Contacts of the helix formed by residues 207 - 219 (chain B) in PDB entry 4BVH
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 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE 2.7 24.8 + - - -
151B PRO* 3.7 18.6 - - + +
152B SER* 2.9 33.4 + - - +
206B PRO* 1.3 75.3 - - - +
208B VAL* 1.3 67.4 + - - +
209B THR* 2.8 38.5 + - - -
210B HIS* 2.9 23.8 + - - +
211B TYR* 3.1 18.1 + - - -
367B VAL* 3.9 6.2 - - + +
1397B CL 4.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN* 1.3 74.9 + - - +
209B THR* 1.3 55.7 + - - +
211B TYR* 3.3 6.9 + - - +
212B PHE* 2.8 28.1 + - - +
367B VAL* 4.6 14.8 - - + +
370B VAL* 4.2 12.3 - - + -
371B GLU* 4.1 35.2 - - + +
374B VAL* 5.8 0.9 - - + -
383B MET* 3.7 24.2 - - + -
387B VAL* 4.7 8.3 - - + -
1397B CL 4.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.5 41.0 + - + -
207B ASN* 2.8 24.1 + - - -
208B VAL* 1.3 70.8 - - - +
210B HIS* 1.4 63.9 + - - +
212B PHE* 3.3 4.2 + - - +
213B LEU* 3.2 27.4 + - + +
318B LEU* 4.0 17.9 - - + -
366B VAL* 3.8 23.9 - - + +
367B VAL* 4.0 6.2 - - - +
370B VAL* 4.2 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.5 30.0 - - + +
149B SER* 3.4 19.6 + - - -
206B PRO* 3.6 17.0 - - + +
207B ASN* 2.9 45.6 + - - +
209B THR* 1.4 75.8 - - - +
211B TYR* 1.4 60.0 + - - +
213B LEU* 3.1 11.7 + - + +
214B ARG* 2.9 26.0 + - - +
233B LEU* 3.5 39.4 - - + +
234B GLU* 4.2 12.5 + - + -
237B SER* 3.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO* 3.7 46.5 + - + +
207B ASN 3.1 22.9 + - - -
208B VAL* 3.3 3.1 + - + +
210B HIS* 1.4 78.0 - - - +
212B PHE* 1.3 57.2 + - - +
214B ARG* 3.2 7.9 + - + +
215B LEU* 2.9 25.1 + - - +
237B SER* 4.4 17.7 - - - -
383B MET* 3.8 19.7 - - + -
386B LEU* 3.5 19.7 - - + +
387B VAL* 3.9 18.2 - - + -
390B GLU* 3.8 35.7 - - + +
391B THR* 3.7 24.7 - - + +
1395B EDO 4.6 7.4 + - - -
1397B CL 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 5.8 1.6 - - + -
208B VAL 2.8 14.2 + - - +
209B THR 3.5 7.9 - - - +
210B HIS 3.2 0.2 - - - -
211B TYR* 1.3 75.0 - - - +
213B LEU* 1.3 74.1 + - + +
215B LEU* 3.2 3.1 + - + +
216B LEU* 3.0 38.3 + - + +
316B LEU* 4.1 22.7 - - + -
318B LEU* 5.1 4.9 - - + -
343B ILE* 5.8 1.3 - - + -
370B VAL* 3.6 28.9 - - + -
373B LEU* 3.7 25.8 - - + -
374B VAL* 3.6 19.3 - - + -
377B LEU* 3.8 13.7 - - + -
379B TRP* 3.6 28.7 - + - -
383B MET* 3.9 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.9 29.2 - - + -
144B VAL* 4.1 20.6 - - + -
148B ILE* 4.6 9.0 - - + -
209B THR 3.2 16.4 + - - +
210B HIS* 3.1 13.3 + - - +
212B PHE* 1.3 88.4 - - + +
214B ARG* 1.3 63.5 + - - +
216B LEU* 3.3 10.7 + - + +
217B HIS* 3.1 20.8 + - - +
222B LEU* 4.5 5.1 - - + +
225B LEU* 3.9 30.7 - - + -
234B GLU* 5.3 2.7 - - + -
239B ILE* 3.8 6.6 - - + +
316B LEU* 5.3 0.4 - - + -
318B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS 2.9 12.8 + - - +
211B TYR* 3.2 14.1 + - + +
213B LEU* 1.3 77.1 - - - +
215B LEU* 1.3 56.7 + - - +
217B HIS* 3.2 9.4 + - - +
218B ASP* 2.8 61.1 + - - +
237B SER 2.8 40.4 + - - +
238B GLY* 3.4 26.9 + - - -
239B ILE* 3.7 11.1 - - + +
386B LEU* 4.0 17.5 - - + +
389B ARG* 5.9 1.4 - - - +
390B GLU* 3.5 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR 2.9 16.5 + - - +
212B PHE* 3.2 10.1 + - - +
214B ARG* 1.3 73.6 - - - +
216B LEU* 1.3 62.3 + - - +
218B ASP* 3.2 13.1 + - + +
219B LYS* 2.9 50.6 + - + +
379B TRP* 3.7 28.3 - - + -
382B GLU* 4.3 15.0 - - + +
383B MET* 3.6 43.7 - - + +
386B LEU* 4.1 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 5.0 9.0 - - + -
140B VAL* 4.2 20.6 - - + -
142B VAL* 4.2 12.8 - - + -
212B PHE* 3.0 24.9 + - + +
213B LEU* 3.5 19.1 - - + +
214B ARG 3.3 0.2 - - - -
215B LEU* 1.3 77.0 - - - +
217B HIS* 1.4 62.6 + - - +
219B LYS* 3.4 4.4 + - - -
221B LEU* 3.1 45.0 + - + +
222B LEU* 4.3 11.7 - - + -
316B LEU* 4.1 24.0 - - + -
379B TRP* 3.6 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU 3.1 10.0 + - - +
214B ARG* 3.2 14.1 + - - +
216B LEU* 1.4 80.6 - - - +
218B ASP* 1.3 74.0 + - - +
220B GLY* 2.9 20.8 + - - -
222B LEU* 3.8 21.4 - - + +
238B GLY 4.8 0.9 - - - -
239B ILE* 4.4 5.8 - - + -
240B PRO* 3.5 40.5 - - + +
243B LYS* 3.8 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 2.8 56.9 + - - +
215B LEU* 3.2 16.7 + - + +
217B HIS* 1.3 85.7 - - - +
219B LYS* 1.3 59.3 + - + +
220B GLY 3.2 3.0 + - - -
386B LEU* 4.6 7.8 - - - +
389B ARG* 5.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.0 26.9 + - - +
267A ASP* 5.3 3.0 + - - -
135B ARG* 4.7 11.8 + - - +
215B LEU* 2.9 33.2 + - + +
216B LEU 3.9 0.9 - - - +
217B HIS 3.1 0.4 - - - -
218B ASP* 1.3 75.6 - - - +
220B GLY* 1.3 60.9 + - - +
221B LEU* 3.4 25.5 + - + +
379B TRP* 3.4 43.0 - - + +
382B GLU* 3.0 37.5 + - - -
----------------------------------------------------------
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