Contacts of the helix formed by residues 279 - 298 (chain A) in PDB entry 3NC0
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 TYR 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LEU* 3.9 37.0 - - + +
239A GLY* 4.2 5.2 + - - -
242A PHE* 3.5 35.0 - + + -
243A GLU* 3.7 39.8 + - + -
276A VAL* 4.1 12.8 - - + +
278A GLN* 1.3 114.1 + - + +
280A GLU* 1.3 63.5 + - - +
281A GLU 3.1 3.4 - - - -
282A GLN* 2.9 28.6 + - - +
283A PHE* 2.9 30.5 + - + -
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER 5.2 4.4 - - - +
278A GLN 3.7 3.8 + - - +
279A TYR* 1.3 74.9 - - - +
281A GLU* 1.3 61.1 + - - +
283A PHE* 3.9 9.4 + - - +
284A GLU* 3.3 28.0 + - - +
336A LEU* 4.0 21.0 - - + +
339A LYS* 3.0 29.0 + - - -
340A ARG* 2.7 35.3 + - - -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR 3.0 1.0 + - - -
280A GLU* 1.3 76.7 - - - +
282A GLN* 1.3 85.1 + - - +
284A GLU* 3.1 20.0 + - + +
285A THR* 3.3 18.8 + - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.4 48.2 + - + +
243A GLU* 5.9 1.6 - - - +
247A ILE* 4.7 7.8 - - + +
279A TYR* 2.9 40.2 - - - +
281A GLU* 1.3 93.0 + - - +
283A PHE* 1.3 57.7 + - - +
285A THR* 2.9 10.0 + - - -
286A LEU* 2.8 31.9 + - - +
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PHE* 3.5 36.1 - + - -
271A ILE 3.6 14.6 - - - -
274A VAL* 4.2 12.1 - - + -
276A VAL* 4.6 11.9 - - + -
279A TYR* 2.9 42.3 + - + -
280A GLU* 4.1 9.0 - - - +
281A GLU 3.2 0.6 - - - -
282A GLN* 1.3 76.4 - - - +
284A GLU* 1.3 63.9 + - - +
286A LEU* 3.6 9.3 - - + +
287A PHE* 3.0 25.6 + - - +
329A PHE* 3.6 20.7 - + + -
333A HIS* 3.2 48.7 - + + -
336A LEU* 5.2 6.1 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 3.3 27.9 - - - +
281A GLU* 3.1 11.4 + - + +
283A PHE* 1.3 78.6 - - - +
285A THR* 1.3 61.5 + - + +
287A PHE* 3.4 5.0 + - - +
288A THR* 3.0 29.9 + - - +
336A LEU* 3.8 17.7 - - + +
337A LEU* 5.4 2.7 - - - -
340A ARG* 3.4 32.9 + - - +
342A ASN* 4.3 6.6 + - - -
343A LEU* 3.2 36.4 - - + +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLU* 3.3 16.3 + - + +
282A GLN* 2.9 19.9 + - - -
284A GLU* 1.3 73.0 - - + +
286A LEU* 1.3 66.8 + - - +
287A PHE 3.1 1.8 - - - -
288A THR* 3.4 7.8 + - - +
289A LEU* 2.8 40.4 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.6 29.8 - - + +
251A ILE* 3.6 17.8 - - + +
268A LEU* 3.5 39.5 - - + +
271A ILE* 4.1 18.8 - - + -
272A ALA* 4.8 8.1 - - + -
282A GLN 2.8 18.6 + - - +
283A PHE* 3.6 19.7 - - + +
285A THR* 1.3 76.6 + - - +
287A PHE* 1.3 61.7 + - - +
289A LEU* 5.4 0.2 - - - -
290A THR* 2.8 35.9 + - - +
325A PHE* 5.1 5.2 - - + -
329A PHE* 4.9 5.2 - - + -
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE 3.0 16.9 + - - +
284A GLU* 3.7 4.5 - - - +
285A THR 3.1 0.2 - - - -
286A LEU* 1.3 74.8 - - - +
288A THR* 1.3 72.3 + - + +
289A LEU 3.1 1.1 - - - -
290A THR* 3.0 7.3 + - - -
291A MET* 3.0 45.3 + - + +
325A PHE* 4.6 15.5 - + - -
326A LEU* 5.0 3.8 - - + -
329A PHE* 3.4 32.1 - + + -
330A LEU* 4.4 4.5 - - + -
337A LEU* 3.5 41.1 - - + -
343A LEU 5.4 0.4 - - - -
346A ALA* 3.8 24.5 - - + -
347A LEU* 4.2 2.5 - - - -
350A ALA* 3.5 28.3 - - + -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLU 3.0 12.0 + - - +
285A THR* 3.4 10.4 + - - +
287A PHE* 1.3 82.0 - - + +
289A LEU* 1.3 64.5 + - - +
291A MET* 3.7 9.3 + - - +
292A MET* 3.2 27.6 + - - +
342A ASN 5.6 0.9 - - - +
343A LEU* 3.5 32.8 - - + +
