Contacts of the helix formed by residues 246 - 258 (chain G) in PDB entry 1R8Y
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 CYS 246 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174G HIS* 4.7 0.2 - - - -
177G TYR 4.8 0.2 - - - -
178G ASP* 3.6 23.1 - - - +
181G LEU* 4.1 15.3 - - - -
244G PRO 3.2 8.1 + - - -
245G HIS* 1.3 74.2 - - - +
247G LEU* 1.3 66.2 + - - +
248G ALA* 3.3 4.7 - - + +
249G SER* 3.1 18.0 + - - +
250G PHE* 3.0 22.2 + - - +
7246G BME 2.1 48.5 - - + -
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Residues in contact with LEU 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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174G HIS* 4.2 7.4 - - - +
178G ASP* 3.0 27.1 + - - +
245G HIS 4.0 0.4 + - - -
246G CYS* 1.3 70.8 - - - +
248G ALA* 1.3 58.6 + - - +
250G PHE* 4.1 0.3 - - - +
251G THR* 2.7 39.6 + - - +
266G VAL* 4.2 11.4 - - + -
273G TYR* 3.7 33.7 - - + +
284G PHE* 3.8 31.6 - - + -
286G HIS* 3.6 29.4 - - + +
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Residues in contact with ALA 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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178G ASP* 4.7 1.4 + - - +
246G CYS* 3.3 3.5 - - + +
247G LEU* 1.3 79.8 - - - +
249G SER* 1.3 66.9 + - - +
251G THR* 3.3 5.7 + - - -
252G GLU* 3.1 25.7 + - + +
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Residues in contact with SER 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G GLN* 5.4 9.2 - - - -
245G HIS* 6.0 1.6 - - - -
246G CYS* 3.1 21.8 + - - +
248G ALA* 1.3 75.3 - - - +
250G PHE* 1.3 68.6 + - - +
252G GLU* 2.9 13.2 + - - +
253G LEU* 2.7 33.0 + - - +
7246G BME 5.7 2.1 - - - +
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Residues in contact with PHE 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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140G PHE* 3.8 29.6 - + + -
157G LEU* 4.2 11.7 - - + -
172G ILE* 3.8 37.0 - - + -
173G ASP 5.0 2.9 - - - -
174G HIS* 3.5 24.0 - + + +
245G HIS* 3.7 30.0 - + + -
246G CYS 3.0 14.1 + - - +
247G LEU 4.2 0.9 - - - +
249G SER* 1.3 78.3 - - - +
251G THR* 1.3 63.6 + - - +
253G LEU* 2.9 11.9 + - + +
254G VAL* 2.8 36.1 + - + +
286G HIS* 3.2 38.8 - + - -
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Residues in contact with THR 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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247G LEU* 2.7 25.8 + - - +
248G ALA* 3.4 9.6 - - - -
250G PHE* 1.3 75.9 - - - +
252G GLU* 1.3 66.7 + - - +
254G VAL* 3.4 7.6 - - - +
255G ARG* 3.0 52.2 + - - +
264G HIS* 3.4 23.6 - - - +
266G VAL* 4.3 3.9 - - + +
286G HIS* 3.7 14.3 - - - -
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Residues in contact with GLU 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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248G ALA 3.1 13.0 + - - +
249G SER* 2.9 16.3 + - - +
251G THR* 1.3 77.2 - - - +
253G LEU* 1.3 59.3 + - + +
255G ARG* 3.6 8.7 + - - +
256G ALA* 2.9 33.0 + - - +
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Residues in contact with LEU 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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150G GLN* 3.5 27.8 - - + +
153G HIS* 4.7 6.1 - - + -
154G ARG* 3.6 52.0 - - + +
157G LEU* 3.7 25.1 - - + +
245G HIS* 4.4 17.0 - - + -
249G SER* 2.7 24.9 + - - +
250G PHE* 2.9 8.5 + - + +
252G GLU* 1.3 73.8 - - + +
254G VAL* 1.3 63.1 + - - +
256G ALA* 3.4 7.7 + - - +
257G ALA* 3.1 20.4 + - - +
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Residues in contact with VAL 254 (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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157G LEU* 4.1 15.0 - - + +
170G LEU* 4.4 11.7 - - + -
172G ILE* 4.1 17.3 - - + -
250G PHE* 2.8 31.8 + - + +
251G THR* 3.4 15.7 - - - +
253G LEU* 1.3 71.8 - - - +
255G ARG* 1.3 68.4 + - - +
257G ALA* 3.1 15.1 + - + +
258G PHE* 3.2 21.6 - - + -
264G HIS* 4.1 18.2 - - + +
286G HIS* 4.7 1.1 - - - +
288G LEU* 3.8 26.0 - - + -
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Residues in contact with ARG 255 (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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251G THR* 3.0 37.0 + - - +
252G GLU* 3.6 8.6 + - - +
254G VAL* 1.3 77.2 - - - +
256G ALA* 1.3 65.0 + - - +
258G PHE* 3.0 15.6 + - - +
259G GLY 3.4 5.7 + - - -
260G GLY* 3.4 13.5 + - - -
262G CYS* 4.4 18.1 - - - -
264G HIS* 3.2 50.5 + - + +
288G LEU* 4.8 1.1 - - - -
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Residues in contact with ALA 256 (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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154G ARG* 5.7 9.9 - - + -
252G GLU 2.9 18.5 + - - +
253G LEU* 3.6 7.4 - - - +
254G VAL 3.3 0.2 - - - -
255G ARG* 1.3 78.2 - - - +
257G ALA* 1.3 54.5 + - - +
259G GLY* 2.8 25.8 + - - +
260G GLY 4.7 1.3 - - - +
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Residues in contact with ALA 257 (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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154G ARG* 5.1 2.7 - - - +
157G LEU* 3.4 40.4 - - + +
158G LYS* 3.9 18.9 - - - +
161G ALA* 3.9 13.9 - - + +
170G LEU* 6.5 0.2 - - + -
253G LEU 3.1 11.7 + - - +
254G VAL* 3.1 14.8 + - + +
256G ALA* 1.3 75.6 - - - +
258G PHE* 1.3 61.5 + - + +
261G ARG* 5.3 0.3 + - - -
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Residues in contact with PHE 258 (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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161G ALA* 3.7 24.0 - - + -
164G VAL* 4.4 4.9 - - + -
170G LEU* 3.9 34.8 - - + -
254G VAL* 3.2 22.9 - - + -
255G ARG 3.0 7.9 + - - +
257G ALA* 1.3 78.9 - - + +
259G GLY* 1.3 51.8 + - - +
260G GLY 3.6 0.8 + - - +
261G ARG* 2.4 46.7 + - - +
262G CYS* 3.8 23.3 - - + -
288G LEU* 3.7 29.2 - - + -
290G LYS* 3.8 51.7 + - + +
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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