Contacts of the helix formed by residues 288 - 305 (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 TRP 288 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.9 32.8 - + + -
115B ILE* 6.4 0.2 - - + -
118B TYR* 3.6 40.6 + + + +
287G THR* 1.3 79.6 - - + +
289G ASN* 1.3 103.1 + - - +
290G GLY 3.4 0.4 - - - -
291G ARG* 4.5 1.7 - - - +
292G LEU* 3.1 36.0 + - + +
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Residues in contact with ASN 289 (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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253G ALA* 3.6 29.9 + - + +
287G THR* 4.2 2.1 - - - +
288G TRP* 1.3 125.4 - - - +
290G GLY* 1.3 57.1 + - - +
292G LEU* 3.4 5.5 + - - +
293G LEU* 3.0 36.2 + - + +
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Residues in contact with GLY 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G VAL* 4.3 13.4 - - - +
253G ALA* 4.1 11.9 - - - +
254G GLU* 5.1 2.2 - - - -
285G PRO* 4.0 11.6 - - - +
287G THR* 3.3 16.9 + - - -
289G ASN* 1.3 80.7 - - - +
291G ARG* 1.3 56.8 + - - +
293G LEU* 3.3 4.4 + - - +
294G ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 291 (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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266A ASP* 3.3 24.7 + - - +
269A TRP* 3.8 51.3 - - + +
282A ASP* 4.6 3.2 + - - -
283A LYS* 4.7 5.7 - - - +
284G TYR* 4.5 12.1 - - - -
285G PRO* 2.7 44.3 + - + +
286G GLN* 4.1 12.8 - - - +
287G THR 3.2 23.4 + - - +
288G TRP* 3.9 2.6 + - - +
289G ASN 3.4 0.4 - - - -
290G GLY* 1.3 74.8 - - - +
292G LEU* 1.3 58.1 + - - +
294G ALA* 3.8 1.4 - - - +
295G ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 5.2 11.9 - - + -
112B PHE* 5.0 20.2 - - + -
288G TRP* 3.1 33.8 + - + +
289G ASN* 3.8 4.9 - - - +
291G ARG* 1.3 77.0 - - - +
293G LEU* 1.3 67.6 + - + +
295G ALA* 3.3 12.9 + - + +
296G THR* 3.2 30.1 + - + +
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Residues in contact with LEU 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G LEU* 3.7 43.7 - - + +
250G VAL* 4.4 9.2 - - + +
253G ALA* 4.2 11.0 - - + -
289G ASN* 3.0 23.2 + - + +
290G GLY 3.8 3.1 - - - +
292G LEU* 1.3 82.0 - - + +
294G ALA* 1.3 61.1 + - - +
296G THR* 2.7 25.6 + - + +
297G PHE* 3.0 30.0 + - + -
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Residues in contact with ALA 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TRP* 4.6 8.5 - - + -
246G ALA* 6.4 0.4 - - - -
250G VAL* 4.6 3.7 - - + +
270G TRP* 4.0 33.2 - - + -
285G PRO* 4.5 10.1 - - + -
290G GLY 2.9 17.9 + - - +
291G ARG* 4.0 3.4 - - - +
293G LEU* 1.3 75.8 - - - +
295G ALA* 1.3 58.7 + - - +
297G PHE* 4.5 4.3 - - - +
298G THR* 2.9 36.9 + - - +
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Residues in contact with ALA 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TRP* 4.8 2.9 - - + -
272A LEU* 3.6 30.9 - - + +
291G ARG 2.9 20.5 + - - +
292G LEU* 3.6 11.7 - - + +
293G LEU 3.2 0.4 - - - -
294G ALA* 1.3 75.4 - - - +
296G THR* 1.3 60.7 + - + +
298G THR* 3.5 11.1 - - - +
299G LEU* 4.5 10.6 - - - +
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Residues in contact with THR 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LEU* 3.2 24.5 - - + +
293G LEU* 2.7 21.6 + - + +
295G ALA* 1.3 81.4 - - + +
297G PHE* 1.3 77.1 + - - +
298G THR 3.3 0.9 + - - -
299G LEU* 3.9 12.9 + - - +
300G ILE* 4.1 12.0 - - - +
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Residues in contact with PHE 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G CYS* 4.3 17.3 - - - -
245G LEU* 3.8 24.5 - - + -
246G ALA* 3.7 31.9 - - + -
249G LEU* 3.8 29.8 - - + -
250G VAL* 6.4 0.4 - - + -
275G LEU* 4.4 4.6 - - - +
293G LEU* 3.0 39.3 + - + +
294G ALA* 3.8 3.1 - - - +
296G THR* 1.3 90.8 + - - +
298G THR* 1.3 58.7 + - - +
299G LEU 3.4 0.4 - - - -
300G ILE* 3.5 8.2 + - + +
301G GLY* 2.9 25.8 + - - -
