Contacts of the helix formed by residues 247 - 262 (chain G) in PDB entry 1RZR
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 THR 247 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221G TYR* 3.8 23.4 - - + +
245G VAL* 2.8 7.5 + - - +
246G GLY* 1.3 79.8 + - - +
248G ASP* 1.3 73.6 + - - +
249G GLU* 2.9 24.2 - - + +
250G MSE 2.9 30.8 - - + +
251G ALA* 3.1 22.0 + - - +
274G PHE 3.5 14.7 + - - -
275G ASP* 5.1 6.4 + - - +
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Residues in contact with ASP 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G THR* 1.3 78.5 - - - +
249G GLU* 1.3 54.6 + - - +
251G ALA* 3.4 5.6 - - - +
252G LEU* 2.7 38.5 + - + +
274G PHE 2.6 46.4 + - - +
275G ASP* 4.9 2.8 + - + +
276G ASN* 3.5 8.6 - - - +
277G THR* 4.2 18.4 - - + +
279G LEU* 5.0 4.9 - - + -
280G SER* 2.9 15.5 + - - +
287G LEU* 2.8 30.3 - - + +
289G SER* 2.9 13.2 + - - -
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Residues in contact with GLU 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ARG* 3.3 30.9 + - - +
282C MSE 3.2 31.2 - - - +
72G ASN* 6.0 0.2 + - - -
73G ILE* 6.2 0.9 - - + -
221G TYR 2.9 20.1 - - - +
222G THR* 4.2 1.9 - - - -
223G TYR* 3.6 28.2 + - + +
247G THR* 2.9 9.0 - - + +
248G ASP* 1.3 76.1 - - - +
250G MSE 1.3 68.2 + - - +
252G LEU* 2.7 19.5 + - - +
253G GLY* 3.0 9.4 + - - -
279G LEU* 4.2 18.3 - - + +
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Residues in contact with MSE 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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183G VAL* 4.1 12.1 - - + -
184G SER* 3.4 17.0 - - - +
185G GLY* 3.4 29.2 - - - +
219G GLY 4.5 0.9 - - - -
220G ASP 2.7 28.9 - - - +
221G TYR* 3.6 20.9 - - + -
222G THR 4.2 8.1 - - - -
225G SER* 3.6 12.6 - - - +
226G GLY* 3.6 2.8 - - - -
245G VAL* 3.5 11.2 - - + -
246G GLY* 4.0 16.8 - - - +
247G THR* 2.9 23.4 - - + +
249G GLU* 1.3 78.4 - - - +
251G ALA* 1.3 56.8 + - - +
253G GLY* 2.8 19.5 + - - +
254G VAL* 3.0 14.0 + - - +
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Residues in contact with ALA 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G VAL* 3.3 27.8 - - + +
247G THR 3.1 20.1 + - - +
248G ASP* 3.2 6.9 + - - +
249G GLU 3.1 0.8 - - - -
250G MSE 1.3 79.1 - - - +
252G LEU* 1.3 57.2 + - - +
254G VAL* 3.7 1.9 - - - +
255G ILE* 2.9 36.3 + - - +
271G ILE* 4.2 6.9 - - + +
273G GLY* 3.9 13.9 - - - +
287G LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MSE 4.1 20.0 - - + +
223G TYR* 3.5 15.8 - - + -
248G ASP 2.7 12.5 + - - +
249G GLU* 2.7 20.0 + - - +
251G ALA* 1.3 73.2 - - - +
253G GLY* 1.3 54.5 + - - -
255G ILE* 3.9 6.8 - - + +
256G HIS* 3.3 40.6 + - + +
279G LEU* 3.6 43.1 - - + -
280G SER* 4.9 0.7 - - - +
282G MSE 5.5 1.3 - - + +
283G VAL* 3.1 45.3 - - + -
287G LEU* 6.0 1.1 - - + -
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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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223G TYR* 3.1 36.9 - - - -
226G GLY 3.0 8.2 - - - +
227G ILE* 3.0 24.2 + - - +
249G GLU 3.0 4.9 + - - -
250G MSE 2.8 6.8 + - - -
252G LEU* 1.3 77.1 - - - +
254G VAL* 1.3 60.2 + - - +
256G HIS 4.9 0.2 - - - -
257G GLY 3.3 10.4 + - - -
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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
----------------------------------------------------------
183G VAL* 4.2 20.4 - - + -
226G GLY* 3.2 18.6 - - - +
230G VAL* 3.1 20.1 - - + +
243G ILE* 3.6 22.4 - - + -
245G VAL* 4.2 15.7 - - + -
250G MSE 3.0 14.4 + - - +
251G ALA* 3.2 10.3 + - - +
253G GLY* 1.3 77.9 - - - +
255G ILE* 1.3 64.6 + - - +
257G GLY 3.2 0.5 + - - -
