Contacts of the helix formed by residues 263 - 276 (chain G) in PDB entry 7CR3
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 263 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 4.2 28.0 - - - +
115A ILE* 4.2 14.7 - - + +
116A LYS* 5.2 2.5 - - + +
251G TYR* 3.4 21.1 - - - -
261G PHE 4.5 0.5 - - - -
262G ASP* 1.3 89.3 + - + +
264G TYR* 1.3 62.5 + - - +
265G ALA* 3.3 16.7 + - - +
266G ASP* 3.4 18.9 + - - +
267G ALA* 3.5 13.0 + - - +
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Residues in contact with TYR 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 6.4 0.2 - - + -
111A VAL* 4.2 17.7 - - + -
114A THR* 4.1 17.0 + - + +
201A ARG* 4.2 29.2 - - - +
205A ILE* 5.0 4.6 - - + +
244G ILE* 3.5 32.7 + - + +
247G SER* 4.5 2.5 - - - -
248G PHE* 3.5 41.5 - + + +
251G TYR* 3.7 24.5 + + + -
263G THR* 1.3 74.6 - - - +
265G ALA* 1.3 59.5 + - - +
267G ALA* 3.5 3.4 + - + +
268G LEU* 3.0 58.5 + - + +
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Residues in contact with ALA 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 4.2 24.4 - - + +
114A THR* 4.5 2.0 - - - +
115A ILE* 4.0 26.2 - - + -
263G THR* 3.2 10.1 + - - +
264G TYR* 1.3 75.3 - - - +
266G ASP* 1.3 62.2 + - - +
268G LEU* 3.1 6.5 + - - +
269G TRP* 2.9 26.0 + - - +
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Residues in contact with ASP 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ARG* 3.3 24.3 + - - +
260G HIS 4.0 11.0 - - - +
261G PHE* 4.7 1.8 - - - -
262G ASP* 4.5 7.9 - - - +
263G THR* 3.4 26.9 + - - +
265G ALA* 1.3 77.3 - - - +
267G ALA* 1.3 58.2 + - - +
269G TRP* 3.2 9.5 + - - +
270G TRP* 2.9 26.5 + - - +
283G LYS* 3.6 28.7 - - + +
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Residues in contact with ALA 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G SER* 2.5 27.0 + - - +
251G TYR* 3.8 24.7 - - + -
261G PHE* 3.5 29.3 - - + -
263G THR 3.5 9.8 + - - +
264G TYR* 3.6 10.8 - - + +
265G ALA 3.2 0.4 - - - -
266G ASP* 1.3 79.0 - - - +
268G LEU* 1.3 55.2 + - - +
270G TRP* 3.2 4.2 + - - +
271G GLY 3.0 19.6 + - - -
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Residues in contact with LEU 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 5.7 3.8 - - + -
111A VAL* 4.0 23.3 - - + -
243G LEU* 4.2 20.6 - - + +
244G ILE* 4.8 9.9 - - + -
247G SER* 3.5 21.3 - - - +
264G TYR* 3.0 50.0 + - + +
265G ALA* 3.1 8.9 + - - +
267G ALA* 1.3 73.0 - - - +
269G TRP* 1.3 65.7 + - - +
271G GLY* 3.3 1.0 + - - -
272G LEU* 3.0 25.6 + - - +
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Residues in contact with TRP 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D TYR* 5.2 1.2 - - + +
285D PRO* 4.0 26.7 + - + -
291D ARG* 3.8 60.8 - - + +
294D ALA* 4.6 9.0 - - + -
295D ALA* 4.8 4.0 - - + -
265G ALA 2.9 13.0 + - - +
266G ASP* 3.4 11.4 - - - +
268G LEU* 1.3 75.4 - - - +
270G TRP* 1.3 64.3 + - - +
272G LEU* 3.4 25.7 + - + +
273G ILE* 3.0 58.2 + - + +
280G TYR* 3.8 16.7 - + - -
282G ASP* 3.7 23.0 + - - -
283G LYS* 4.3 11.7 - - + -
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Residues in contact with TRP 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TRP* 6.3 0.2 - + - -
280A TYR* 3.0 23.5 + + - -
246G ALA* 4.5 6.1 - - + -
247G SER* 4.2 12.1 - - - -
