Contacts of the helix formed by residues 298 - 308 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D PHE 5.0 0.6 + - - -
196D GLN* 3.7 24.6 + - + +
198D ARG* 4.1 4.8 - - - +
206D ARG* 4.7 7.9 - - + +
207D SER* 3.5 31.4 - - - +
210D GLU* 3.2 24.7 - - - +
297D LEU* 1.3 73.8 - - - +
299D LEU* 1.3 66.1 + - - +
300D ASP* 3.7 20.4 - - + +
301D ASP* 2.8 46.6 + - + +
302D PHE 3.1 9.7 + - - -
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D MET* 4.1 14.4 - - + +
210D GLU* 2.9 25.9 + - + -
213D PHE* 3.8 26.0 - - + -
221D PHE* 3.6 31.0 - - + -
232D PHE* 4.0 25.1 - - + -
236D VAL* 4.8 6.7 - - + -
250D LEU* 4.9 2.9 - - + -
252D ILE* 4.2 19.3 - - + -
297D LEU 3.3 4.2 + - - -
298D LEU* 1.3 70.9 - - - +
300D ASP* 1.3 64.7 + - - +
302D PHE* 3.2 15.2 + - + +
303D VAL* 3.0 24.6 + - + +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D SER* 2.6 36.9 + - - -
209D MET* 3.3 36.1 - - + +
298D LEU* 3.7 15.1 - - + +
299D LEU* 1.3 75.3 - - - +
301D ASP* 1.3 58.7 + - - +
303D VAL* 3.4 3.3 + - - +
304D GLU* 3.0 28.6 + - - +
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Residues in contact with ASP 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 3.5 35.5 - - + +
194D PHE 4.6 10.9 + - - +
196D GLN* 4.7 1.9 - - - +
297D LEU* 4.5 8.4 - - + +
298D LEU* 2.8 42.0 + - + +
300D ASP* 1.3 78.2 - - - +
302D PHE* 1.3 57.4 + - - +
304D GLU* 3.4 8.1 + - - +
305D ILE* 2.9 34.5 + - - +
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Residues in contact with PHE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D PHE* 4.2 19.3 - + - -
235D ILE* 3.9 18.8 - - + -
236D VAL* 3.7 28.9 - - + -
249D HIS* 5.6 2.0 - - + -
250D LEU* 3.6 39.3 - - + -
297D LEU* 4.3 15.6 - - + +
298D LEU 3.1 6.6 + - - +
299D LEU* 3.2 9.4 + - + +
301D ASP* 1.3 72.7 - - - +
303D VAL* 1.3 68.3 + - - +
305D ILE* 3.1 11.6 + - + +
306D ILE* 2.9 36.8 + - + +
329D PHE* 5.7 3.1 - + - -
341D PHE* 3.7 38.8 - + - -
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D MET* 3.6 29.4 - - + -
227D LEU* 4.2 14.1 - - + -
232D PHE* 4.0 21.5 - - + -
299D LEU* 3.0 18.8 + - + +
300D ASP 3.5 9.2 - - - +
302D PHE* 1.3 77.6 - - - +
304D GLU* 1.3 54.2 + - - +
306D ILE* 3.2 9.1 + - - +
307D LYS* 2.7 68.3 + - + +
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 2.6 31.3 + - - +
300D ASP 3.0 14.8 + - - +
301D ASP* 3.6 11.9 - - - +
302D PHE 3.3 0.2 - - - -
303D VAL* 1.3 76.2 - - - +
305D ILE* 1.3 56.5 + - - +
307D LYS* 4.0 4.9 - - - +
308D SER* 3.0 35.9 + - - +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 3.6 39.7 - - + +
297D LEU* 4.1 26.7 - - + -
301D ASP 2.9 21.2 + - - +
302D PHE* 3.1 10.7 + - + +
304D GLU* 1.3 75.7 - - - +
306D ILE* 1.3 61.9 + - - +
308D SER* 3.2 14.1 + - - -
309D GLN* 2.9 26.7 + - - +
320D VAL* 3.8 36.3 - - + -
322D ILE* 5.2 0.2 - - + -
329D PHE* 5.9 1.1 - - + -
341D PHE* 4.3 18.6 - - + -
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Residues in contact with ILE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU* 5.4 0.9 - - + -
230D TYR* 3.6 50.7 - - + +
232D PHE* 4.6 9.4 - - + -
235D ILE* 4.3 4.3 - - + -
302D PHE* 2.9 27.0 + - + +
303D VAL* 3.4 14.8 - - - +
305D ILE* 1.3 78.3 - - + +
307D LYS* 1.3 66.0 + - + +
309D GLN* 3.1 27.9 + - + +
311D LEU* 4.8 0.2 - - - +
331D LEU* 4.9 3.1 - - + -
338D VAL* 3.9 30.1 - - + -
341D PHE* 4.1 26.7 - - + -
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Residues in contact with LYS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D TYR 4.1 9.5 + - - -
226D LYS* 3.9 27.5 + - - +
227D LEU* 3.9 13.0 - - + -
230D TYR* 3.9 33.1 + - + +
303D VAL* 2.7 40.5 + - + +
304D GLU* 4.0 5.4 - - - +
306D ILE* 1.3 71.5 - - + +
308D SER* 1.3 56.8 + - - +
309D GLN 3.1 9.5 + - - +
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 5.5 1.0 + - - -
304D GLU* 3.0 21.9 + - - +
305D ILE* 3.2 11.4 + - - -
307D LYS* 1.3 75.1 - - - +
309D GLN* 1.3 63.1 + - - +
310D ASP 3.8 1.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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