.8 2.1 - - - +
185B MET* 3.3 40.0 - - + +
186B ILE 3.3 0.4 - - - -
187B PRO* 1.3 73.9 - - - +
189B ALA* 1.3 59.9 + - - +
191B CYS* 3.9 3.8 + - - +
192B LEU* 3.6 24.8 + - - +
305B LEU* 4.2 7.5 - - + +
334B VAL* 4.0 16.7 - - + +
336B TYR* 4.9 4.0 - - + -
362B ARG* 2.5 58.9 + - - +
380B VAL* 4.0 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B MET 3.1 19.8 + - - +
186B ILE* 3.6 5.8 - - - +
187B PRO 3.1 0.4 - - - -
188B ASP* 1.3 75.8 - - - +
190B GLU* 1.3 65.1 + - - +
192B LEU* 3.4 6.0 + - - +
193B LYS* 3.1 22.5 + - - +
305B LEU* 3.7 18.4 - - + +
308B TYR* 3.9 16.2 - - + -
309B LEU* 4.8 4.1 - - + +
312B PHE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.0 32.5 - - - -
439A GLU* 5.7 1.2 - - - +
440A LEU* 5.9 1.4 - - - +
442A TYR* 3.2 32.8 + - - +
87B HIS* 3.0 24.4 + - - +
148B LYS* 4.2 4.9 + - - +
176B PHE* 5.1 0.2 - - + -
178B ILE* 4.0 12.1 - - + -
186B ILE* 3.0 13.2 + - - +
187B PRO* 2.9 12.4 + - + +
189B ALA* 1.3 77.0 - - - +
191B CYS* 1.3 63.4 + - - +
193B LYS* 3.1 8.6 + - - +
194B ILE* 2.9 40.4 + - + +
312B PHE* 4.4 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 4.7 6.7 - - - -
178B ILE* 4.5 9.2 - - - -
187B PRO 3.2 14.2 + - - -
188B ASP 4.1 6.7 - - - +
190B GLU* 1.3 77.6 - - - +
192B LEU* 1.3 59.0 + - - +
194B ILE* 3.2 8.4 + - - +
195B MET* 2.9 28.7 + - - +
336B TYR* 3.7 20.0 - - + +
380B VAL* 3.9 33.0 - - - -
381B GLY* 4.1 8.1 - - - -
382B LEU* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASP 3.6 15.2 + - - +
189B ALA 3.4 6.9 + - - +
190B GLU 3.2 0.6 - - - -
191B CYS* 1.3 76.9 - - - +
193B LYS* 1.3 62.8 + - - +
195B MET* 3.3 9.6 + - + +
196B CYS* 3.1 29.2 + - - -
209B VAL* 4.5 12.6 - - + -
211B VAL* 4.4 15.3 - - + -
305B LEU* 4.2 20.0 - - + -
309B LEU* 3.7 31.2 - - + -
314B ILE* 4.6 3.8 - - + -
318B ILE* 4.8 4.9 - - + -
334B VAL* 5.8 0.2 - - + -
336B TYR* 3.5 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 4.4 4.6 - - - -
432A TRP* 4.0 28.5 - - + -
433A ASP* 3.0 32.7 + - - -
87B HIS* 4.3 1.3 - - + -
189B ALA 3.1 13.1 + - - +
190B GLU* 3.1 11.3 + - - +
192B LEU* 1.3 76.7 - - - +
194B ILE* 1.3 57.5 + - - +
196B CYS* 3.4 1.6 + - - +
197B GLU* 2.9 46.6 + - - +
312B PHE* 3.2 40.8 + - + -
313B GLY 5.2 0.2 + - - -
314B ILE* 3.5 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B CYS* 3.6 16.8 - - - -
84B PHE* 3.6 27.1 - - + -
87B HIS* 3.4 37.0 - - + +
176B PHE* 3.5 39.9 - - + -
190B GLU* 2.9 24.6 + - + +
191B CYS* 3.2 7.6 + - - +
193B LYS* 1.3 74.8 - - - +
195B MET* 1.3 65.1 + - - +
197B GLU* 3.2 8.5 + - - +
198B ILE* 3.0 24.8 + - + +
382B LEU* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B CYS 2.9 12.9 + - - +
192B LEU* 3.5 16.6 - - + +
194B ILE* 1.3 79.0 - - - +
196B CYS* 1.3 60.8 + - - +
198B ILE* 3.3 4.0 + - - +
