Contacts of the helix formed by residues 208 - 218 (chain A) in PDB entry 1RVB
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 SER 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.5 18.6 - - - -
206A PHE* 3.4 2.3 - - - +
207A ASP* 1.3 81.6 - - - +
209A GLU* 1.3 63.3 + - - +
210A ASP* 3.5 14.2 + - - +
211A GLU* 3.1 24.4 + - - +
212A PHE* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE 4.9 9.6 - - - +
130A ALA* 5.4 0.9 - - - -
131A HIS* 4.2 24.4 + - - +
174A TRP* 3.7 50.9 + - + +
208A SER* 1.3 74.3 - - - +
210A ASP* 1.3 60.4 + - - +
212A PHE* 3.3 6.4 + - + +
213A LEU* 2.9 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 3.1 11.6 + - - +
209A GLU* 1.3 77.6 - - - +
211A GLU* 1.3 63.0 + - - +
213A LEU* 3.6 12.1 + - - +
214A ASP* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 3.5 11.5 - - + -
207A ASP* 2.8 27.7 + - + +
208A SER* 3.1 20.8 + - - +
210A ASP* 1.3 73.4 - - - +
212A PHE* 1.3 66.4 + - - +
214A ASP* 3.5 1.8 + - - +
215A TYR* 3.0 24.4 + - - +
233A ILE* 4.3 2.0 - - - -
236A TYR* 3.8 23.9 + - + +
237A ARG* 2.8 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 5.8 4.0 - - + -
173A LYS* 4.1 26.0 - - + -
174A TRP* 3.5 28.0 - - + -
177A ALA* 3.3 33.4 - - + -
189A ILE* 4.1 18.2 - - + -
206A PHE* 3.8 21.0 - + + -
208A SER 3.1 11.8 + - - +
209A GLU* 3.4 13.9 - - + +
211A GLU* 1.3 78.9 - - - +
213A LEU* 1.3 90.4 + - + +
215A TYR* 3.2 0.7 + - - +
216A TRP* 3.1 50.7 + + + -
----------------------------------------------------------
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
----------------------------------------------------------
114A ILE* 4.5 16.4 - - + -
125A PHE* 4.1 30.5 - - + -
209A GLU* 2.9 34.0 + - + +
210A ASP* 3.9 12.1 - - - +
211A GLU 3.4 0.2 - - - -
212A PHE* 1.3 95.7 - - + +
214A ASP* 1.3 58.1 + - - +
216A TRP* 3.3 4.0 + - - +
217A ARG* 2.9 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP 3.1 16.0 + - - +
211A GLU* 4.0 0.7 - - - +
213A LEU* 1.3 77.7 - - - +
215A TYR* 1.3 65.5 + - - +
217A ARG* 3.3 8.1 + - - +
218A ASN* 3.0 33.4 + - - +
230A TYR* 3.7 1.6 + - - -
236A TYR* 2.7 32.1 + - - +
244A ARG* 3.0 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 2.7 37.9 + - + -
206A PHE* 3.6 17.7 - + + -
211A GLU 3.0 19.1 + - - +
212A PHE 3.5 4.7 - - - +
214A ASP* 1.3 76.3 - - - +
216A TRP* 1.3 78.7 + + - +
219A TYR* 3.2 34.8 + + - +
230A TYR* 2.6 40.5 + + - -
231A ASN 3.6 2.3 - - - -
232A ASN* 3.2 32.0 + - - -
233A ILE* 3.8 4.9 - - + -
236A TYR* 3.5 39.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.6 38.7 - + + +
114A ILE* 3.7 23.0 - - + +
115A ARG* 2.9 22.7 + - - -
177A ALA* 4.7 0.2 - - - +
178A GLY 3.1 28.9 + - - -
179A ASP* 3.9 7.6 - - - -
180A LEU 3.6 32.1 - - - -
181A ALA* 3.7 5.4 - - - -
189A ILE* 3.6 27.7 - - + +
206A PHE* 3.8 4.7 - + - -
212A PHE* 3.1 45.1 + + + +
213A LEU* 4.1 1.3 - - - +
215A TYR* 1.3 87.9 - + - +
217A ARG* 1.3 59.9 + - - +
218A ASN 3.3 0.2 - - - -
219A TYR* 3.5 38.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 2.8 37.9 + - + +
115A ARG* 3.1 34.9 + - + +
125A PHE* 4.0 24.9 - - - -
213A LEU* 2.9 47.2 + - - +
214A ASP* 3.3 9.4 + - - +
216A TRP* 1.3 77.3 - - - +
218A ASN* 1.3 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.9 1.1 - - - +
214A ASP* 3.0 38.0 + - - -
217A ARG* 1.3 85.9 - - - +
219A TYR* 1.3 63.9 + - - +
220A GLU* 3.4 2.6 + - - -
229A LYS* 2.9 38.7 + - - +
230A TYR* 3.1 23.6 + - + +
239A TRP* 4.3 8.2 - - + -
244A ARG* 3.4 16.6 + - - +
----------------------------------------------------------
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