Contacts of the helix formed by residues 231 - 241 (chain C) in PDB entry 6GYS
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 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558B LEU* 4.9 9.4 - - + -
561B GLY* 4.0 22.0 - - - +
562B LEU* 4.4 17.3 - - + -
230C ASP* 1.3 84.7 + - - +
232C ARG* 1.3 61.4 + - - +
233C LEU 3.1 0.4 - - - -
234C VAL* 3.0 31.5 + - + +
235C GLN* 2.9 31.1 + - - +
263C THR* 4.2 1.1 - - + +
264C PHE* 4.5 27.8 - - + +
267C PHE* 5.0 13.6 - - + -
289C LEU* 4.8 11.2 - - + -
292C ILE* 4.5 20.2 - - + -
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Residues in contact with ARG 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.5 14.1 - - - +
560B LYS* 4.0 1.8 + - - +
561B GLY* 3.2 38.4 - - - +
155C ASP* 2.7 31.1 + - - -
158C TYR* 3.2 62.9 - - + +
159C TRP* 4.0 17.4 - - + +
161C ALA* 6.5 0.2 - - + -
162C LEU* 4.7 14.7 - - + +
220C LEU* 6.0 1.6 - - + -
230C ASP* 2.6 34.0 + - + +
231C ILE* 1.3 75.9 - - - +
233C LEU* 1.3 55.3 + - - +
235C GLN* 3.4 12.6 + - - +
236C ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TYR* 5.9 1.7 - - + -
220C LEU* 3.8 34.4 - - + +
225C PHE* 3.7 31.0 - - + -
229C PRO* 5.9 1.8 - - + -
230C ASP 3.0 16.7 + - - +
232C ARG* 1.3 77.9 - - - +
234C VAL* 1.3 57.8 + - + +
236C ALA* 3.3 5.9 + - + +
237C TYR* 2.9 29.1 + - + +
256C LEU* 3.8 19.3 - - + -
259C GLN* 3.9 26.0 - - + +
260C CYS* 4.0 10.1 - - - -
263C THR* 4.0 16.2 - - - +
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Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ILE* 3.0 30.3 + - + +
233C LEU* 1.3 76.0 - - + +
235C GLN* 1.3 58.4 + - - +
237C TYR* 3.2 1.6 + - - +
238C LEU* 2.9 37.4 + - + +
260C CYS* 3.6 39.7 - - + +
263C THR* 4.4 10.8 - - - -
264C PHE* 4.7 1.6 - - + +
292C ILE* 3.7 25.8 - - + -
296C LEU* 4.2 22.4 - - + -
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Residues in contact with GLN 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B GLY 4.4 8.3 - - - +
562B LEU* 3.4 29.8 - - - +
129C SER* 3.4 35.6 + - - +
130C ILE* 4.3 13.6 - - - +
159C TRP* 6.0 0.3 - - - -
162C LEU* 4.4 15.5 - - + +
231C ILE* 2.9 21.3 + - + +
232C ARG* 3.8 12.3 - - - +
234C VAL* 1.3 76.8 - - - +
236C ALA* 1.3 56.9 + - - +
238C LEU* 3.4 7.2 + - + +
239C ILE* 2.9 34.1 + - - +
288C THR* 4.6 1.0 - - - +
292C ILE* 3.5 22.5 - - + +
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Residues in contact with ALA 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ALA* 4.7 7.4 - - + +
162C LEU* 4.3 8.8 - - + +
165C SER* 4.0 23.3 - - - +
216C SER* 6.0 0.2 - - - +
220C LEU* 4.8 15.0 - - + -
232C ARG 2.9 18.7 + - - +
233C LEU* 3.6 6.5 - - - +
235C GLN* 1.3 75.4 - - - +
237C TYR* 1.3 58.5 + - - +
239C ILE* 3.3 4.1 + - - +
240C LEU* 2.9 37.5 + - + +
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Residues in contact with TYR 237 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C LEU* 2.9 19.3 + - + +
234C VAL 3.2 2.2 + - - +
236C ALA* 1.3 77.1 - - - +
238C LEU* 1.3 62.0 + - + +
240C LEU* 3.3 9.1 + - + +
241C ALA* 2.9 37.8 + - + +
245C PHE* 4.8 11.2 - + - -
253C ALA* 2.8 34.5 + - + -
256C LEU* 3.8 26.7 - - + -
257C LEU* 3.5 25.1 - - + +
260C CYS* 3.6 20.4 - - - -
296C LEU* 4.5 9.2 - - + -
299C CYS* 4.7 6.5 - - + -
303C GLN* 2.6 36.5 + - - -
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLY 4.9 7.6 - - - +
129C SER* 5.5 5.2 - - - -
234C VAL* 2.9 25.9 + - + +
235C GLN* 3.8 5.6 - - - +
237C TYR* 1.3 76.3 - - + +
239C ILE* 1.3 67.7 + - - +
241C ALA* 3.8 5.3 + - - +
242C THR* 3.5 16.5 + - - +
292C ILE* 3.5 43.1 - - + +
295C ARG* 3.5 39.0 - - + +
296C LEU* 3.7 15.3 - - + +
299C CYS* 3.7 17.0 - - - -
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU* 4.8 6.5 - - + +
126C TYR* 4.9 6.1 - - + -
129C SER* 3.7 28.5 - - - +
130C ILE* 6.4 0.2 - - + -
162C LEU* 4.9 3.1 - - + -
165C SER* 3.4 34.1 - - - +
166C VAL* 4.1 15.0 - - + +
169C MET* 3.8 37.6 - - + +
235C GLN 2.9 20.5 + - - +
236C ALA* 3.4 10.8 - - - +
237C TYR 3.2 0.2 - - - -
238C LEU* 1.3 77.8 - - - +
240C LEU* 1.3 61.3 + - - +
241C ALA 3.2 0.5 + - - -
242C THR* 2.8 29.1 + - + +
243C THR* 4.8 0.2 - - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C SER* 3.7 36.1 - - - +
168C THR* 3.8 25.6 - - + +
169C MET 5.0 0.7 - - - +
213C ALA* 5.0 12.1 - - + +
216C SER* 5.6 3.4 - - - -
217C LEU* 4.4 29.6 - - + -
220C LEU* 6.3 0.2 - - + -
236C ALA* 2.9 24.2 + - + +
237C TYR* 3.3 9.2 + - + +
239C ILE* 1.3 75.7 - - + +
241C ALA* 1.3 58.5 + - - +
242C THR 3.2 0.2 + - - -
243C THR* 2.7 33.4 + - + +
245C PHE* 3.8 23.8 - - + +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C TYR* 2.9 29.9 + - + +
238C LEU 4.2 5.2 - - - +
239C ILE 3.2 1.0 - - - -
240C LEU* 1.3 75.1 - - - +
242C THR* 1.3 62.4 + - - +
243C THR 3.2 9.0 + - - +
245C PHE* 5.7 1.1 - - - -
246C PRO* 4.4 19.8 - - + +
299C CYS* 3.8 30.0 - - + -
303C GLN* 5.1 1.3 - - - +
456C HIS* 5.2 1.0 + - - -
457C PRO* 5.4 0.9 - - - +
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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