Contacts of the helix formed by residues 223 - 233 (chain B) in PDB entry 3VAS
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 GLU 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 1.3 74.0 - - - +
224B SER* 1.3 57.8 + - - +
226B ALA* 3.0 7.7 + - - +
227B GLU* 2.8 54.7 + - - +
240B VAL* 4.2 4.0 - - + -
264B ILE* 4.3 3.8 - - - -
265B THR 3.0 16.5 + - - +
266B ARG* 2.9 56.2 + - - +
269B ASN* 5.3 4.0 + - - -
295B ILE* 3.9 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.9 20.4 - - - +
222B ASN* 3.0 17.6 + - - -
223B GLU* 1.3 79.0 - - - +
225B GLU* 1.3 60.5 + - - +
227B GLU* 3.7 14.3 + - - +
228B ALA* 3.2 23.0 + - - +
295B ILE* 5.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASN* 4.1 2.9 - - - +
196B LEU* 3.5 21.4 - - + +
197B SER* 2.8 36.2 + - - +
198B ALA* 3.7 24.4 - - - +
199B PRO* 3.7 11.5 - - + +
202B SER* 4.4 4.1 + - - +
221B GLY* 3.4 9.0 - - - -
222B ASN* 2.8 53.2 + - - +
224B SER* 1.3 73.3 + - - +
226B ALA* 1.3 60.9 + - - +
228B ALA* 3.3 2.3 + - - +
229B TYR* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.9 3.8 - - - +
222B ASN 2.9 18.3 + - - +
223B GLU 3.0 4.7 + - - +
225B GLU* 1.3 76.1 - - - +
227B GLU* 1.3 58.1 + - - +
229B TYR* 3.4 1.6 + - - +
230B GLY 3.0 23.6 + - - -
239B THR* 4.1 1.0 - - - +
240B VAL* 4.1 15.9 - - + -
243B THR* 3.1 31.4 + - + -
264B ILE* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 2.8 45.5 + - - +
224B SER* 3.9 13.3 - - - +
226B ALA* 1.3 73.1 - - - +
228B ALA* 1.3 61.0 + - - +
230B GLY 3.5 0.3 + - - -
231B GLU* 3.1 25.8 + - - +
239B THR* 3.8 16.4 - - + +
240B VAL* 3.8 17.5 - - + +
266B ARG* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.8 25.6 - - + +
202B SER* 4.5 2.2 - - - -
203B GLN* 3.8 26.5 - - + +
224B SER 3.2 17.0 + - - +
225B GLU 3.3 4.0 + - - +
227B GLU* 1.3 76.1 - - - +
229B TYR* 1.3 67.5 + - - +
231B GLU* 3.5 7.2 + - - +
232B VAL* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.9 5.6 - - + -
202B SER* 3.5 26.4 - - - +
206B THR* 5.8 0.2 - - + -
209B VAL* 4.0 9.4 - - + -
210B ASP* 2.5 29.9 + - - -
213B ILE* 3.7 15.5 - - + +
225B GLU 2.9 17.5 + - - +
226B ALA* 3.7 4.5 - - - +
228B ALA* 1.3 77.1 - - - +
230B GLY* 1.3 61.7 + - - +
232B VAL* 3.3 3.4 + - - +
233B HIS* 2.7 52.6 + + + -
235B LEU* 5.1 0.7 - - + -
243B THR* 3.5 22.9 - - + -
246B TYR* 3.3 32.7 - + + -
247B ILE* 3.7 21.9 - - + +
250B LEU* 3.6 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA 3.0 10.7 + - - -
229B TYR* 1.3 77.8 - - - +
231B GLU* 1.3 53.3 - - - +
233B HIS 3.1 1.6 + - - -
234B GLY 3.0 8.7 + - - -
235B LEU* 2.7 40.8 + - - -
239B THR* 3.6 15.3 - - - -
243B THR* 3.2 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLN* 4.9 10.7 + - - -
227B GLU 3.1 17.6 + - - +
228B ALA* 3.9 5.7 - - - +
229B TYR 3.4 0.2 - - - -
230B GLY* 1.3 74.4 - - - +
232B VAL* 1.3 63.5 + - + +
234B GLY* 3.2 12.6 + - - -
236B LEU* 4.4 20.4 - - + +
239B THR* 4.1 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER 3.8 3.1 - - - +
203B GLN* 3.9 34.3 - - + +
206B THR* 3.5 36.3 - - + +
228B ALA 3.3 16.3 + - - +
229B TYR* 3.7 2.5 - - - +
230B GLY 3.3 0.2 - - - -
231B GLU* 1.3 81.5 - - + +
233B HIS* 1.3 66.8 + - + +
234B GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER 5.4 0.4 - - - -
206B THR* 3.6 25.5 - - + +
210B ASP* 2.6 27.9 + - - -
229B TYR* 2.7 58.0 + + - +
230B GLY 3.1 3.7 + - - +
232B VAL* 1.3 80.3 - - + +
234B GLY* 1.3 62.0 + - - +
235B LEU* 3.3 22.8 + - + +
246B TYR* 3.7 31.6 - + + -
----------------------------------------------------------
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