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Residues in contact with THR 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 3.8 26.9 - - + -
273A ILE* 6.5 0.4 - - - -
276A THR* 4.5 4.9 - - - +
278A ILE* 3.7 25.0 - - - +
275G LEU* 4.9 6.9 - - - +
294G ALA* 2.9 22.9 + - - +
295G ALA* 3.5 17.3 - - - +
297G PHE* 1.3 73.7 - - - +
299G LEU* 1.3 70.4 + - + +
300G ILE 3.0 1.6 - - - -
301G GLY 4.4 0.2 - - - +
302G VAL* 3.0 36.0 + - - +
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Residues in contact with LEU 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 4.4 27.2 + - + +
272A LEU* 4.5 8.1 - - + -
276A THR* 4.3 12.6 - - + -
305A PHE* 3.5 38.1 - - + +
295G ALA 4.5 9.6 - - - +
296G THR* 3.9 8.0 + - - +
297G PHE 3.4 0.4 - - - -
298G THR* 1.3 82.4 - - + +
300G ILE* 1.3 67.5 + - + +
302G VAL* 4.5 4.7 - - + -
303G SER* 3.1 24.5 + - - -
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Residues in contact with ILE 300 (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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236A TRP* 4.8 16.6 - - + -
242G CYS* 3.7 18.4 - - - -
296G THR 4.1 13.0 - - - +
297G PHE* 3.5 10.2 + - + +
298G THR 3.0 0.2 - - - -
299G LEU* 1.3 90.6 - - + +
301G GLY* 1.3 65.7 + - - +
302G VAL 3.5 0.2 - - - -
303G SER* 3.4 3.4 + - - -
304G PHE* 3.0 51.4 + - + -
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Residues in contact with GLY 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G CYS* 4.2 7.8 - - - -
275G LEU* 3.6 35.9 - - - -
297G PHE 2.9 12.2 + - - -
300G ILE* 1.3 76.3 - - - +
302G VAL* 1.3 63.1 + - - +
304G PHE* 2.9 14.4 + - - -
305G PHE* 3.0 18.1 + - - +
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Residues in contact with VAL 302 (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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276A THR* 4.7 17.7 - - + +
278A ILE* 4.5 7.6 - - + -
305A PHE 5.4 7.0 - - - +
309A ALA* 5.0 1.0 - - - +
274G THR 3.9 14.4 - - - +
275G LEU* 3.5 13.4 - - + +
277G THR* 3.7 28.4 - - + +
298G THR* 3.0 35.2 + - - +
299G LEU* 4.4 5.2 - - + +
301G GLY* 1.3 74.0 - - - +
303G SER* 1.3 68.7 + - - +
305G PHE 4.2 0.7 - - - -
306G ALA* 3.5 24.4 + - - +
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Residues in contact with SER 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 4.5 5.7 + - - -
305A PHE 5.1 2.8 + - - -
308A PRO* 4.0 23.6 - - - +
309A ALA* 4.2 19.1 + - - +
312A LEU* 5.8 5.8 - - - +
299G LEU 3.1 20.5 + - - -
300G ILE* 3.4 6.0 + - - -
301G GLY 3.0 1.0 - - - -
302G VAL* 1.3 84.8 - - - +
304G PHE* 1.3 62.5 + - - +
305G PHE 3.5 0.2 - - - -
306G ALA 4.0 0.2 + - - -
307G LEU* 3.4 25.1 + - - +
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Residues in contact with PHE 304 (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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221A LEU* 3.5 45.8 - - + -
312A LEU* 5.5 5.6 - - + -
235G ALA* 3.8 22.3 - - - +
236G TRP* 5.4 1.4 - - - -
238G ILE* 4.2 22.2 - - + -
239G GLY* 3.9 23.5 - - - -
242G CYS* 5.0 3.1 - - + -
300G ILE* 3.0 45.8 + - + +
301G GLY* 2.9 5.3 + - - +
303G SER* 1.3 81.7 - - - +
305G PHE* 1.3 60.4 + - - +
306G ALA 3.3 1.3 + - - -
307G LEU* 3.9 31.6 + - + +
308G PRO* 4.2 4.9 - - - +
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Residues in contact with PHE 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU* 3.5 36.8 - - + -
302D VAL* 5.4 7.4 - - - +
303D SER* 5.1 3.5 + - - -
236G TRP* 5.1 15.3 + + - -
239G GLY* 3.2 37.5 - - - -
240G PHE* 4.4 3.4 - - + -
243G LEU* 4.1 19.5 - - + -
272G LEU* 5.0 6.3 - - + -
275G LEU* 3.3 55.0 - - + +
276G THR* 4.1 14.6 - - + +
301G GLY* 3.0 11.0 + - - +
304G PHE* 1.3 78.3 - - - +
306G ALA* 1.3 58.0 + - - +
307G LEU 3.5 1.1 - - - -
308G PRO* 4.1 12.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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