Contacts of the helix formed by residues 214 - 229 (chain B) in PDB entry 3MYV
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 ASN 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B MSE 3.4 14.5 - - - +
205B SER 3.5 6.5 - - - +
206B GLU 3.2 22.8 + - - -
207B GLU 3.2 24.0 + - - +
208B LYS* 4.0 5.2 - - - +
209B ASN* 5.0 6.1 - - + +
212B ARG 3.9 2.3 + - - +
213B MSE 1.3 72.7 - - - +
215B LYS* 1.3 66.2 + - - +
216B TYR* 3.4 9.3 + - - +
217B ALA* 3.1 21.4 + - - +
218B ALA 3.0 18.5 + - - -
252B TYR* 3.0 24.3 + - - -
275B PHE 4.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.3 37.9 + - + +
202B THR* 5.1 6.3 + - - +
204B MSE 3.6 26.6 + - + +
205B SER 2.9 23.9 + - - +
206B GLU* 3.9 29.0 + - + +
214B ASN* 1.3 71.2 - - - +
216B TYR* 1.3 57.9 + - + +
218B ALA* 3.3 4.1 + - - +
219B ARG* 2.9 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 3.8 47.3 + - + -
214B ASN* 3.2 18.1 + - - +
215B LYS* 1.3 77.1 - - - +
217B ALA* 1.3 56.6 - - - +
219B ARG* 3.2 10.0 + - - +
220B ALA* 2.9 28.4 + - - +
242B LEU* 3.6 25.5 - - + +
245B ASP* 3.9 13.3 + - + +
246B ALA* 4.1 23.1 - - - -
249B SER* 3.1 28.7 + - - -
251B SER* 4.4 6.1 + - - -
252B TYR* 3.5 26.9 - + + -
275B PHE* 3.8 20.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B MSE 3.9 14.8 - - + -
214B ASN* 3.1 27.5 + - - +
216B TYR* 1.3 75.8 - - - +
218B ALA* 1.3 57.6 + - - +
220B ALA* 3.2 2.4 + - - +
221B LEU 2.9 25.3 + - - -
275B PHE* 3.6 32.7 - - + +
276B PHE* 4.0 9.0 - - + -
358B LEU* 3.5 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 4.4 3.8 - - + -
197B LEU* 4.0 16.4 - - + +
201B VAL* 3.9 15.3 - - + -
204B MSE 3.5 33.2 - - + -
213B MSE 4.8 5.3 - - - +
214B ASN 3.0 10.3 + - - +
215B LYS* 3.7 4.7 - - - +
217B ALA* 1.3 73.7 - - - +
219B ARG* 1.3 56.9 + - - +
221B LEU* 3.4 7.8 + - - +
222B LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.7 33.1 - - + +
206B GLU* 4.6 9.5 + - - -
215B LYS* 2.9 34.4 + - - +
216B TYR* 3.5 11.3 - - - +
218B ALA* 1.3 73.9 - - - +
220B ALA* 1.3 60.5 + - - +
222B LEU* 3.3 2.8 + - - -
223B ALA* 2.9 26.9 + - - +
238B LEU* 3.4 31.4 - - + +
241B GLN* 3.7 19.8 - - - +
242B LEU* 3.8 40.0 - - + +
245B ASP* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR 2.9 13.1 + - - +
217B ALA 3.2 8.0 + - - +
219B ARG* 1.3 76.6 - - - +
221B LEU* 1.3 62.7 + - - +
223B ALA* 3.2 6.4 + - - +
224B ARG* 3.1 20.8 + - - +
242B LEU* 3.4 14.5 - - + +
275B PHE* 3.7 25.8 - - + -
358B LEU* 4.1 13.4 - - + +
362B GLU* 5.5 1.0 - - - +
363B VAL* 3.7 13.0 - - + -
366B ILE* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA 4.2 10.3 - - - +
145B LEU* 4.0 40.4 - - + +
148B PHE* 4.6 1.8 - - + -
197B LEU* 3.8 22.0 - - + -
213B MSE 4.3 12.6 - - - -
217B ALA 2.9 16.5 + - - +
218B ALA* 3.6 5.2 - - - +
220B ALA* 1.3 76.9 - - - +
222B LEU* 1.3 56.6 + - - +
224B ARG* 3.2 31.5 + - - +
225B ILE* 2.9 46.0 + - + +
357B VAL* 6.6 0.2 - - + -
358B LEU* 3.7 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 4.3 13.2 - - + +
197B LEU* 3.6 28.9 - - + +
198B GLU* 3.8 28.0 - - + +
