Contacts of the helix formed by residues 254 - 264 (chain C) in PDB entry 2RIB
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 PHE 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C PRO* 1.3 69.5 - - - +
255C THR* 1.3 67.3 + - - +
257C ALA* 3.1 2.8 + - - +
258C GLN* 2.8 65.7 + - - +
268C LEU* 3.3 24.9 - - + -
292C PHE* 3.3 23.4 - + + -
293C LEU 3.6 15.3 - - - -
294C SER 3.9 8.1 - - - -
295C MET 5.0 0.2 - - - -
296C THR* 3.5 24.7 - - + -
331C CYS* 3.3 32.8 - - + -
345C CYS* 3.0 25.4 + - + +
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C PRO* 3.4 3.1 + - - +
254C PHE* 1.3 87.9 - - - +
256C GLU* 1.3 62.2 + - + +
258C GLN* 3.5 10.8 + - - +
259C LEU* 3.1 28.7 + - + +
345C CYS* 4.7 2.4 + - - +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LYS* 3.6 25.7 + - + +
253C PRO* 3.3 36.1 + - + +
254C PHE 3.2 0.6 - - - -
255C THR* 1.3 78.3 - - + +
257C ALA* 1.3 66.1 + - - +
259C LEU* 3.4 7.4 + - - +
260C LEU* 3.1 29.9 + - + +
348C LYS* 5.7 0.4 + - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LYS* 4.2 4.6 - - + +
253C PRO 3.0 16.8 + - - +
254C PHE* 3.5 7.6 - - - +
256C GLU* 1.3 75.6 - - - +
258C GLN* 1.3 62.7 + - - +
260C LEU* 3.3 6.1 + - - +
261C CYS* 3.2 27.5 + - - -
268C LEU* 3.9 17.7 - - + -
292C PHE* 4.8 6.7 - - + -
351C VAL* 3.8 32.0 - - + +
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Residues in contact with GLN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PHE* 2.8 47.7 + - + +
255C THR* 3.6 11.4 - - - +
257C ALA* 1.3 78.0 - - - +
259C LEU* 1.3 62.9 + - - +
261C CYS* 3.4 2.6 + - - +
262C THR* 3.0 39.9 + - + +
268C LEU* 3.7 23.6 + - + +
294C SER* 4.9 4.0 + - - -
307C PRO* 5.2 12.7 - - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C THR* 3.1 19.2 + - + +
256C GLU* 3.7 7.6 - - - +
257C ALA 3.3 0.2 - - - -
258C GLN* 1.3 74.1 - - - +
260C LEU* 1.3 60.6 + - - +
262C THR* 2.8 24.1 + - - +
263C GLN* 2.9 56.7 + - + +
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B PHE* 4.3 17.4 - - + -
235B PRO* 6.0 3.1 - - + -
286B ALA* 5.7 8.5 - - + -
250C PHE* 3.8 34.8 - - + -
252C LYS* 4.3 15.3 - - + -
256C GLU* 3.1 20.3 + - + +
257C ALA* 3.3 11.0 + - - +
259C LEU* 1.3 77.0 - - + +
261C CYS* 1.3 62.7 + - - +
263C GLN* 3.5 12.0 + - - +
264C ALA* 3.1 24.4 + - - +
351C VAL* 4.5 7.6 - - + -
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Residues in contact with CYS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ALA 3.2 15.1 + - - -
258C GLN 3.8 5.6 - - - +
260C LEU* 1.3 81.0 - - - +
262C THR* 1.3 60.7 + - - +
264C ALA* 3.1 10.4 + - - +
265C GLY 3.3 0.2 + - - -
266C GLY* 2.9 25.7 + - - -
267C GLN* 3.4 20.9 - - - -
268C LEU* 3.6 23.3 - - - +
351C VAL* 4.4 2.0 - - - -
352C VAL 4.1 0.4 - - - -
353C CYS* 2.0 56.3 - - + -
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLN* 3.0 26.0 + - + +
259C LEU* 2.8 34.0 + - - +
261C CYS* 1.3 75.7 - - - +
263C GLN* 1.3 62.3 + - - +
265C GLY* 3.1 14.2 + - - -
266C GLY 3.4 12.6 - - - +
267C GLN* 5.0 7.6 - - + -
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Residues in contact with GLN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLN* 5.8 1.6 + - - -
282B GLN* 4.2 17.4 + - - +
259C LEU* 2.9 55.7 + - + +
260C LEU* 4.0 12.2 - - - +
262C THR* 1.3 76.6 - - - +
264C ALA* 1.3 58.6 + - - +
265C GLY 3.1 1.8 + - - -
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LYS* 3.9 16.0 - - - +
233B LEU 6.1 0.2 - - - -
234B PHE* 3.8 28.9 - - + -
260C LEU 3.1 17.6 + - - +
261C CYS* 3.1 7.4 + - - +
263C GLN* 1.3 76.4 - - - +
265C GLY* 1.3 60.7 + - - +
266C GLY 3.4 0.2 - - - -
355C PHE* 3.5 19.7 - - + -
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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