199B LEU* 3.1 35.6 + - + +
209B VAL* 3.7 30.7 - - + -
336B TYR* 4.2 28.0 - - - -
338B ALA* 3.6 32.1 - - + +
358B ALA* 4.2 19.5 - - + -
359B ALA 4.8 2.9 - - - +
382B LEU* 4.2 20.4 - - + -
384B ILE* 5.1 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU 3.1 11.3 + - - +
193B LYS 3.8 0.7 - - - +
195B MET* 1.3 76.4 - - - +
197B GLU* 1.3 63.3 + - - +
200B SER* 2.7 34.1 + - - +
207B PHE* 3.7 29.9 - - + -
209B VAL* 4.3 16.4 - - - -
314B ILE* 3.5 50.0 - - + -
317B LYS* 4.5 10.5 - - + -
318B ILE* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.9 11.7 - - - +
433A ASP* 4.8 5.8 - - - +
83B CYS* 3.7 10.3 - - - -
86B ARG* 3.1 41.0 + - - +
87B HIS* 2.6 32.2 + - - -
193B LYS* 2.9 36.3 + - - +
194B ILE* 3.2 7.1 + - - +
196B CYS* 1.3 77.5 - - - +
198B ILE* 1.3 59.2 + - - +
200B SER* 3.9 3.6 - - - -
201B SER* 3.2 28.1 + - - +
314B ILE* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 4.5 4.9 - - + +
80B ILE* 3.5 42.2 - - + +
83B CYS* 3.6 20.9 - - + -
84B PHE* 3.8 24.7 - - + -
194B ILE* 3.0 16.6 + - + +
195B MET 3.8 3.6 - - - +
197B GLU* 1.3 74.0 - - - +
199B LEU* 1.3 64.2 + - + +
200B SER 3.1 1.6 - - - -
201B SER* 3.0 6.3 + - - -
202B LEU* 2.8 42.5 + - + +
384B ILE* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MET* 3.1 25.2 + - + +
198B ILE* 1.3 81.0 - - + +
200B SER* 1.3 61.0 + - - +
202B LEU* 3.9 22.5 + - + +
203B GLN* 3.8 10.0 + - - -
204B ILE* 4.0 20.2 + - + +
205B GLY 4.8 2.8 - - - +
207B PHE* 3.5 52.3 - - + -
338B ALA* 3.9 25.6 - - + -
339B VAL 6.2 0.2 - - - -
357B VAL* 3.6 24.9 - - + -
358B ALA* 5.1 5.2 - - + -
384B ILE* 5.5 4.3 - - + -
389B ILE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B CYS* 2.7 23.7 + - - +
197B GLU* 3.9 4.7 - - - -
198B ILE 3.1 0.6 - - - -
199B LEU* 1.3 77.3 - - - +
201B SER* 1.3 59.2 + - - +
203B GLN* 3.0 26.0 + - - +
205B GLY 5.9 1.3 - - - -
207B PHE* 3.6 16.4 - - - -
317B LYS* 4.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.7 28.9 - - - +
86B ARG* 5.7 3.5 + - - -
197B GLU* 3.2 17.7 + - - +
198B ILE* 3.0 2.5 + - - -
200B SER* 1.3 74.4 - - - +
202B LEU* 1.3 64.8 + - - +
203B GLN* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.1 30.7 - - + +
79B VAL* 3.8 24.2 - - + -
80B ILE* 4.7 3.6 - - + -
198B ILE* 2.8 36.5 + - + +
199B LEU* 4.0 16.2 - - + +
200B SER 3.2 0.2 - - - -
201B SER* 1.3 78.1 - - - +
203B GLN* 1.3 69.8 + - - +
204B ILE* 3.9 16.3 - - + +
389B ILE* 3.7 37.0 - - + -
393B VAL* 4.7 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 3.8 0.6 + - - -
200B SER 3.0 21.9 + - - +
201B SER* 3.6 11.8 - - - +
202B LEU* 1.3 82.0 - - - +
204B ILE* 1.3 60.9 + - - +
205B GLY 3.5 5.8 + - - +
396B ARG* 3.9 39.3 + - - +
----------------------------------------------------------
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