201B VAL* 4.5 11.7 - - + -
218B ALA 2.9 18.0 + - - +
219B ARG* 3.7 4.9 - - + +
221B LEU* 1.3 75.2 - - - +
223B ALA* 1.3 57.8 + - - +
225B ILE* 4.4 3.1 - - + +
226B TYR* 2.8 70.8 + - + +
238B LEU* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ARG 2.9 14.4 + - - +
220B ALA* 3.2 11.9 + - - +
222B LEU* 1.3 77.3 - - - +
224B ARG* 1.3 61.2 + - - +
226B TYR* 3.5 8.5 + - - +
227B LEU* 3.1 19.1 + - - +
235B ALA* 3.7 22.9 - - - +
238B LEU* 3.6 15.8 - - + +
239B ALA* 4.3 10.1 - - + +
242B LEU* 5.4 1.1 - - + -
363B VAL* 5.5 1.1 - - + -
366B ILE* 3.9 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.8 2.4 - - - +
148B PHE* 3.9 19.8 - - - -
152B ARG* 3.7 11.1 - - - +
220B ALA 3.1 12.2 + - - +
221B LEU* 3.2 24.0 + - - +
223B ALA* 1.3 76.5 - - - +
225B ILE* 1.3 57.8 + - - +
227B LEU* 3.0 6.8 + - + +
228B TYR* 2.9 55.7 + - + -
357B VAL* 3.0 23.4 + - - +
358B LEU* 3.4 12.6 - - - +
362B GLU* 2.7 46.1 + - - +
366B ILE* 3.7 10.6 - - + +
413B ARG* 6.2 0.9 - - - +
422B HIS* 3.6 8.2 - - - -
513B EDO 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA 4.7 1.1 - - - +
148B PHE* 3.8 30.7 - - + -
190B TYR* 3.9 19.0 - - + -
193B ILE* 3.8 22.9 - - + -
194B ILE* 3.8 25.6 - - + -
197B LEU* 3.7 26.5 - - + -
221B LEU* 2.9 31.3 + - + +
222B LEU* 3.9 5.6 - - + +
224B ARG* 1.3 72.6 - - - +
226B TYR* 1.3 65.5 + - - +
228B TYR* 3.2 7.8 + - - +
229B HIS* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 3.8 18.2 - - + -
198B GLU* 2.5 38.5 + - - +
222B LEU* 2.8 49.4 + - + +
223B ALA 3.5 4.7 - - - +
225B ILE* 1.3 72.1 - - - +
227B LEU* 1.3 60.0 + - - +
229B HIS* 3.2 8.2 + - - -
231B ASP* 2.9 46.9 + - - +
234B LYS* 3.7 46.2 - - + +
235B ALA* 3.8 14.4 - - + +
238B LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR* 5.0 2.9 - - - +
223B ALA 3.1 13.0 + - - +
224B ARG* 3.0 11.0 + - + +
226B TYR* 1.3 75.2 - - - +
228B TYR* 1.3 64.8 + - + +
230B ASP* 3.0 14.4 + - - +
232B ASN* 3.6 26.4 + - - +
235B ALA* 3.8 7.1 - - + +
366B ILE* 4.3 14.4 - - + +
369B GLU* 3.4 21.5 - - + +
370B ALA* 3.9 29.8 - - + +
373B LYS* 4.6 3.3 + - - +
413B ARG* 3.4 30.1 - - - +
429B ARG* 3.5 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 3.5 22.2 - + + -
152B ARG* 3.0 38.1 + - + -
158B TYR* 3.9 12.8 + - - +
159B THR* 3.7 18.0 + - - +
190B TYR* 3.4 21.9 + - + +
224B ARG* 2.9 47.0 + - + +
225B ILE 3.6 7.0 - - - +
227B LEU* 1.3 78.3 - - + +
229B HIS* 1.3 59.2 + - - +
230B ASP 3.2 1.4 + - - -
413B ARG* 6.0 1.1 - - - -
422B HIS* 4.9 6.7 + - - -
425B PHE* 3.2 22.5 - + + +
426B ASP* 4.0 7.6 + - - -
429B ARG* 3.6 48.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.4 54.0 + + - -
187B ALA 5.1 0.2 + - - -
190B TYR* 3.5 32.1 - + + +
191B ASP* 4.4 14.6 + - - -
194B ILE* 3.3 17.3 - - + +
225B ILE 2.9 16.8 + - - +
226B TYR 3.5 5.2 - - - +
227B LEU 3.1 0.4 - - - -
228B TYR* 1.3 76.0 - - - +
230B ASP* 1.3 67.2 + - - +
231B ASP* 2.6 35.5 + - - +
----------------------------------------------------------
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