Contacts of the helix formed by residues 246 - 253 (chain G) 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 LEU 246 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G SER 3.1 1.0 - - - -
245G PRO* 1.3 88.2 - - + +
247G ALA* 1.3 68.6 - - - +
248G CYS 3.2 0.2 - - - -
249G GLY* 3.1 13.4 + - - +
251G VAL* 2.9 36.9 + - + +
252G SER* 5.0 2.5 - - - +
304G PRO* 3.8 37.7 - - + +
307G ALA* 3.9 13.0 - - + -
308G ILE* 4.1 8.5 - - + -
333G ASN* 4.2 6.3 - - - +
1001G NAP 3.1 60.6 + - + +
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Residues in contact with ALA 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G GLU* 5.7 0.2 - - - -
218G HIS* 3.7 33.0 - - + +
220G PHE* 4.9 3.4 - - + -
244G SER* 2.8 17.1 + - - -
245G PRO 3.3 1.2 - - - -
246G LEU* 1.3 82.6 - - - +
248G CYS* 1.3 71.4 + - - +
250G ILE* 3.4 29.7 + - + +
251G VAL* 4.0 10.1 - - + -
273G LEU* 4.8 0.2 - - - +
285G GLN* 6.0 0.2 - - - +
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Residues in contact with CYS 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G TRP* 3.8 21.1 - - - -
244G SER* 4.2 6.2 - - - -
247G ALA* 1.3 75.0 - - - +
249G GLY* 1.3 55.0 + - - +
250G ILE 3.3 1.9 + - - -
255G TYR* 4.6 4.2 + - - -
264G ARG* 3.4 42.4 - - - +
272G TRP* 4.4 15.7 - - - -
273G LEU* 4.0 23.2 - - + +
1001G NAP 2.7 35.9 + - - +
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Residues in contact with GLY 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LEU* 3.1 11.5 + - - +
248G CYS* 1.3 76.4 - - - +
250G ILE* 1.3 61.7 + - - +
251G VAL 3.1 2.7 - - - -
252G SER* 2.7 31.6 + - - -
254G LYS* 4.4 2.1 - - - +
255G TYR* 4.2 10.6 - - - -
1001G NAP 3.2 31.5 + - - -
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Residues in contact with ILE 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G PHE* 4.9 7.2 - - + -
246G LEU 3.2 0.8 + - - +
247G ALA* 3.4 26.9 - - + +
248G CYS 3.3 1.4 + - - -
249G GLY* 1.3 77.1 - - - +
251G VAL* 1.3 60.4 + - - +
252G SER 3.0 5.0 + - - -
253G GLY* 3.1 11.8 + - - -
254G LYS 4.8 0.2 + - - -
255G TYR* 3.9 11.6 - - + -
273G LEU* 4.1 12.6 - - + -
276G LYS* 5.7 4.3 - - + -
277G ILE* 3.6 42.6 - - + +
282G GLY* 5.9 1.6 - - - +
285G GLN* 4.0 26.2 - - + +
286G GLN* 4.6 7.8 - - - +
289G LEU* 3.2 18.1 - - + +
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Residues in contact with VAL 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G HIS* 5.1 4.7 - - + -
219G MET* 4.9 14.1 - - + -
220G PHE* 4.2 22.0 - - + -
245G PRO 4.5 3.4 - - - +
246G LEU* 2.9 38.3 + - + +
247G ALA* 4.0 10.8 - - + +
250G ILE* 1.3 76.9 - - - +
252G SER* 1.3 61.4 + - - +
253G GLY 3.2 0.2 - - - -
289G LEU* 4.1 11.7 - - + -
303G LEU* 3.2 27.9 - - + +
307G ALA* 3.5 30.3 - - + -
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Residues in contact with SER 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LEU* 5.0 2.9 - - - +
249G GLY* 2.7 21.4 + - - -
251G VAL* 1.3 78.6 - - - +
253G GLY* 1.3 62.0 + - - +
254G LYS* 3.2 25.2 + - - +
293G GLN* 5.4 1.4 - - - +
303G LEU* 4.4 10.7 - - - +
304G PRO* 4.0 19.3 - - - +
1001G NAP 3.6 31.2 - - - -
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Residues in contact with GLY 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ILE 3.1 7.6 + - - -
251G VAL 3.2 1.6 - - - -
252G SER* 1.3 79.2 + - - +
254G LYS* 1.3 63.1 + - - +
255G TYR 3.1 5.1 + - - -
256G ASP* 3.3 17.3 + - - +
286G GLN* 3.4 18.7 + - - -
289G LEU* 3.8 12.1 - - - -
303G LEU* 5.1 1.8 - - - -
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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