Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 2RHB
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 LEU 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE 5.2 0.2 + - - -
196A GLN* 3.9 30.8 - - - +
198A ARG* 5.2 0.2 - - - +
206A ARG* 4.7 9.9 - - + +
207A SER* 3.8 13.7 - - - +
210A GLU* 3.6 27.8 - - - +
297A LEU* 1.3 73.8 - - - +
299A LEU* 1.3 68.1 + - - +
300A ASP* 3.5 32.5 - - + +
301A ASP* 2.8 42.0 + - - +
302A PHE* 3.0 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.8 14.8 - - + +
210A GLU* 3.3 24.0 + - + +
213A PHE* 3.7 25.1 - - + -
221A PHE* 3.3 32.8 - - + -
232A PHE* 3.8 25.8 - - + -
236A VAL* 4.6 2.5 - - + -
250A LEU* 3.9 21.1 - - + -
252A ILE* 4.1 15.9 - - + -
297A LEU 3.2 5.9 + - - -
298A LEU* 1.3 71.7 - - - +
300A ASP* 1.3 53.2 + - - +
302A PHE* 3.1 4.4 + - + +
303A VAL* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 2.7 35.8 + - - -
209A MET* 3.5 31.5 + - + +
298A LEU* 3.1 19.0 - - + +
299A LEU* 1.3 74.8 + - - +
301A ASP* 1.3 58.9 + - - +
303A VAL* 3.3 4.3 + - - +
304A GLU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.4 39.6 - - + +
194A PHE 4.7 7.1 + - - +
196A GLN* 4.9 2.1 + - - -
297A LEU* 4.1 13.6 - - + +
298A LEU* 2.8 34.8 + - + +
300A ASP* 1.3 75.9 - - - +
302A PHE* 1.3 59.7 + - - +
304A GLU* 3.4 8.1 + - - +
305A ILE* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 3.9 22.0 - + - -
235A ILE* 3.9 18.4 - - + -
236A VAL* 3.9 16.8 - - + -
249A HIS* 6.1 1.3 - - + -
250A LEU* 3.7 44.6 - - + -
297A LEU* 4.2 14.2 - - + +
298A LEU 3.0 9.3 + - - +
299A LEU* 3.6 7.2 - - + +
301A ASP* 1.3 72.5 - - - +
303A VAL* 1.3 56.2 + - - +
305A ILE* 3.1 12.6 + - + +
306A ILE* 2.8 50.5 + - + +
329A PHE* 5.4 6.7 - + - -
341A PHE* 3.8 35.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.6 32.8 - - + -
225A TYR* 6.3 0.7 - - + -
227A LEU* 4.2 16.6 - - + -
232A PHE* 3.7 25.4 - - + -
299A LEU* 2.8 23.6 + - + +
300A ASP 3.6 4.9 - - - +
302A PHE* 1.3 71.3 - - - +
304A GLU* 1.3 58.6 + - - +
306A ILE* 3.7 6.8 - - - +
307A LYS* 2.9 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 2.6 35.4 + - - +
300A ASP 2.9 18.2 + - - +
301A ASP* 3.5 7.5 - - - +
303A VAL* 1.3 75.4 - - - +
305A ILE* 1.3 67.7 + - - +
307A LYS* 4.0 3.2 - - - +
308A SER* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.1 38.4 - - + +
297A LEU* 4.9 10.3 - - + -
301A ASP 2.8 34.4 + - - +
302A PHE* 3.2 14.1 - - + +
304A GLU* 1.3 76.3 - - - +
306A ILE* 1.3 64.8 + - - +
308A SER* 3.0 17.1 + - - -
309A GLN* 3.3 18.1 - - - +
320A VAL* 3.2 39.9 - - + -
329A PHE* 6.2 0.2 - - + -
341A PHE* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 5.2 0.7 - - + -
230A TYR* 3.6 36.8 - - + +
232A PHE* 4.1 21.5 - - + -
235A ILE* 3.8 28.9 - - + -
302A PHE* 2.8 36.4 + - + +
303A VAL* 3.7 6.3 - - - +
305A ILE* 1.3 75.9 - - + +
307A LYS* 1.3 67.4 + - + +
309A GLN* 3.3 26.4 + - + +
331A LEU* 5.4 1.3 - - + -
338A VAL* 4.1 13.8 - - + +
341A PHE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR 3.3 20.0 + - - -
226A LYS* 3.6 16.3 + - - +
227A LEU* 3.7 21.9 - - + +
230A TYR* 3.6 42.4 + - + +
303A VAL* 2.9 34.4 + - + +
304A GLU* 4.2 2.9 - - - +
306A ILE* 1.3 73.1 - - + +
308A SER* 1.3 56.9 + - - +
309A GLN 3.0 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.1 19.6 + - - +
305A ILE* 3.0 15.9 + - - -
306A ILE 3.3 0.2 - - - -
307A LYS* 1.3 75.0 - - - +
309A GLN* 1.3 67.0 + - - +
310A ASP 4.4 0.3 + - - -
----------------------------------------------------------
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