Contacts of the strand formed by residues 267 - 276 (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 THR 267 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243G GLN 4.4 0.3 - - - +
244G LYS 4.3 0.5 - - - -
245G ARG* 3.2 61.3 + - + +
265G PRO 3.3 1.2 + - - +
266G GLY* 1.3 72.1 - - - -
268G TYR* 1.3 62.0 + - - +
290G ARG* 4.1 20.3 + - - +
291G PHE 3.3 10.2 + - - -
292G GLU* 4.2 18.8 - - + +
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Residues in contact with TYR 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G ALA* 3.7 1.9 - - - +
222G SER* 2.6 28.8 + - - -
224G MET* 3.5 18.8 - - - +
242G ILE* 4.0 2.5 - - + -
243G GLN 3.3 14.4 - - - +
244G LYS* 3.9 17.7 - - + -
262G LEU* 3.6 21.1 - - + -
265G PRO* 3.7 27.8 - - + +
266G GLY 4.4 0.2 - - - -
267G THR* 1.3 75.7 + - - +
269G THR* 1.3 62.4 + - - +
270G VAL* 3.1 36.8 - - + -
289G GLN 3.9 0.2 - - - +
290G ARG* 3.4 3.9 - - - +
291G PHE* 2.8 65.8 + + + -
293G CYS* 4.0 3.4 - - - -
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Residues in contact with THR 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G GLN 3.8 0.7 - - - +
242G ILE* 3.5 0.9 - - - -
243G GLN* 2.9 44.9 + - - +
268G TYR* 1.3 75.3 + - - +
270G VAL* 1.3 70.4 + - - +
288G PRO* 3.7 24.7 - - + -
289G GLN 3.4 20.4 - - - +
290G ARG* 3.9 25.2 + - + +
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Residues in contact with VAL 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G MET* 3.9 21.4 - - + +
224G MET* 3.4 27.4 - - + -
240G LEU* 4.5 4.9 - - + -
241G GLN 3.3 8.3 - - - +
242G ILE* 4.1 10.5 - - + -
268G TYR* 3.1 37.2 - - + -
269G THR* 1.3 78.4 - - - +
271G GLN* 1.3 80.2 + - - +
286G SER* 4.4 1.0 + - - -
287G THR 4.2 1.7 - - - +
288G PRO* 3.5 3.4 - - - +
289G GLN* 3.1 33.9 + - - +
291G PHE* 4.8 0.2 - - + -
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Residues in contact with GLN 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G LEU* 3.5 1.0 - - - -
241G GLN* 2.9 51.4 + - + +
270G VAL* 1.3 85.3 - - - +
272G ILE* 1.3 60.8 + - - +
285G TRP* 3.6 28.9 - - + +
286G SER* 3.0 30.0 - - - +
288G PRO* 3.8 30.2 - - + +
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Residues in contact with ILE 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G PRO* 4.2 2.3 - - - +
211G PRO* 3.7 40.8 - - + +
213G MET* 4.6 19.1 - - + -
226G TRP* 3.5 42.8 - - + +
238G TYR* 4.1 4.3 - - + -
239G GLU 3.3 12.3 - - - +
240G LEU* 3.6 18.8 - - + -
271G GLN* 1.3 75.5 - - - +
273G ARG* 1.3 68.9 + - - +
284G ALA 4.0 0.9 - - - +
285G TRP* 3.6 3.8 - - - -
286G SER* 2.8 41.1 + - - +
289G GLN* 5.8 0.4 - - - +
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Residues in contact with ARG 273 (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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211G PRO* 4.5 3.4 - - - -
238G TYR* 3.4 5.6 - - - +
239G GLU* 3.0 62.8 + - + +
272G ILE* 1.3 77.5 - - - +
274G ALA* 1.3 61.8 + - - +
275G ARG* 4.1 8.1 - - - +
282G LEU* 3.6 31.9 - - + +
283G SER* 3.3 26.1 + - - +
284G ALA 3.4 10.8 - - - +
285G TRP* 3.4 50.5 - - + +
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Residues in contact with ALA 274 (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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208G LEU* 4.5 2.7 - - + -
211G PRO* 4.2 3.9 - - + +
228G MET* 3.8 37.2 - - + -
236G PHE* 4.3 6.1 - - + -
237G ARG 3.4 4.7 - - - +
238G TYR* 3.8 14.4 - - + -
273G ARG* 1.3 73.9 - - - +
275G ARG* 1.3 60.4 + - - +
276G GLU 4.3 0.2 - - - -
282G LEU* 3.4 8.8 - - - +
283G SER* 2.9 37.7 + - - +
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Residues in contact with ARG 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G PHE* 3.3 6.3 - - - -
237G ARG* 2.8 60.1 + - + +
238G TYR* 5.8 0.2 - - - -
239G GLU* 2.8 30.6 + - + +
253G GLN* 5.7 1.0 + - - -
273G ARG* 4.1 8.3 - - - +
274G ALA* 1.3 74.8 - - - +
276G GLU* 1.3 71.1 + - - +
277G ARG* 3.5 0.6 + - - +
280G GLU* 3.4 46.9 + - - +
281G PHE 3.4 3.8 - - - -
282G LEU* 3.6 30.9 - - + +
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Residues in contact with GLU 276 (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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208G LEU* 3.9 7.2 - - + +
233G ASN* 3.7 17.7 - - + +
235G LYS* 3.5 19.3 + - - +
236G PHE* 3.9 4.3 - - + -
275G ARG* 1.3 71.6 - - - +
277G ARG* 1.3 62.2 + - - +
278G VAL* 3.2 15.5 + - - +
279G TYR* 2.8 28.8 + - - +
280G GLU* 2.9 30.7 + - - +
281G PHE* 3.0 52.2 + - + +
116I TRP* 3.1 30.7 + - - -
120I ASN* 5.0 1.0 - - - +
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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