Contacts of the helix formed by residues 292 - 299 (chain M) in PDB entry 2RCR
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 TRP 292 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H ALA* 5.3 2.9 - - + -
191M HIS* 3.1 42.5 + + + +
193M ASN 3.9 13.2 - - - +
194M LEU* 4.2 11.4 - - + +
196M TYR* 4.2 14.7 - - + +
197M ASN* 3.4 40.5 - - + +
198M PRO* 4.0 16.6 - - + -
199M PHE* 4.3 13.7 - + - -
281M GLY 4.1 3.8 - - - -
284M LEU* 4.5 5.4 - - + -
285M SER* 3.4 38.9 + - - +
289M VAL* 3.6 34.3 - - + +
291M ASN* 1.3 70.9 + - - +
293M TYR* 1.3 69.4 + - - +
294M VAL 3.1 2.2 - - - -
295M TRP* 2.9 43.6 + + + +
296M GLY 3.5 1.9 + - - -
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Residues in contact with TYR 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M GLY* 4.6 11.9 - - - -
193M ASN* 4.8 2.1 - - + +
196M TYR* 4.3 34.4 - + + +
291M ASN* 3.5 12.4 + - - +
292M TRP* 1.3 77.5 - - - +
294M VAL* 1.3 75.8 + - + +
296M GLY* 3.1 4.9 + - - -
297M GLN* 2.5 63.6 + - + +
302M ALA* 5.2 4.0 - - + -
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Residues in contact with VAL 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291M ASN* 3.1 37.9 - - + +
293M TYR* 1.3 89.8 - - + +
295M TRP* 1.3 52.3 + - - +
297M GLN* 3.1 3.7 - - - -
298M ASN* 2.4 60.9 + - - +
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Residues in contact with TRP 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 4.1 19.9 - - + +
13H ALA* 3.2 45.3 - - + +
14H SER* 3.6 19.7 - - - -
17H ILE* 5.0 5.6 - - + -
196M TYR 4.7 4.9 - - - +
198M PRO* 3.7 35.2 - - + -
199M PHE* 6.0 0.4 - + - -
289M VAL* 4.2 19.0 - - + +
291M ASN 4.4 1.4 + - - +
292M TRP* 2.9 30.2 + + + +
294M VAL* 1.3 77.5 - - - +
296M GLY* 1.3 55.5 + - - +
298M ASN* 2.8 26.5 + - + +
299M HIS* 2.9 39.0 + + - +
301M MET* 4.5 22.2 - - + -
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Residues in contact with GLY 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M TYR* 4.9 11.4 - - - +
292M TRP 3.5 2.8 + - - -
293M TYR 3.1 7.4 + - - -
295M TRP* 1.3 84.3 - - - +
297M GLN* 1.3 55.9 + - - +
298M ASN 3.2 0.2 + - - -
299M HIS* 3.8 0.8 - - - -
300M GLY 2.8 27.2 + - - -
301M MET* 2.8 37.7 + - - +
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Residues in contact with GLN 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M TYR* 2.5 69.7 + - + +
294M VAL 3.1 3.6 - - - +
296M GLY* 1.3 72.6 - - - +
298M ASN* 1.3 56.8 + - - +
299M HIS 3.3 4.0 - - - -
300M GLY* 4.6 5.4 - - - +
301M MET 3.5 2.6 + - - -
302M ALA* 3.7 20.7 - - + +
303M PRO 4.5 8.5 + - - +
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Residues in contact with ASN 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ASN* 3.0 33.2 + - - +
294M VAL* 2.4 44.6 + - - +
295M TRP* 2.8 13.4 + - - +
297M GLN* 1.3 75.4 - - - +
299M HIS* 1.3 73.1 + - + +
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Residues in contact with HIS 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ASN* 4.9 14.4 + - - -
10H PHE* 5.9 5.2 - + - -
11H ASP* 5.1 9.9 - - + +
14H SER* 3.8 25.9 + - - -
295M TRP* 2.9 47.8 + + - +
296M GLY 4.1 1.1 - - - +
297M GLN 4.8 0.9 - - - -
298M ASN* 1.3 98.5 + - + +
300M GLY* 1.3 57.6 + - - +
301M MET* 5.0 15.5 - - + -
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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