Contacts of the helix formed by residues 206 - 218 (chain A) in PDB entry 2VRB
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 PHE 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.7 20.4 - + + -
161A ILE* 4.4 10.4 - - + +
163A THR* 3.9 20.0 - - + -
165A ALA* 3.7 30.3 - - + -
166A GLY 4.7 2.7 + - - +
168A GLY 4.5 5.0 + - - -
170A VAL* 3.8 22.9 - - + -
204A TRP* 4.0 15.9 - + - -
205A THR* 1.3 70.9 - - - +
207A ASP* 1.3 66.1 + - - +
209A LEU* 3.8 24.3 - - + +
210A ALA* 3.1 23.2 + - - +
223A HIS* 3.5 33.4 - - + +
252A TYR* 3.6 25.1 - + - -
255A ILE* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 5.8 4.9 - - - -
205A THR* 3.3 9.9 + - - +
206A PHE* 1.3 76.9 - - - +
208A GLU* 1.3 62.1 + - - +
210A ALA* 3.3 4.9 + - - +
211A GLN* 3.1 21.1 + - - +
223A HIS* 3.4 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO 4.1 4.4 - - - +
204A TRP* 3.3 33.2 - - - +
205A THR* 3.1 18.2 + - - +
207A ASP* 1.3 77.2 - - - +
209A LEU* 1.3 65.7 + - - +
211A GLN* 3.3 9.0 + - + +
212A ILE* 3.0 47.9 + - + +
277A LEU* 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE 4.3 9.4 - - - +
148A VAL* 4.0 19.5 - - + -
152A LEU* 4.7 10.5 - - + -
161A ILE* 3.8 15.9 - - + -
204A TRP* 3.7 29.5 - - + -
205A THR 2.8 17.2 + - - +
206A PHE* 3.8 24.0 - - + +
207A ASP 3.3 0.2 - - - -
208A GLU* 1.3 73.5 - - - +
210A ALA* 1.3 55.4 - - - +
212A ILE* 3.4 4.6 + - + +
213A LEU* 2.9 27.3 + - + +
277A LEU* 4.3 11.7 - - + -
281A VAL* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.8 16.4 - - + +
206A PHE 3.1 15.4 + - - +
207A ASP* 3.6 5.6 - - - +
208A GLU 3.2 0.2 - - - -
209A LEU* 1.3 78.4 - - - +
211A GLN* 1.3 58.8 + - - +
213A LEU* 3.5 4.4 + - - +
214A SER* 2.9 32.1 + - - -
221A VAL* 3.5 16.6 - - - +
222A VAL* 3.7 3.6 - - - -
223A HIS 3.5 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP 3.1 12.1 + - - +
208A GLU* 3.3 13.0 + - + +
210A ALA* 1.3 75.4 - - - +
212A ILE* 1.3 59.9 + - + +
214A SER* 3.3 10.7 + - - -
215A GLU* 3.0 56.3 + - - +
221A VAL 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 3.0 35.5 + - + +
209A LEU* 3.6 6.5 - - - +
211A GLN* 1.3 75.5 - - + +
213A LEU* 1.3 65.7 + - - +
215A GLU* 3.1 15.6 + - - +
216A VAL* 2.9 24.8 + - + +
277A LEU* 3.5 38.4 - - + -
278A LYS* 3.7 40.6 - - + +
281A VAL* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 4.2 21.3 - - + +
155A SER* 4.1 18.4 - - - -
156A THR* 3.5 22.0 - - - +
161A ILE* 4.2 11.0 - - + -
209A LEU* 2.9 21.6 + - + +
210A ALA 3.7 4.5 - - - +
212A ILE* 1.3 74.2 - - - +
214A SER* 1.3 57.2 + - - +
216A VAL* 4.6 0.2 - - - -
217A SER* 2.8 37.0 + - - -
221A VAL* 3.7 33.4 - - + -
281A VAL* 4.2 13.2 - - + +
285A LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA 2.9 20.7 + - - -
211A GLN* 3.4 15.8 - - - -
212A ILE 3.2 0.2 - - - -
213A LEU* 1.3 75.8 - - - +
215A GLU* 1.3 60.3 + - - +
218A GLY* 2.9 30.5 + - - -
219A LYS 3.2 15.5 + - - -
220A LYS* 3.8 8.9 - - - +
221A VAL 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.0 45.2 + - - +
212A ILE* 3.1 15.9 + - - +
214A SER* 1.3 77.9 - - - +
216A VAL* 1.3 62.5 + - - +
218A GLY* 3.9 5.0 + - - -
278A LYS* 2.6 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 2.9 19.2 + - + +
213A LEU 4.1 2.2 - - - +
215A GLU* 1.3 78.7 - - - +
217A SER* 1.3 62.6 + - - +
218A GLY* 3.6 0.3 + - - -
278A LYS* 3.9 30.7 - - + +
281A VAL* 4.2 13.0 - - + -
282A LYS* 4.0 33.0 - - + -
285A LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 4.1 27.8 + - - +
213A LEU* 2.8 26.8 + - - +
216A VAL* 1.3 76.9 - - - +
218A GLY* 1.3 58.3 + - - +
219A LYS* 2.9 28.5 + - - +
221A VAL* 4.8 0.3 - - - +
285A LEU* 5.1 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER 2.9 14.9 + - - -
215A GLU 3.9 4.7 + - - -
216A VAL 3.4 3.2 - - - -
217A SER* 1.3 77.4 - - - +
219A LYS* 1.3 57.7 + - - +
220A LYS 4.3 0.5 + - - -
----------------------------------------------------------
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