Contacts of the helix formed by residues 250 - 259 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235F ILE* 4.8 1.7 + - + -
236F VAL* 3.8 27.1 + - + +
248F LEU 3.3 0.7 - - - +
249F HIS* 1.3 86.3 - - + +
251F MET* 1.3 67.8 + - - +
252F ILE* 4.0 14.1 - - + +
253F GLY* 3.0 12.8 + - - -
254F LEU* 3.2 16.0 - - - +
294F VAL* 4.3 1.1 - - - -
295F ILE* 3.4 23.3 - - + +
296F ASP* 4.5 0.2 - - - -
297F LEU* 3.5 40.6 - - + +
299F LEU* 5.5 3.8 - - + +
302F PHE* 3.8 43.3 - - + -
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Residues in contact with MET 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F ARG 3.9 17.5 - - - +
200F LEU* 3.7 36.3 - - + -
203F PHE* 3.8 22.0 - - + -
250F LEU* 1.3 74.1 - - - +
252F ILE* 1.3 61.7 + - - +
254F LEU* 3.1 24.6 + - + -
255F ALA* 3.1 18.0 + - - +
265F LEU* 4.7 6.1 - - + -
278F TYR* 6.0 2.9 - - - -
294F VAL* 3.8 19.5 - - + +
295F ILE 3.3 7.9 + - - -
296F ASP* 3.5 33.4 - - + +
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Residues in contact with ILE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F ARG* 5.4 0.7 - - - +
203F PHE* 3.6 26.3 - - + -
210F GLU* 3.5 31.4 - - + +
213F PHE* 3.8 13.0 - - + -
214F LEU* 3.6 24.9 - - + -
236F VAL* 4.3 8.3 - - + -
250F LEU* 4.0 21.1 - - + +
251F MET* 1.3 76.3 - - - +
253F GLY* 1.3 62.2 + - - +
255F ALA* 3.5 2.4 - - - +
256F LYS* 2.9 28.6 + - - +
296F ASP* 4.5 1.7 + - - +
297F LEU 5.4 2.2 - - - +
299F LEU* 3.7 34.3 - - + -
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Residues in contact with GLY 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F PHE* 4.2 11.7 - - - -
236F VAL* 3.4 25.1 - - - -
237F TYR* 4.4 4.4 - - - +
248F LEU* 3.6 13.1 - - - +
250F LEU 3.0 8.7 + - - -
252F ILE* 1.3 81.8 - - - +
254F LEU* 1.3 61.3 + - - +
256F LYS* 3.4 4.7 + - - +
257F ARG* 3.2 17.7 + - - +
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Residues in contact with LEU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LEU* 3.6 6.7 - - + -
248F LEU* 3.3 33.7 - - + +
250F LEU 3.2 24.9 - - - +
251F MET* 3.1 26.1 + - + +
253F GLY* 1.3 72.7 - - - +
255F ALA* 1.3 55.2 + - - +
257F ARG* 3.2 4.0 + - - +
258F SER* 2.8 36.9 + - - -
263F LEU* 3.9 15.5 - - + +
265F LEU* 3.7 23.8 - - + -
280F ILE* 3.7 25.8 - - + -
294F VAL* 3.8 18.8 - - + -
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Residues in contact with ALA 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LEU* 3.4 13.6 - - + +
203F PHE* 3.7 42.0 - - + -
214F LEU* 4.5 8.3 - - + +
251F MET 3.1 11.4 + - - +
252F ILE* 3.3 10.7 + - + +
254F LEU* 1.3 75.9 - - - +
256F LYS* 1.3 61.8 + - - +
258F SER* 3.4 15.3 + - - -
259F GLN* 3.5 13.3 + - - +
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F PHE* 3.5 41.2 + - + +
214F LEU* 3.6 23.1 - - + +
216F LEU 3.5 14.9 + - - -
217F ALA* 4.5 6.8 - - - +
218F MET* 4.6 1.2 - - - +
237F TYR* 3.3 32.3 + - + -
252F ILE 2.9 17.0 + - - +
253F GLY 3.5 6.1 - - - +
255F ALA* 1.3 75.1 - - - +
257F ARG* 1.3 64.8 + - - +
258F SER 3.5 0.2 + - - -
259F GLN* 3.5 26.3 + - - +
260F ASP* 4.3 11.1 + - - +
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Residues in contact with ARG 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F TYR 5.3 1.8 - - - +
240F PHE* 3.1 61.4 - - + +
248F LEU* 4.9 0.2 - - + -
253F GLY 3.2 9.6 + - - +
254F LEU* 3.2 8.8 + - - +
256F LYS* 1.3 77.7 - - - +
258F SER* 1.3 65.9 + - - +
260F ASP* 3.0 24.3 + - - +
261F SER* 2.9 43.2 + - - +
263F LEU* 4.5 8.1 - - + -
282F ASP* 2.7 34.0 + - - -
284F GLN* 3.7 18.2 - - - +
285F THR* 4.6 4.4 - - - +
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Residues in contact with SER 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LEU* 3.5 28.9 - - - +
254F LEU 2.8 19.4 + - - -
255F ALA* 3.4 10.8 - - - -
256F LYS 3.2 0.2 - - - -
257F ARG* 1.3 77.1 - - - +
259F GLN* 1.3 62.8 + - - +
260F ASP 3.0 2.4 + - - -
261F SER* 3.5 19.2 + - - -
262F PRO* 4.4 4.5 - - - +
263F LEU* 4.5 8.4 + - - +
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Residues in contact with GLN 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F LEU* 3.3 52.2 + - + +
215F GLU* 5.7 2.0 - - - +
255F ALA 3.7 10.8 - - - +
256F LYS* 3.5 20.4 - - - +
257F ARG 3.3 0.4 - - - -
258F SER* 1.3 76.5 - - - +
260F ASP* 1.3 66.6 + - - +
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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