250G VAL* 3.7 34.1 - - + -
261G PHE* 3.5 33.2 - + + -
266G ASP 2.9 10.6 + - - +
267G ALA 3.2 12.1 + - - +
269G TRP* 1.3 78.8 - - - +
271G GLY* 1.3 86.0 + - - +
273G ILE* 3.1 5.8 + - + +
274G THR* 3.0 49.9 + - + +
275G LEU* 6.2 2.2 - - + -
283G LYS* 2.9 34.1 + - + -
285G PRO* 3.7 14.4 - - + +
294G ALA* 4.0 23.3 - - + -
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Residues in contact with GLY 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G LEU* 3.5 20.0 - - - -
247G SER* 4.4 3.1 - - - -
267G ALA 3.0 13.1 + - - -
268G LEU 3.3 0.8 + - - -
270G TRP* 1.3 92.8 - - - +
272G LEU* 1.3 62.1 + - - +
274G THR* 4.1 2.5 - - - -
275G LEU* 3.0 32.6 + - - +
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Residues in contact with LEU 272 (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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295D ALA* 3.6 40.6 - - + +
298D THR* 3.8 22.2 - - + -
299D LEU* 4.5 11.2 - - + -
243G LEU* 3.6 16.0 - - + +
268G LEU 3.0 17.1 + - - +
269G TRP* 3.9 22.2 - - + +
271G GLY* 1.3 76.2 - - - +
273G ILE* 1.3 56.1 + - + +
275G LEU* 5.1 1.8 - - - -
276G THR* 2.5 45.0 + - + +
305G PHE* 5.0 6.7 - - + -
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Residues in contact with ILE 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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280A TYR* 5.9 1.3 - - + -
298D THR* 6.5 0.4 - - + -
269G TRP* 3.0 67.3 + - + +
270G TRP* 3.1 5.4 + - + +
272G LEU* 1.3 81.5 - - + +
274G THR* 1.3 63.9 + - + +
276G THR* 3.3 3.1 + - - -
278G ILE* 3.1 42.0 + - + +
279G GLY* 3.3 5.9 + - - +
280G TYR* 3.6 47.3 - - + +
282G ASP* 5.3 3.6 - - - +
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Residues in contact with THR 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 4.2 18.4 - - - +
280A TYR* 3.1 35.0 - - + +
270G TRP* 3.0 39.7 + - + +
271G GLY* 3.4 9.4 + - - -
273G ILE* 1.3 78.8 - - + +
275G LEU* 1.3 72.2 + - - +
276G THR 3.1 2.5 - - - -
277G THR* 2.7 26.2 + - - +
279G GLY 4.9 2.9 - - - +
302G VAL* 3.9 9.3 - - - +
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Residues in contact with LEU 275 (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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239G GLY 4.6 0.2 - - - +
242G CYS* 4.5 3.4 - - - +
243G LEU* 3.7 31.0 - - + +
246G ALA* 5.5 7.6 - - + -
270G TRP* 6.2 2.5 - - + -
271G GLY* 3.0 17.9 + - - +
272G LEU* 4.8 1.8 - - - +
274G THR* 1.3 91.3 + - - +
276G THR* 1.3 59.8 + - - +
277G THR* 3.2 1.3 + - - +
297G PHE 4.4 8.7 - - - +
298G THR* 4.9 7.9 - - - +
301G GLY* 3.6 26.2 - - - -
302G VAL* 3.5 20.7 - - + +
305G PHE* 3.3 51.7 - - + +
306G ALA* 6.1 0.2 - - - +
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Residues in contact with THR 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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277D THR* 3.9 13.0 - - - +
298D THR* 4.5 7.6 + - - +
299D LEU* 4.3 8.5 - - + -
302D VAL* 4.7 15.7 - - + +
272G LEU* 2.5 38.6 + - + +
273G ILE 3.3 8.3 + - - -
274G THR 3.1 0.2 - - - -
275G LEU* 1.3 76.4 - - + +
277G THR* 1.3 73.4 + - - +
278G ILE* 3.2 19.8 + - - +
305G PHE* 4.1 25.6 - - + +
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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