Contacts of the strand formed by residues 236 - 243 (chain G) in PDB entry 5UWC
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 PHE 236 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G LEU* 3.7 26.0 - - + -
228G MET* 3.7 38.4 - - + -
230G SER* 4.1 6.5 - - - -
233G ASN* 3.2 42.0 - - + -
234G ARG* 3.5 17.6 + - - -
235G LYS* 1.3 79.0 - - - +
237G ARG* 1.3 59.9 + - - +
238G TYR* 3.4 27.9 - - + +
256G ASP* 3.4 19.8 + - - -
274G ALA* 4.3 3.8 - - + -
275G ARG 3.3 14.4 - - - +
276G GLU* 3.9 5.6 - - - -
277G ARG* 3.2 23.8 + - - +
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Residues in contact with ARG 237 (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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236G PHE* 1.3 70.5 - - - +
238G TYR* 1.3 68.0 + - - +
253G GLN* 5.7 9.4 + - - +
254G VAL 3.6 6.8 - - - +
255G ARG* 3.5 41.1 - - + +
274G ALA* 3.4 4.2 - - - +
275G ARG* 2.8 58.0 + - + +
277G ARG* 3.8 12.5 - - + +
201I CIT 2.6 58.2 + - - -
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Residues in contact with TYR 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 4.1 9.4 - - + -
226G TRP* 3.6 42.0 - + + -
228G MET* 3.1 30.6 - - + +
236G PHE* 3.4 32.3 - - + +
237G ARG* 1.3 78.8 - - - +
239G GLU* 1.3 65.4 + - - +
240G LEU* 4.2 4.0 - - + -
253G GLN* 3.7 6.3 - - - +
254G VAL* 2.8 40.1 + - + +
256G ASP* 4.9 1.3 - - - -
257G ARG 3.6 23.8 - - - -
258G THR* 4.2 10.3 - - + +
272G ILE* 4.1 6.7 - - + -
273G ARG 3.4 5.8 - - - +
274G ALA* 3.8 26.0 - - + -
275G ARG* 5.8 0.2 - - - -
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Residues in contact with GLU 239 (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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238G TYR* 1.3 72.6 - - - +
240G LEU* 1.3 61.5 + - - +
251G THR* 4.0 13.3 - - + +
252G GLU 3.4 3.4 - - - -
253G GLN* 3.2 35.0 + - - +
272G ILE* 3.3 7.1 - - - +
273G ARG* 3.0 60.6 + - + -
275G ARG* 2.8 39.4 + - + +
282G LEU* 4.7 1.3 - - - +
285G TRP* 3.4 18.8 - - + -
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Residues in contact with LEU 240 (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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213G MET* 5.2 0.4 - - - -
224G MET* 3.5 32.1 - - + -
226G TRP* 3.8 17.5 - - + -
238G TYR* 4.3 6.1 - - + -
239G GLU* 1.3 75.1 - - - +
241G GLN* 1.3 60.9 + - - +
242G ILE* 3.6 9.2 + - + +
250G ILE 3.3 2.9 - - - +
251G THR* 3.2 4.3 - - - -
252G GLU* 2.8 44.7 + - + +
254G VAL* 4.4 9.2 - - + -
260G PHE* 3.8 33.4 - - + -
270G VAL* 4.5 4.5 - - + -
271G GLN 3.5 4.3 - - - +
272G ILE* 3.6 29.8 - - + -
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Residues in contact with GLN 241 (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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240G LEU* 1.3 69.5 - - - +
242G ILE* 1.3 60.1 + - - +
243G GLN 4.2 0.2 + - - -
249G VAL* 4.2 25.8 - - + +
250G ILE 3.4 3.4 - - - +
251G THR* 3.4 22.2 + - - +
269G THR 3.8 0.7 - - - +
270G VAL* 3.3 6.2 - - - -
271G GLN* 2.9 53.5 + - + +
285G TRP* 3.7 37.3 + - + -
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Residues in contact with ILE 242 (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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224G MET* 4.5 3.6 - - + -
240G LEU* 4.1 25.1 - - + +
241G GLN* 1.3 77.4 - - - +
243G GLN* 1.3 63.2 + - - +
244G LYS* 4.0 13.5 + - + -
248G PRO 4.4 0.9 - - - +
249G VAL* 3.5 3.8 - - - +
250G ILE* 2.7 49.5 + - + +
252G GLU* 4.4 7.6 - - + +
260G PHE* 4.2 26.0 - - + -
262G LEU* 4.0 32.5 - - + -
268G TYR* 4.0 11.2 - - + -
269G THR 3.5 2.9 - - - -
270G VAL* 4.1 16.8 - - + -
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Residues in contact with GLN 243 (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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241G GLN 4.2 0.4 - - - -
242G ILE* 1.3 71.5 - - - +
244G LYS* 1.3 80.2 + - - +
246G MET 5.2 0.2 - - - +
247G GLN 2.6 30.7 + - - +
248G PRO* 4.1 1.8 - - - +
249G VAL* 3.2 29.5 + - + +
267G THR 4.4 0.2 - - - +
268G TYR* 3.3 5.1 - - - -
269G THR* 2.9 47.8 + - - +
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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