Contacts of the helix formed by residues 215 - 225 (chain B) in PDB entry 3VI7
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 ALA 215 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.1 11.2 - - + -
208B TYR* 3.5 41.3 - - + -
212B ARG 3.1 2.0 + - - -
214B ARG* 1.3 78.2 - - - +
216B GLU* 1.4 65.5 + - - +
217B ILE 3.2 2.9 - - - -
218B ILE* 3.0 19.4 + - - +
219B ARG* 3.2 26.0 + - - +
252B PRO* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 2.9 38.3 + - + +
213B GLY 3.5 8.0 + - - +
214B ARG 3.4 2.2 - - - -
215B ALA* 1.4 76.3 - - - +
217B ILE* 1.3 57.6 + - - +
219B ARG* 3.0 34.9 + - - +
220B TYR* 2.9 42.2 + - + -
233B ARG* 4.7 0.7 + - - -
355B ILE* 3.6 18.4 - - + -
390B TRP* 2.9 24.2 + - - -
394B ARG* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLY 4.9 0.6 + - - -
214B ARG 4.1 15.9 - - - +
215B ALA 3.1 0.2 + - - -
216B GLU* 1.3 77.6 - - - +
218B ILE* 1.3 69.4 + - + +
220B TYR* 3.4 1.2 + - - +
221B ILE* 3.1 35.1 + - + +
264B SER* 4.4 3.4 - - - +
265B LEU* 4.3 9.2 - - + -
268B ALA* 4.1 14.8 - - + -
348B TRP* 3.8 33.7 - - + +
351B PHE* 3.6 32.1 - - + -
352B TYR* 3.7 37.9 - - + +
355B ILE* 3.5 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.0 28.7 - - + -
214B ARG 4.6 0.2 - - - +
215B ALA 3.0 9.1 + - - +
217B ILE* 1.3 81.4 - - + +
219B ARG* 1.3 64.4 + - - +
221B ILE* 3.1 9.5 + - - +
222B PHE* 3.0 48.7 + - + -
252B PRO* 4.2 9.4 - - + -
254B LEU* 5.1 0.4 - - + -
264B SER* 3.9 30.1 - - - +
267B ILE* 3.6 33.4 - - + -
268B ALA* 4.4 5.2 - - - +
271B LEU* 3.7 11.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
206B LEU* 3.6 16.1 - - + +
208B TYR* 3.8 16.4 - - - +
209B PHE 3.4 15.8 + - - -
211B MET 2.7 28.3 + - - -
212B ARG* 3.5 9.3 + - - +
215B ALA* 3.6 14.0 - - - +
216B GLU* 3.0 27.1 + - - +
218B ILE* 1.3 77.4 - - - +
220B TYR* 1.3 60.8 + - - +
222B PHE* 3.5 2.1 + - - +
223B ALA* 3.0 23.2 + - - +
229B TYR* 3.4 23.3 + - - +
231B ASP* 2.7 25.5 + - - -
232B HIS 5.5 0.2 + - - -
233B ARG* 3.3 21.6 - - - +
390B TRP* 3.5 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLU* 2.9 42.0 + - + +
217B ILE 3.6 8.5 - - - +
219B ARG* 1.3 77.0 - - - +
221B ILE* 1.3 59.3 + - - +
223B ALA* 3.3 7.3 + - - +
224B TYR* 2.8 31.9 + - - +
351B PHE* 3.9 30.2 - + + -
354B GLU* 2.6 34.8 + - - -
355B ILE* 3.5 22.6 - - + +
358B THR* 5.5 0.7 + - - -
381B VAL* 4.7 4.0 - - + -
387B VAL* 3.9 25.8 - - + +
390B TRP* 3.7 17.7 - + - -
391B ILE* 3.7 9.9 - - + +
394B ARG* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.1 25.6 + - + +
218B ILE* 3.1 7.1 + - - +
220B TYR* 1.3 79.7 - - - +
222B PHE* 1.3 58.5 + - + +
224B TYR* 3.1 2.1 + - - +
225B LEU* 2.9 55.0 + - + +
268B ALA* 3.6 41.3 - - + +
271B LEU* 3.7 22.4 - - + -
272B THR* 3.8 21.1 - - + -
277B LEU* 4.2 8.5 - - + -
348B TRP* 4.3 3.4 - - + -
351B PHE* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 3.8 35.2 - + - -
206B LEU* 4.8 0.4 - - + -
218B ILE* 3.0 40.5 + - + +
219B ARG 3.8 1.3 - - - +
221B ILE* 1.3 77.5 - - + +
223B ALA* 1.3 62.4 + - - +
225B LEU* 3.6 0.8 + - - -
226B ASP* 2.9 18.2 + - - -
227B ILE* 2.9 40.6 + - + +
229B TYR* 3.4 55.6 - + + -
254B LEU* 4.0 14.8 - - + -
271B LEU* 3.7 33.0 - - + -
----------------------------------------------------------
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 3.0 17.8 + - - +
220B TYR* 3.6 6.5 - - - +
222B PHE* 1.3 76.5 - - - +
224B TYR* 1.3 64.5 + - - +
226B ASP* 3.1 14.2 + - - +
229B TYR* 5.2 1.2 - - - -
386B ALA* 3.4 25.3 - - - +
387B VAL* 5.1 2.0 - - - -
390B TRP* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR 2.8 17.5 + - - +
221B ILE 3.1 2.0 + - - +
223B ALA* 1.3 78.2 - - - +
225B LEU* 1.3 71.6 + - + +
226B ASP* 3.4 1.4 + - - +
276B ASP* 2.8 33.1 + - - -
277B LEU* 3.5 30.5 - - + -
346B VAL* 4.1 17.1 - - + +
351B PHE* 3.6 28.0 - + + -
384B ILE* 4.0 28.0 - - + -
386B ALA* 3.9 13.5 - - + +
387B VAL* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 2.9 33.4 + - + +
222B PHE* 4.3 0.4 - - + +
224B TYR* 1.3 95.3 - - + +
226B ASP* 1.3 70.8 + - - +
227B ILE* 3.3 32.2 + - + +
271B LEU* 3.6 24.0 - - + +
275B THR* 3.9 29.8 - - + +
276B ASP* 5.5 0.9 - - - +
277B LEU* 4.4 3.8 - - + -
----------------------------------------------------------
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