Contacts of the helix formed by residues 263 - 275 (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 ILE 263 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230H ILE* 4.4 11.2 - - + +
233H PHE* 3.5 33.7 - - + -
234H SER* 3.9 25.1 - - - +
237H PHE* 4.1 29.6 - - + -
259H ASP 3.9 10.3 - - - +
260H ILE* 2.9 20.1 + - + +
262H ALA* 1.3 78.3 - - - +
264H ILE* 1.3 70.4 + - + +
265H PRO* 3.3 3.4 - - - -
266H TYR* 3.2 13.9 + - - +
267H TYR* 3.4 31.2 - - + -
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Residues in contact with ILE 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260H ILE* 3.0 38.7 + - + +
261H VAL* 4.0 17.3 - - + +
263H ILE* 1.3 78.2 - - + +
265H PRO* 1.3 70.4 - - + +
267H TYR* 3.6 4.2 + - - +
268H VAL* 3.0 44.8 + - + +
292H PHE* 3.9 15.3 - - + -
295H MET* 4.8 6.1 - - - -
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Residues in contact with PRO 265 (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 3.1 19.7 - - - +
262H ALA 4.3 3.1 - - - +
263H ILE* 3.4 5.2 - - - +
264H ILE* 1.3 92.8 - - + +
266H TYR* 1.3 53.9 + - - +
268H VAL* 3.8 1.0 - - - +
269H THR* 2.6 40.0 + - - +
292H PHE* 3.3 36.9 - - + +
295H MET* 4.0 15.3 - - + -
296H ARG* 3.5 31.9 - - + +
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Residues in contact with TYR 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H TYR* 3.7 18.6 - - - -
214H GLN* 4.5 0.8 + - - -
218H PHE* 5.8 0.2 - - - -
223H PHE* 3.4 28.4 - + - -
226H GLU* 3.8 26.1 + - + +
227H THR* 2.8 39.9 + - + +
230H ILE* 3.5 36.1 - - + -
231H ILE* 6.2 2.0 - - + -
263H ILE 3.2 11.0 + - - +
265H PRO* 1.3 79.5 - - - +
267H TYR* 1.3 79.0 + + - +
269H THR* 3.3 5.3 + - - -
270H ILE* 3.2 49.4 + - + +
296H ARG* 5.4 0.8 - - - +
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Residues in contact with TYR 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H ILE* 3.8 14.2 - - + +
231H ILE* 5.3 5.9 - - - +
234H SER* 2.7 33.1 + - - -
263H ILE* 3.4 38.7 + - + -
264H ILE* 4.3 4.3 - - - +
265H PRO 3.5 0.2 - - - -
266H TYR* 1.3 90.4 - + - +
268H VAL* 1.3 63.5 + - + +
270H ILE* 3.4 14.3 + - + +
271H PHE* 3.1 23.6 + - - +
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Residues in contact with VAL 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H ILE* 3.0 41.9 + - + +
265H PRO 3.8 2.5 - - - +
267H TYR* 1.3 77.9 - - + +
269H THR* 1.3 57.7 + - - +
271H PHE* 3.5 10.9 + - + +
272H LEU* 2.9 42.1 + - + +
292H PHE* 3.8 36.8 - - + -
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Residues in contact with THR 269 (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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210H ILE* 3.6 47.8 - - + +
212H TYR* 4.6 6.2 + - - +
214H GLN* 4.1 7.4 - - - +
265H PRO* 2.6 24.0 + - - +
266H TYR* 3.5 5.7 - - - -
267H TYR 3.2 0.2 - - - -
268H VAL* 1.3 74.8 - - - +
270H ILE* 1.3 62.8 + - - +
272H LEU* 3.4 8.1 + - - +
273H THR* 2.9 29.7 + - + +
289H VAL* 4.4 11.1 + - + +
292H PHE* 4.5 11.3 - - - +
293H ARG* 6.0 0.5 - - - -
296H ARG* 6.0 1.6 - - - -
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Residues in contact with ILE 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H GLN* 3.2 24.5 - - - +
223H PHE* 5.9 2.5 - - + -
266H TYR* 3.2 44.8 + - + +
267H TYR* 3.6 17.3 - - + +
269H THR* 1.3 76.0 - - - +
271H PHE* 1.3 63.4 + - - +
273H THR* 3.0 16.6 + - - +
274H GLU* 3.0 30.3 + - + +
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Residues in contact with PHE 271 (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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267H TYR 3.1 13.2 + - - +
268H VAL* 3.6 12.6 - - + +
270H ILE* 1.3 80.6 - - - +
272H LEU* 1.3 72.0 + - + +
274H GLU* 3.6 2.9 + - - +
275H SER* 2.6 55.7 + - - -
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Residues in contact with LEU 272 (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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268H VAL* 2.9 39.4 + - + +
269H THR* 3.8 5.4 - - - +
271H PHE* 1.3 92.9 - - + +
273H THR* 1.3 61.7 + - - +
275H SER* 3.6 1.3 + - - -
276H ASN* 2.9 35.5 + - - +
285H VAL* 3.6 23.8 - - + +
288H VAL* 3.6 30.3 - - + -
289H VAL* 3.9 30.3 - - + +
292H PHE* 4.6 1.8 - - + -
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Residues in contact with THR 273 (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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202H PHE* 5.6 0.6 - - - -
206H SER* 5.4 2.0 - - - -
210H ILE* 3.4 31.9 - - + -
214H GLN* 2.8 17.9 + - - +
269H THR* 2.9 19.1 + - + +
270H ILE* 3.0 10.6 + - - -
272H LEU* 1.3 75.8 - - + +
274H GLU* 1.3 69.7 + - - +
276H ASN 3.2 26.5 - - - +
277H LYS* 3.3 12.7 + - - +
282H PHE* 3.8 22.7 - - + -
289H VAL* 5.3 1.6 - - + -
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Residues in contact with GLU 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H GLN* 4.7 6.9 - - - +
270H ILE* 3.0 30.7 + - + +
271H PHE* 4.3 3.8 - - - +
273H THR* 1.3 91.4 + - - +
275H SER* 1.3 60.0 + - - +
276H ASN 3.3 0.6 + - - -
277H LYS* 3.5 41.1 + - - +
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Residues in contact with SER 275 (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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271H PHE* 2.6 47.0 + - - -
272H LEU* 4.0 5.6 - - - -
273H THR 3.2 0.2 - - - -
274H GLU* 1.3 76.9 - - - +
276H ASN* 1.3 71.5 + - - +
277H LYS 3.9 1.1 - - - -
281H GLN* 3.5 10.8 + - - -
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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