Contacts of the helix formed by residues 227 - 236 (chain G) in PDB entry 6V01
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 ILE 227 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225G SER* 4.6 0.4 - - - +
226G ALA* 1.3 80.2 - - + +
228G ARG* 1.3 63.5 + - - +
229G GLY 3.3 0.4 - - - -
230G ILE* 3.3 26.6 + - + +
231G ARG* 4.1 15.3 + - - +
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Residues in contact with ARG 228 (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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225G SER* 3.6 35.1 + - - +
226G ALA 3.2 0.8 - - - -
227G ILE* 1.3 79.5 - - - +
229G GLY* 1.3 71.5 + - - +
231G ARG* 3.2 39.1 + - - +
232G PHE* 4.1 9.6 + - - +
278J TYR* 3.8 19.9 + - - +
282J LEU* 4.3 23.9 - - + +
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Residues in contact with GLY 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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212G VAL* 4.6 11.0 - - - -
225G SER 3.8 5.5 + - - -
226G ALA 3.7 7.3 + - - -
227G ILE 3.3 0.8 - - - -
228G ARG* 1.3 91.9 - - - +
230G ILE* 1.3 65.7 + - - +
231G ARG 3.2 0.6 + - - -
232G PHE* 3.6 4.5 + - - +
233G LEU* 3.5 28.5 + - - +
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Residues in contact with ILE 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G SER* 4.4 5.6 - - - +
160G GLU* 4.3 21.0 - - + +
209G SER* 4.6 10.3 - - - +
212G VAL* 3.8 24.2 - - + -
213G LEU* 3.7 33.2 - - + -
226G ALA 4.3 4.9 - - - +
227G ILE* 3.4 22.9 - - + +
228G ARG 3.1 0.8 - - - -
229G GLY* 1.3 76.8 - - - +
231G ARG* 1.3 59.3 + - - +
233G LEU* 3.6 4.0 - - + +
234G GLN* 2.9 53.0 + - - +
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Residues in contact with ARG 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G LEU* 4.4 2.8 - - + +
140G SER* 3.5 27.0 + - - +
141G VAL* 4.7 14.0 - - + +
143G SER* 2.8 27.0 + - - -
144G THR* 4.1 22.3 - - - +
227G ILE* 4.1 11.7 + - - +
228G ARG* 3.2 41.0 + - - +
229G GLY 3.2 0.8 - - - -
230G ILE* 1.3 78.1 - - - +
232G PHE* 1.3 56.7 + - - +
234G GLN* 3.3 5.0 + - - +
235G ILE* 2.9 37.0 + - + +
278J TYR* 3.9 24.9 - - + +
281J TYR* 5.8 6.5 - - - -
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Residues in contact with PHE 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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228G ARG* 4.1 10.5 + - - +
229G GLY* 3.6 7.7 + - - +
230G ILE 3.4 0.2 - - - -
231G ARG* 1.3 78.4 - - - +
233G LEU* 1.3 67.9 + - + +
234G GLN 3.1 0.2 - - - -
235G ILE* 3.2 6.3 + - + -
236G LEU* 3.0 56.8 + - + +
275J PHE* 3.7 20.0 - + - -
278J TYR* 4.2 25.3 + + + +
279J PHE* 3.9 27.1 - + - -
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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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160G GLU* 5.0 2.2 - - - +
204G ILE* 4.9 11.7 - - + +
205G VAL* 4.5 13.4 - - - +
208G ALA* 3.7 44.9 - - + +
209G SER* 3.7 19.3 - - - +
212G VAL* 4.3 12.1 - - + -
229G GLY 3.5 18.7 + - - +
230G ILE* 3.6 5.2 - - + +
232G PHE* 1.3 85.8 - - + +
234G GLN* 1.3 55.2 + - - +
236G LEU* 4.2 15.7 - - + -
237G ARG* 3.3 24.8 + - - +
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Residues in contact with GLN 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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133G VAL* 4.2 8.3 - - - +
136G CYS* 2.5 43.0 + - - +
137G LEU* 3.5 19.2 - - + +
140G SER* 2.9 22.9 + - - -
156G LEU* 5.5 3.8 - - - +
160G GLU* 2.8 27.8 + - - +
230G ILE* 2.9 27.5 + - + +
231G ARG* 3.8 4.3 - - - +
232G PHE 3.1 0.2 - - - -
233G LEU* 1.3 78.6 - - - +
235G ILE* 1.3 61.4 + - - +
236G LEU 3.4 0.9 - - - -
237G ARG* 3.3 34.1 + - - +
238G MET* 4.7 0.9 + - - +
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Residues in contact with ILE 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G LEU* 3.7 25.8 - - + -
141G VAL* 6.2 3.6 - - + -
231G ARG* 2.9 24.5 + - + +
232G PHE* 3.6 6.7 - - + +
234G GLN* 1.3 76.6 - - - +
236G LEU* 1.3 62.5 + - - +
237G ARG 3.1 1.8 + - - -
238G MET* 3.1 22.6 + - + +
239G LEU 4.6 0.3 + - - -
271J LEU* 6.3 0.2 - - + -
274J ILE* 4.3 24.9 - - + +
275J PHE* 4.1 33.2 - - + -
278J TYR* 4.1 39.3 - - + -
299J TYR* 4.9 6.5 - - + +
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Residues in contact with LEU 236 (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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201G ILE* 4.5 22.2 - - + +
204G ILE* 6.3 1.8 - - + -
205G VAL* 3.7 24.1 - - + +
232G PHE* 3.0 60.3 + - + +
233G LEU* 4.4 12.3 - - + -
234G GLN 3.4 0.4 - - - -
235G ILE* 1.3 77.2 - - - +
237G ARG* 1.3 59.5 + - - +
238G MET 3.2 2.2 + - - -
239G LEU* 3.4 24.1 + - + +
240G HIS* 4.1 4.0 + - - +
275J PHE* 3.9 20.6 - - + -
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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