258G ALA* 3.0 23.4 + - - +
271G ILE* 3.2 22.7 - - + -
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Residues in contact with ILE 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 ALA 2.9 21.9 + - - +
252G LEU* 3.9 5.4 - - - +
254G VAL* 1.3 79.1 - - - +
256G HIS* 1.3 66.5 + - - +
257G GLY 3.0 0.2 + - - -
258G ALA* 3.1 10.4 + - - +
259G GLN* 3.1 16.6 + - - +
265G VAL* 3.3 32.2 - - + +
271G ILE* 3.7 28.5 - - + -
283G VAL* 4.1 19.7 - - + -
285G PRO* 3.9 19.3 - - + +
287G LEU* 4.1 29.8 - - + -
330G SER* 4.7 3.1 - - - +
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Residues in contact with HIS 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MSE 3.3 34.5 - - - -
283C VAL* 3.6 12.9 + - - -
284C ARG 4.5 0.2 + - - -
223G TYR* 2.8 34.5 + - + +
227G ILE* 5.6 0.7 - - + -
252G LEU* 3.3 19.9 + - + +
253G GLY 4.8 0.4 - - - +
255G ILE* 1.3 78.3 - - - +
257G GLY* 1.3 57.3 - - - +
259G GLN* 3.0 22.7 + - - +
260G ASP* 2.8 44.7 + - - +
283G VAL* 4.1 18.0 - - + +
284G ARG* 3.7 25.6 + - + +
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Residues in contact with GLY 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G ILE* 3.7 21.8 - - - +
230G VAL* 4.4 8.7 - - - -
253G GLY 3.3 15.4 + - - -
254G VAL 3.2 6.7 + - - -
255G ILE 3.0 1.6 - - - -
256G HIS* 1.3 79.8 - - - +
258G ALA* 1.3 61.6 + - - +
260G ASP* 3.2 5.8 + - - +
261G ARG* 3.2 24.2 + - - +
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Residues in contact with ALA 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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230G VAL* 4.1 15.2 - - + +
234G LEU* 4.5 5.4 - - + -
254G VAL 3.0 11.7 + - - +
255G ILE* 3.7 7.6 - - - +
257G GLY* 1.3 73.8 - - - +
259G GLN* 1.3 59.1 + - - +
261G ARG* 3.0 9.9 + - - +
262G GLY 2.8 25.1 + - - -
263G LEU* 3.0 16.2 + - + +
265G VAL* 5.3 3.8 - - + -
269G LEU* 3.7 31.4 - - + -
271G ILE* 5.3 1.3 - - + -
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Residues in contact with GLN 259 (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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255G ILE* 3.1 7.4 + - - +
256G HIS* 3.0 21.0 + - - +
258G ALA* 1.3 77.0 - - - +
260G ASP* 1.3 62.4 + - - +
261G ARG 3.0 1.4 + - - -
262G GLY* 3.2 12.1 + - - -
263G LEU 3.2 12.3 - - - +
264G ASN* 3.8 17.3 + - - +
265G VAL* 3.3 34.1 - - + +
266G PRO* 5.7 0.4 - - - +
284G ARG* 2.7 66.3 + - - +
285G PRO* 4.1 3.6 - - - +
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Residues in contact with ASP 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G TYR* 5.1 2.1 + - - -
227G ILE* 4.9 9.1 - - + +
256G HIS* 2.8 33.7 + - - +
257G GLY* 3.2 7.5 + - - +
259G GLN* 1.3 73.0 - - - +
261G ARG* 1.3 60.3 + - - +
284G ARG* 4.4 15.6 + - - -
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Residues in contact with ARG 261 (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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231G GLU* 2.8 55.6 + - + +
234G LEU* 3.9 24.9 - - + +
257G GLY 3.2 13.5 + - - +
258G ALA* 3.0 12.3 + - - +
259G GLN 2.9 0.8 - - - -
260G ASP* 1.3 80.0 + - + +
262G GLY* 1.3 57.0 + - - +
263G LEU* 4.5 6.2 - - + +
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Residues in contact with GLY 262 (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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258G ALA 2.8 2.4 + - - -
259G GLN 3.2 7.9 + - - -
261G ARG* 1.3 80.8 - - - +
263G LEU* 1.3 70.9 + - - +
264G ASN* 4.2 2.3 + - - -
268G ASP* 4.3 1.9 - - - +
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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