Contacts of the helix formed by residues 230 - 241 (chain J) 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 ASP 230 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85I LEU* 3.4 8.2 - - + +
557I SER 2.9 22.3 - - - +
558I LEU* 3.6 6.8 - - - -
561I GLY* 3.1 18.2 + - - -
158J TYR* 3.6 25.0 - - + -
225J PHE* 5.8 0.2 - - - +
229J PRO* 1.3 74.9 - - - +
231J ILE* 1.3 79.5 + - - +
232J ARG* 2.7 37.6 + - + +
233J LEU* 3.2 21.7 + - - +
234J VAL 4.2 0.3 + - - -
263J THR* 3.4 8.1 - - - +
267J PHE* 3.7 11.3 - - - -
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Residues in contact with ILE 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558I LEU* 3.8 22.4 - - + -
561I GLY* 3.4 35.0 - - - +
562I LEU* 4.1 9.0 - - + -
230J ASP* 1.3 78.8 + - - +
232J ARG* 1.3 60.1 + - - +
233J LEU 3.2 1.1 - - - -
234J VAL* 3.3 9.9 + - + +
235J GLN* 2.9 32.8 + - + +
264J PHE* 3.6 32.1 - - + -
267J PHE* 4.1 5.8 - - + -
289J LEU* 3.8 16.6 - - + -
292J ILE* 3.7 28.3 - - + -
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Residues in contact with ARG 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I LEU* 3.8 1.4 - - - +
560I LYS 3.7 4.5 - - - -
561I GLY* 3.2 25.1 - - - -
155J ASP* 2.4 31.9 + - - +
158J TYR* 3.2 55.5 - - + +
159J TRP* 2.8 51.6 - - + +
162J LEU* 3.5 26.7 + - + +
220J LEU* 6.1 0.4 - - - -
230J ASP* 2.7 31.0 + - + -
231J ILE* 1.3 77.5 - - - +
233J LEU* 1.3 59.2 + - - +
235J GLN* 4.3 1.6 - - - -
236J ALA* 2.9 33.1 + - - +
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Residues in contact with LEU 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J TYR* 5.9 1.6 - - - -
220J LEU* 4.3 20.9 - - + -
225J PHE* 3.6 49.8 - - + -
229J PRO* 4.5 2.0 - - + -
230J ASP* 3.2 17.0 + - - +
231J ILE 3.2 0.2 - - - -
232J ARG* 1.3 77.5 - - - +
234J VAL* 1.3 58.6 + - - +
236J ALA* 3.3 5.0 + - + +
237J TYR* 2.9 28.9 + - + +
256J LEU* 4.2 14.8 - - + -
259J GLN* 4.1 16.6 - - + +
260J CYS* 4.6 5.6 - - - +
263J THR* 3.3 28.0 - - + +
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Residues in contact with VAL 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J ASP 4.6 0.7 - - - +
231J ILE* 3.3 13.4 + - + +
233J LEU* 1.3 76.5 - - + +
235J GLN* 1.3 58.4 + - - +
238J LEU* 2.9 47.2 + - + +
260J CYS* 3.7 49.1 - - + +
263J THR* 4.4 18.6 - - + -
264J PHE* 4.5 7.2 - - + -
292J ILE* 3.7 26.5 - - + -
296J LEU* 4.5 11.4 - - + -
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Residues in contact with GLN 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561I GLY 4.3 8.3 - - - +
562I LEU* 3.6 18.4 - - - +
129J SER* 2.9 48.6 + - - +
130J ILE* 3.4 18.3 + - + +
159J TRP* 5.6 0.7 - - - -
162J LEU* 3.6 25.1 - - + +
231J ILE* 2.9 25.3 + - - +
232J ARG* 4.7 1.0 - - - -
234J VAL* 1.3 75.5 - - - +
236J ALA* 1.3 58.9 + - - +
238J LEU* 4.9 1.1 - - - -
239J ILE* 3.2 17.5 + - - +
291J ARG* 3.6 11.9 - - - +
292J ILE* 3.4 24.2 - - + +
