Contacts of the helix formed by residues 222 - 235 (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 222 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220G ASP* 2.8 39.2 + - + +
221G TYR* 1.3 81.9 - - - +
223G TYR* 1.3 66.0 + - - +
224G ASP* 3.6 10.7 + - - +
225G SER* 2.6 35.0 + - - -
226G GLY* 3.2 2.6 + - - -
228G GLU* 5.4 0.2 + - - -
249G GLU* 4.2 4.7 - - - -
250G MSE 4.0 4.6 - - - +
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Residues in contact with TYR 223 (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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281C THR* 3.7 37.1 + - - +
282C MSE 3.6 32.3 - - + -
283C VAL 5.3 0.2 + - - -
286C GLN* 4.6 6.0 + - - -
222G THR* 1.3 71.8 - - - +
224G ASP* 1.3 71.8 + - - +
226G GLY 3.1 9.0 + - - -
227G ILE* 3.2 27.3 + - + +
249G GLU* 3.6 27.5 - - + +
252G LEU* 3.5 24.9 - - + -
253G GLY* 3.1 35.5 - - - -
256G HIS* 2.8 34.7 + + - +
260G ASP* 5.1 1.6 + - - -
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Residues in contact with ASP 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G THR* 3.1 10.0 + - - +
223G TYR* 1.3 81.7 - - - +
225G SER* 1.3 51.0 + - - +
226G GLY 2.8 5.6 - - - -
227G ILE* 2.5 41.6 + - + +
228G GLU* 2.7 33.4 + - + +
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Residues in contact with SER 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G GLY* 4.0 8.0 - - - -
220G ASP* 2.5 52.2 + - - -
222G THR* 2.6 23.1 + - - -
224G ASP* 1.3 77.2 - - - +
226G GLY* 1.3 52.4 + - - +
228G GLU* 3.5 15.2 + - - +
229G ALA* 2.7 36.8 + - - +
250G MSE 3.6 8.2 - - - -
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Residues in contact with GLY 226 (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* 5.2 1.1 - - - -
222G THR 3.2 1.7 + - - -
223G TYR 3.1 9.0 + - - -
224G ASP 2.8 1.4 - - - -
225G SER* 1.3 84.8 + - - +
227G ILE* 1.3 53.5 + - - +
229G ALA* 4.6 1.1 - - - -
230G VAL* 2.6 38.5 + - - +
250G MSE 3.6 23.8 - - - -
253G GLY 3.0 7.1 - - - +
254G VAL* 3.2 9.8 - - - +
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Residues in contact with ILE 227 (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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286C GLN* 6.2 0.2 - - - +
223G TYR* 3.4 42.2 - - + +
224G ASP* 2.5 27.7 + - + +
226G GLY* 1.3 74.8 - - - +
228G GLU* 1.3 59.0 + - + +
230G VAL* 3.7 3.0 + - - +
231G GLU* 3.2 35.3 + - - +
253G GLY* 3.0 16.4 - - - +
257G GLY* 3.7 21.6 - - - +
260G ASP* 4.9 9.2 - - + +
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Residues in contact with GLU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G ASP* 2.7 34.1 + - + +
225G SER* 3.6 11.4 + - - +
227G ILE* 1.3 78.1 - - + +
229G ALA* 1.3 63.7 + - - +
230G VAL 3.2 0.4 - - - -
231G GLU* 3.2 19.4 - - - +
232G LYS* 3.1 26.1 + - - +
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Residues in contact with ALA 229 (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* 3.2 37.5 - - + -
217G VAL* 3.9 21.3 - - + -
219G GLY* 5.4 4.5 - - - +
225G SER 2.7 20.6 + - - +
226G GLY 4.2 3.4 - - - +
227G ILE 3.5 0.2 - - - -
228G GLU* 1.3 73.7 - - - +
230G VAL* 1.3 58.0 + - - +
232G LYS* 4.1 1.5 - - - +
233G LEU* 2.7 35.1 + - - +
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Residues in contact with VAL 230 (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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226G GLY 2.6 30.3 - - - +
227G ILE* 4.0 4.9 - - - +
229G ALA* 1.3 74.5 - - - +
231G GLU* 1.3 56.3 + - - +
232G LYS 3.1 1.6 - - - -
233G LEU* 3.0 6.7 + - + -
234G LEU* 2.7 59.4 + - + +
243G ILE* 4.3 10.5 - - + -
253G GLY 3.9 2.2 - - - +
254G VAL* 3.1 48.0 - - + +
257G GLY* 4.4 2.5 - - - -
258G ALA* 4.1 14.6 - - + +
269G LEU* 4.7 1.8 - - + -
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Residues in contact with GLU 231 (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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227G ILE* 3.2 29.0 + - - +
228G GLU* 3.2 27.6 - - - +
230G VAL* 1.3 79.4 - - - +
232G LYS* 1.3 63.7 + - - +
234G LEU* 3.4 7.2 + - - +
235G GLU* 3.1 20.4 + - - +
261G ARG* 2.8 49.9 + - + +
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Residues in contact with LYS 232 (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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217G VAL* 4.4 19.5 - - + -
228G GLU 3.1 18.0 + - - +
229G ALA* 4.2 6.1 - - - +
230G VAL 3.1 0.6 - - - -
231G GLU* 1.3 78.2 - - - +
233G LEU* 1.3 59.7 + - + +
235G GLU* 2.8 43.2 + - - +
236G GLU* 3.7 0.3 + - - -
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Residues in contact with LEU 233 (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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181G ALA* 4.1 14.6 - - + -
183G VAL* 3.6 13.7 - - + -
214G SER 4.5 3.1 - - - +
215G TYR* 3.9 23.9 - - + +
217G VAL* 3.0 37.2 - - + -
229G ALA 2.7 26.0 + - - +
230G VAL* 3.0 5.7 + - + +
232G LYS* 1.3 76.2 - - + +
234G LEU* 1.3 60.6 + - + +
235G GLU 3.1 0.4 - - - -
236G GLU* 3.6 12.6 + - - +
239G LYS* 4.1 1.7 - - - +
240G PRO* 3.8 26.9 - - + +
243G ILE* 4.1 21.1 - - + -
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Residues in contact with LEU 234 (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* 2.7 43.6 + - + +
231G GLU* 3.9 5.2 - - - +
232G LYS 3.1 0.4 - - - -
233G LEU* 1.3 75.1 - - + +
235G GLU* 1.3 57.1 + - - +
236G GLU 3.0 11.6 + - - +
239G LYS* 3.6 36.1 + - + +
240G PRO* 5.4 3.6 - - + +
243G ILE* 6.2 0.7 - - + -
258G ALA* 4.5 7.0 - - + -
261G ARG* 3.9 37.2 - - + +
263G LEU* 4.2 27.4 - - + -
269G LEU* 4.8 10.3 - - + -
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Residues in contact with GLU 235 (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 3.1 11.5 + - - +
232G LYS* 2.8 30.5 + - - +
234G LEU* 1.3 76.9 - - - +
236G GLU* 1.3 57.2 + - - +
237G ASP* 5.7 0.2 - - - +
261G ARG* 6.0 0.2 - - - +
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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