Contacts of the helix formed by residues 250 - 259 (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 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235D ILE 4.6 1.6 + - - -
236D VAL* 4.0 25.3 + - + -
248D LEU* 3.2 3.0 - - - +
249D HIS* 1.3 88.4 - - + +
251D MET* 1.3 64.8 + - - +
252D ILE* 4.2 13.7 - - + -
253D GLY* 3.1 12.3 + - - -
254D LEU* 3.3 14.2 - - - +
294D VAL* 4.6 0.2 - - - -
295D ILE* 3.3 11.4 - - + +
297D LEU* 3.3 46.9 - - + +
299D LEU* 4.9 5.4 - - + -
302D PHE* 3.6 51.6 - - + -
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Residues in contact with MET 251 (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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198D ARG 4.1 12.3 - - - +
199D ASP 4.3 2.0 - - - +
200D LEU* 3.4 54.3 - - + +
203D PHE* 3.6 22.0 - - + -
249D HIS 4.0 0.2 + - - -
250D LEU* 1.3 71.7 - - - +
252D ILE* 1.3 58.0 + - - +
254D LEU* 2.9 36.0 + - + +
255D ALA 3.2 7.8 + - - +
265D LEU* 5.7 3.4 - - + -
278D TYR* 6.1 3.1 - - - -
294D VAL* 4.2 14.8 - - + +
295D ILE 3.0 9.9 + - - +
296D ASP* 3.3 36.0 - - + +
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Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.6 33.9 - - + -
210D GLU* 3.6 45.1 - - + +
213D PHE* 3.6 29.8 - - + -
214D LEU* 4.0 10.1 - - + -
236D VAL* 4.7 2.7 - - + -
250D LEU* 4.2 20.8 - - + +
251D MET* 1.3 77.8 - - - +
253D GLY* 1.3 55.1 + - - +
255D ALA* 3.2 4.0 + - - +
256D LYS* 2.8 33.4 + - - +
296D ASP* 4.4 1.4 + - - +
297D LEU 5.1 2.2 - - - +
299D LEU* 4.2 18.4 - - + -
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Residues in contact with GLY 253 (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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213D PHE* 4.2 12.6 - - - -
236D VAL* 3.4 24.5 - - - -
237D TYR 3.9 4.7 - - - +
248D LEU* 3.4 14.9 - - - +
250D LEU* 3.1 9.0 + - - +
251D MET 3.0 1.6 + - - -
252D ILE* 1.3 82.1 - - - +
254D LEU* 1.3 55.0 + - - +
256D LYS* 3.5 4.0 - - - +
257D ARG* 3.2 21.7 + - - +
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Residues in contact with LEU 254 (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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200D LEU* 3.8 15.3 - - + -
248D LEU* 3.5 30.7 - - + +
250D LEU 3.3 18.2 - - - +
251D MET* 2.9 13.8 + - + +
253D GLY* 1.3 73.0 - - - +
255D ALA* 1.3 55.7 + - - +
256D LYS 3.2 0.2 - - - -
257D ARG* 3.2 2.7 + - - +
258D SER* 2.8 37.1 + - - -
263D LEU* 3.9 16.0 - - + +
265D LEU* 3.9 30.3 - - + -
280D ILE* 3.9 24.2 - - + -
294D VAL* 3.8 21.1 - - + -
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Residues in contact with ALA 255 (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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200D LEU* 3.8 13.6 - - + +
203D PHE* 3.6 44.2 - - + -
214D LEU* 4.2 7.2 - - + -
251D MET 3.2 3.3 + - - +
252D ILE* 3.2 11.4 + - - +
254D LEU* 1.3 78.1 - - - +
256D LYS* 1.3 61.6 + - - +
258D SER* 3.4 5.6 + - - -
259D GLN* 3.2 25.3 + - - +
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Residues in contact with LYS 256 (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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213D PHE* 2.9 32.7 + - + +
214D LEU* 2.8 35.3 + - + +
215D GLU 4.3 1.0 + - - -
216D LEU 2.6 31.1 + - - -
217D ALA* 4.5 4.4 - - - +
218D MET 5.4 0.2 - - - +
237D TYR* 3.8 26.6 - - + +
252D ILE 2.8 16.8 + - - +
253D GLY 3.5 6.7 - - - +
255D ALA* 1.3 75.0 - - - +
257D ARG* 1.3 66.1 + - + +
259D GLN* 3.2 25.0 + - - +
260D ASP* 4.0 11.1 - - - +
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Residues in contact with ARG 257 (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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237D TYR 4.9 2.2 - - - +
240D PHE* 3.0 68.3 - - + +
253D GLY 3.2 14.5 + - - +
254D LEU* 3.2 3.8 + - - +
256D LYS* 1.3 80.2 - - + +
258D SER* 1.3 60.8 + - - +
260D ASP* 3.2 16.5 + - - +
261D SER* 2.9 50.7 + - - +
263D LEU* 3.9 14.4 - - + -
282D ASP* 3.2 23.2 + - - -
284D GLN* 3.9 17.0 - - - +
285D THR* 4.4 5.5 - - - +
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Residues in contact with SER 258 (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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200D LEU* 3.5 27.1 - - - +
254D LEU 2.8 20.2 + - - -
255D ALA* 3.4 11.2 - - - -
256D LYS 3.1 0.2 - - - -
257D ARG* 1.3 73.3 - - - +
259D GLN* 1.3 61.3 + - - +
260D ASP 2.9 7.4 + - - -
261D SER 3.4 20.2 + - - +
262D PRO* 5.1 2.6 - - - +
263D LEU* 4.4 10.7 + - - +
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Residues in contact with GLN 259 (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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214D LEU* 3.2 61.2 + - - +
255D ALA 3.2 8.9 + - - +
256D LYS* 3.2 16.4 + - - +
258D SER* 1.3 76.6 - - - +
260D ASP* 1.3 66.4 + - - +
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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