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Residues in contact with ALA 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J ALA* 3.8 17.0 - - + +
162J LEU* 3.5 7.6 - - + +
165J SER* 3.5 24.8 - - - +
216J SER* 5.3 0.7 - - - +
220J LEU* 5.8 7.9 - - + -
232J ARG 2.9 19.7 + - - +
233J LEU* 3.8 4.3 - - + +
235J GLN* 1.3 77.1 - - - +
237J TYR* 1.3 58.9 + - - +
238J LEU 3.3 0.4 - - - -
239J ILE 3.2 1.2 + - - -
240J LEU* 2.9 35.1 + - + +
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Residues in contact with TYR 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J LEU* 2.9 20.1 + - + +
234J VAL 3.3 0.8 + - - +
236J ALA* 1.3 78.3 - - - +
238J LEU* 1.3 64.3 + - + +
240J LEU* 3.2 16.5 + - + +
241J ALA* 2.9 37.5 + - + +
245J PHE* 5.6 7.2 - + - -
246J PRO* 5.6 0.7 - - + -
253J ALA* 2.7 34.1 + - + +
256J LEU* 3.6 30.1 - - + -
257J LEU* 3.5 28.3 - - + +
260J CYS* 3.6 28.0 - - - -
299J CYS* 4.4 9.0 - - + -
303J GLN* 2.9 25.4 + - - -
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Residues in contact with LEU 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLY 5.0 0.9 - - - +
129J SER* 4.2 15.7 - - - +
234J VAL* 2.9 30.0 + - + +
237J TYR* 1.3 82.4 - - + +
239J ILE* 1.3 61.7 + - - +
241J ALA* 4.1 4.6 - - - +
242J THR* 3.3 20.4 + - - +
292J ILE* 3.4 42.6 - - + +
295J ARG* 3.4 46.9 + - + +
296J LEU* 3.8 8.5 - - + +
299J CYS* 3.6 17.9 - - + -
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Residues in contact with ILE 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J LEU* 4.4 14.8 - - + +
126J TYR* 4.7 6.1 - - + -
129J SER* 3.9 21.8 - - - +
130J ILE* 5.3 3.6 - - + -
162J LEU* 5.9 0.2 - - + -
165J SER* 3.4 31.9 - - - +
166J VAL* 3.7 20.2 - - + -
169J MET* 3.7 35.9 - - + +
235J GLN 3.2 17.7 + - - +
236J ALA 3.2 8.2 + - - +
237J TYR 3.1 0.4 - - - -
238J LEU* 1.3 77.8 - - - +
240J LEU* 1.3 60.9 + - - +
241J ALA 3.2 1.8 - - - -
242J THR* 2.7 29.7 + - + -
243J THR* 5.3 0.3 - - - +
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Residues in contact with LEU 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J SER* 3.7 26.0 - - - +
168J THR* 3.7 32.8 - - + +
169J MET* 5.7 0.7 - - - -
213J ALA* 4.4 11.7 - - + +
216J SER* 5.0 7.0 - - - +
217J LEU* 4.7 23.3 - - + -
220J LEU* 5.6 3.8 - - + -
236J ALA* 2.9 25.0 + - + +
237J TYR* 3.8 15.0 - - + +
239J ILE* 1.3 75.7 - - - +
241J ALA* 1.3 56.8 + - - +
242J THR 3.2 0.7 - - - -
243J THR* 3.3 22.7 + - - +
245J PHE* 3.7 30.4 - - + +
256J LEU* 6.4 0.7 - - + -
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Residues in contact with ALA 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J TYR* 2.9 28.2 + - + +
238J LEU* 4.5 3.1 - - - +
239J ILE 3.2 0.6 - - - -
240J LEU* 1.3 74.2 - - - +
242J THR* 1.3 62.9 + - - +
243J THR 3.2 9.8 - - - +
245J PHE* 5.6 0.2 - - - -
246J PRO* 3.7 25.6 - - + +
299J CYS* 3.7 29.7 - - - -
456J HIS* 6.0 0.5 - - - -
457J PRO* 5.3 1.4 - - - +
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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