Contacts of the helix formed by residues 263 - 275 (chain B) in PDB entry 2R9R
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 ILE 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B ILE* 4.4 11.4 - - + +
233B PHE* 3.5 33.9 - - + -
234B SER* 4.0 24.9 - - - +
237B PHE* 4.1 28.7 - - + -
259B ASP 3.9 8.7 - - - +
260B ILE* 2.8 22.1 + - + +
262B ALA* 1.3 78.4 - - - +
264B ILE* 1.3 72.5 + - + +
265B PRO* 3.2 4.1 - - - -
266B TYR* 3.2 12.6 + - - +
267B TYR* 3.5 31.4 + - + -
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ILE* 3.0 38.3 + - + +
261B VAL* 4.0 13.0 - - + +
263B ILE* 1.3 78.9 - - + +
265B PRO* 1.3 67.8 - - + +
267B TYR* 3.6 4.6 + - - +
268B VAL* 2.9 45.0 + - + +
292B PHE* 3.9 15.3 - - + -
295B MET* 4.7 6.5 - - - -
514B PGW 4.2 35.2 - - + -
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Residues in contact with PRO 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL 3.1 19.7 - - - +
262B ALA 4.2 3.4 - - - +
263B ILE* 3.3 6.3 - - - +
264B ILE* 1.3 92.3 - - + +
266B TYR* 1.3 53.6 + - - +
268B VAL* 3.7 1.2 - - - +
269B THR* 2.6 40.3 + - - +
292B PHE* 3.5 37.1 - - + +
295B MET* 4.1 21.1 - - + -
296B ARG* 3.6 26.5 - - + +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B TYR* 3.7 19.1 - - - -
214B GLN* 4.5 0.9 + - - -
223B PHE* 3.4 24.2 - + - -
226B GLU* 3.8 26.3 + - + +
227B THR* 2.6 46.0 + - + +
230B ILE* 3.7 34.5 - - + -
231B ILE* 6.2 0.7 - - + -
263B ILE* 3.2 9.9 + - - +
265B PRO* 1.3 77.7 - - - +
267B TYR* 1.3 79.2 + + - +
269B THR* 3.1 7.1 + - - -
270B ILE* 3.1 47.5 + - + +
296B ARG* 5.4 0.6 - - - +
513B PGW 4.1 16.0 - - + +
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Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 3.8 13.9 - - + +
231B ILE* 5.3 2.6 - - - +
234B SER* 2.7 33.2 + - - -
263B ILE* 3.5 39.9 + - + -
264B ILE* 4.3 4.9 - - - +
265B PRO 3.5 0.4 - - - -
266B TYR* 1.3 95.0 - + - +
268B VAL* 1.3 63.6 + - + +
270B ILE* 3.4 14.2 + - + +
271B PHE* 3.0 23.2 + - - +
513B PGW 4.8 17.6 - - + +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 2.9 41.5 + - + +
265B PRO 3.7 3.1 - - - +
267B TYR* 1.3 75.3 - - + +
269B THR* 1.3 62.2 + - - +
271B PHE* 3.5 10.9 + - + +
272B LEU* 2.9 39.7 + - + +
292B PHE* 3.8 39.5 - - + -
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Residues in contact with THR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 3.5 46.6 - - + +
212B TYR* 4.6 6.0 + - - +
214B GLN* 4.1 7.2 - - - +
265B PRO* 2.6 24.8 + - - +
266B TYR* 3.1 5.9 + - - -
268B VAL* 1.3 75.8 - - - +
270B ILE* 1.3 66.3 + - - +
272B LEU* 3.2 7.8 + - - +
273B THR* 2.9 27.8 + - + +
289B VAL* 4.5 11.1 + - + +
292B PHE* 4.5 10.9 - - - +
293B ARG* 5.7 0.3 + - - -
296B ARG* 6.1 1.0 - - - -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 3.1 23.3 - - - +
266B TYR* 3.1 44.9 + - + +
267B TYR* 3.5 17.3 - - + +
268B VAL 3.3 0.2 - - - -
269B THR* 1.3 76.0 - - - +
271B PHE* 1.3 65.8 + - - +
273B THR* 3.0 15.9 + - - -
274B GLU* 3.0 29.8 + - + +
513B PGW 4.1 34.3 - - + -
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B TYR 3.0 14.1 + - - +
268B VAL* 3.7 13.0 - - + +
270B ILE* 1.3 81.9 - - - +
272B LEU* 1.3 73.7 + - + +
274B GLU* 3.9 3.5 - - - +
275B SER* 2.5 54.1 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B VAL* 2.9 38.9 + - + +
269B THR* 3.7 5.4 - - - +
270B ILE 3.2 0.2 - - - -
271B PHE* 1.3 92.3 - - + +
273B THR* 1.3 62.6 + - - +
275B SER* 4.6 0.9 - - - -
276B ASN* 2.9 35.8 + - - +
285B VAL* 3.7 23.3 - - + +
288B VAL* 3.6 31.0 - - + -
289B VAL* 3.8 30.3 - - + +
292B PHE* 4.6 1.8 - - + -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PHE* 5.7 0.5 - - - -
206B SER* 5.4 2.7 - - - -
210B ILE* 3.4 33.0 - - + -
214B GLN* 2.7 19.8 + - - +
269B THR* 2.9 17.1 + - + +
270B ILE 3.0 10.0 + - - -
272B LEU* 1.3 74.6 - - + +
274B GLU* 1.3 73.9 + - - +
276B ASN 3.2 23.5 - - - +
277B LYS* 3.3 11.6 + - - +
282B PHE* 3.8 22.4 - - + -
289B VAL* 5.2 1.3 - - + -
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 4.5 0.5 - - - +
270B ILE* 3.0 29.3 + - + +
271B PHE* 4.2 3.4 - - - +
273B THR* 1.3 91.6 + - - +
275B SER* 1.3 59.3 + - - +
276B ASN 3.3 1.1 + - - -
277B LYS* 3.5 35.2 + - - +
513B PGW 3.2 31.1 - - + +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PHE* 2.5 49.2 + - - -
272B LEU* 4.5 1.1 - - - -
273B THR 3.2 0.4 - - - -
274B GLU* 1.3 77.3 - - - +
276B ASN* 1.3 76.5 + - - +
277B LYS 3.8 0.7 - - - -
281B GLN* 3.5 11.0 + - - -
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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