Contacts of the helix formed by residues 285 - 296 (chain H) 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 VAL 285 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H LEU* 3.6 33.9 - - + +
276H ASN* 3.8 23.1 - - + +
281H GLN 3.3 9.4 + - - +
282H PHE* 2.8 23.3 + - + +
284H ASN* 1.3 79.0 - - - +
286H ARG* 1.3 66.8 + - - +
287H ARG* 3.2 3.8 - - - +
288H VAL* 3.1 19.4 + - + +
289H VAL* 3.1 26.6 + - + +
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Residues in contact with ARG 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H TYR* 3.0 43.2 + - - -
208H SER 6.0 0.2 - - - -
209H THR* 3.0 34.9 + - + +
282H PHE* 2.8 17.3 + - + +
283H GLN 4.0 11.1 + - - +
284H ASN 3.7 0.8 - - - -
285H VAL* 1.3 78.6 - - - +
287H ARG* 1.3 58.5 + - + +
289H VAL* 3.2 8.7 + - - +
290H GLN* 2.8 68.3 + - - +
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Residues in contact with ARG 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H GLN 5.4 0.4 + - - +
284H ASN* 4.4 16.7 + - - -
285H VAL* 3.2 1.3 - - - -
286H ARG* 1.3 77.8 - - + +
288H VAL* 1.3 66.8 + - + +
290H GLN* 3.4 13.5 + - - +
291H ILE* 3.0 39.0 + - + +
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Residues in contact with VAL 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 3.6 25.1 - - + -
285H VAL* 3.1 21.9 + - + +
287H ARG* 1.3 84.2 - - + +
289H VAL* 1.3 67.0 + - - +
291H ILE* 3.2 12.0 + - + +
292H PHE* 3.1 46.1 + - + -
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Residues in contact with VAL 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H THR* 3.9 12.3 - - + -
210H ILE* 3.7 33.0 - - + -
269H THR* 4.4 12.5 + - + +
272H LEU* 3.9 27.4 - - + -
273H THR* 5.3 1.6 - - + -
282H PHE* 4.2 18.4 - - + -
285H VAL* 3.1 23.0 + - + +
286H ARG* 3.2 8.9 + - - +
288H VAL* 1.3 76.3 - - - +
290H GLN* 1.3 62.3 + - - +
292H PHE* 3.1 7.9 + - - +
293H ARG* 3.1 19.2 + - - +
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Residues in contact with GLN 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H THR* 3.6 22.4 - - + +
286H ARG* 2.8 59.1 + - - +
287H ARG* 3.6 15.3 - - - +
289H VAL* 1.3 76.5 - - - +
291H ILE* 1.3 64.9 + - + +
293H ARG* 3.1 16.9 + - - +
294H ILE* 3.2 23.2 + - + +
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Residues in contact with ILE 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H ARG* 3.0 28.0 + - + +
288H VAL* 3.5 15.3 - - + +
290H GLN* 1.3 74.8 - - + +
292H PHE* 1.3 67.6 + - + +
294H ILE* 3.4 14.5 + - + +
295H MET* 3.2 33.8 + - + +
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Residues in contact with PHE 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264H ILE* 3.9 21.8 - - + -
265H PRO* 3.3 42.9 - - + +
268H VAL* 3.8 28.7 - - + -
269H THR* 4.5 11.0 - - - +
272H LEU* 4.6 2.2 - - + -
288H VAL* 3.1 46.5 + - + +
289H VAL* 3.1 7.6 + - - +
291H ILE* 1.3 82.1 - - + +
293H ARG* 1.3 65.1 + - - +
295H MET* 3.4 30.8 + - + +
296H ARG* 3.4 7.8 + - - +
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Residues in contact with ARG 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H PHE* 3.4 16.8 + - + -
183H GLU* 3.8 21.4 + - - +
184H THR* 3.9 25.9 - - - +
208H SER 3.1 25.7 + - - -
209H THR* 3.2 20.7 + - - +
210H ILE* 3.2 18.1 + - + +
211H GLY* 3.4 22.1 - - - -
269H THR* 5.6 0.4 + - - -
289H VAL 3.1 11.4 + - - +
290H GLN* 3.1 10.3 + - - +
292H PHE* 1.3 78.0 - - - +
294H ILE* 1.3 63.9 + - + +
296H ARG* 3.1 35.7 - - - +
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Residues in contact with ILE 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H PHE* 4.9 4.7 - - - -
290H GLN* 3.2 21.1 + - + +
291H ILE* 3.6 12.3 - - + +
292H PHE 3.3 0.2 - - - -
293H ARG* 1.3 80.1 - - + +
295H MET* 1.3 61.3 + - - +
296H ARG 3.2 0.5 + - - -
297H ILE* 3.1 32.3 + - + +
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Residues in contact with MET 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H VAL* 4.3 14.4 - - + +
264H ILE* 4.8 7.2 - - - -
265H PRO* 4.0 16.0 - - + +
291H ILE* 3.2 23.8 + - + +
292H PHE* 3.5 45.1 - - + +
293H ARG 3.2 0.4 - - - -
294H ILE* 1.3 75.6 - - - +
296H ARG* 1.3 63.6 + - - +
297H ILE 3.1 0.4 - - - -
298H LEU* 3.1 42.0 + - + +
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Residues in contact with ARG 296 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H PHE* 3.4 30.1 - - + +
183H GLU* 2.9 40.8 + - - -
210H ILE* 3.6 15.9 + - - -
212H TYR* 3.7 12.2 - - - -
226H GLU* 3.0 40.9 + - - +
261H VAL 5.8 0.2 - - - -
262H ALA* 5.9 1.9 - - - +
265H PRO* 3.5 21.5 - - + -
266H TYR* 5.9 0.7 - - - +
292H PHE 3.4 10.5 + - - +
293H ARG* 3.1 28.1 - - - +
294H ILE 3.1 0.4 - - - -
295H MET* 1.3 79.8 - - - +
297H ILE* 1.3 59.8 + - - +
299H ARG* 2.9 46.8 + - - +
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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