346A ALA* 4.0 21.8 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 5.7 1.3 - - + -
248A SER* 4.8 9.2 - - - +
251A ILE* 3.5 40.4 - - + +
252A TYR* 3.5 41.5 - - + +
285A THR* 2.8 28.4 + - + +
286A LEU* 5.4 0.2 - - - -
288A THR* 1.3 78.4 + - - +
290A THR* 1.3 64.9 + - - +
292A MET* 3.5 32.2 + - + +
293A GLN* 3.5 7.6 + - - +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 3.8 13.0 - - - +
255A LEU* 4.4 17.0 - - + -
265A LEU* 5.0 2.5 - - + -
268A LEU* 3.9 8.4 - - + +
286A LEU* 2.8 29.5 + - - +
287A PHE 3.0 8.8 + - - -
289A LEU* 1.3 76.9 - - - +
291A MET* 1.3 66.1 + - - +
293A GLN* 2.9 7.8 + - - +
294A LEU* 2.8 34.5 + - + +
325A PHE* 3.7 32.5 - - + -
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PHE* 3.0 51.9 + - + +
288A THR* 3.9 6.5 - - - +
289A LEU 3.4 0.2 - - - -
290A THR* 1.3 75.0 - - - +
292A MET* 1.3 63.2 + - - +
294A LEU* 3.1 18.2 + - + +
295A LYS* 2.8 25.6 + - - +
325A PHE* 5.1 1.8 - - - -
326A LEU* 4.5 4.3 - - + -
346A ALA* 4.1 13.5 - - + +
349A GLU* 4.2 17.4 - - + +
350A ALA* 3.8 23.3 - - + +
353A TYR* 3.7 35.2 - - + -
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Residues in contact with MET 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TYR* 4.7 13.0 - - + +
288A THR 3.2 15.0 + - - +
289A LEU* 3.6 38.1 - - + +
290A THR 3.2 0.2 - - - -
291A MET* 1.3 78.6 - - + +
293A GLN* 1.3 68.3 + - - +
295A LYS* 3.2 5.5 + - - +
296A GLN* 3.1 27.0 + - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 3.3 35.1 + - + +
252A TYR* 4.6 13.7 + - - +
255A LEU* 4.6 9.4 - - + -
256A ASN* 3.7 33.4 + - + +
289A LEU 3.5 6.2 + - - +
290A THR* 2.9 12.4 + - - +
292A MET* 1.3 82.5 - - - +
294A LEU* 1.3 57.9 + - - +
296A GLN* 3.3 10.2 + - - +
297A MET* 2.8 47.5 + - + +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 5.2 4.9 - - + -
265A LEU* 5.7 4.9 - - + -
290A THR* 2.8 32.6 + - + +
291A MET* 3.4 36.8 - - + +
293A GLN* 1.3 76.6 - - - +
295A LYS* 1.3 59.9 + - - +
297A MET* 3.0 6.7 + - + -
298A LEU* 2.8 37.5 + - + +
318A PHE* 4.6 20.0 - - + -
322A LEU* 4.0 31.4 - - + -
325A PHE* 4.7 1.1 - - + -
326A LEU* 4.5 5.8 - - + -
353A TYR* 3.1 21.5 + - + +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A MET 2.8 18.4 + - - +
292A MET* 3.9 5.2 - - - +
294A LEU* 1.3 73.2 - - - +
296A GLN* 1.3 63.8 + - - +
298A LEU 4.1 1.3 - - - -
299A PRO* 3.9 14.7 - - - +
300A LEU* 3.5 41.3 - - + +
349A GLU* 4.0 20.7 + - - +
353A TYR* 3.4 9.8 + - + +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A MET 3.1 14.9 + - - +
293A GLN* 3.6 15.0 - - - +
295A LYS* 1.3 80.7 - - + +
297A MET* 1.3 67.3 + - + +
299A PRO* 4.8 4.3 - - - +
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Residues in contact with MET 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 3.4 43.7 - - - +
256A ASN* 4.2 22.2 - - + +
257A VAL 5.8 0.2 - - - -
258A PRO* 6.2 0.2 - - + -
261A ARG* 4.0 15.9 - - + +
293A GLN* 2.8 32.9 + - + +
294A LEU* 3.0 6.2 + - - +
296A GLN* 1.3 80.5 - - + +
298A LEU* 1.3 67.6 + - + +
299A PRO* 3.0 13.0 - - - +
318A PHE* 3.6 28.5 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 5.5 4.9 - - - +
294A LEU* 2.8 14.3 + - + +
295A LYS* 4.1 0.4 - - - -
297A MET* 1.3 78.8 - - + +
299A PRO* 1.3 70.0 - - + +
300A LEU 3.5 0.2 + - - -
302A THR* 4.7 4.3 - - + +
304A ILE* 4.5 21.1 - - + -
307A ALA* 5.6 6.7 - - + -
315A GLU* 5.4 11.0 - - + +
318A PHE* 3.6 36.6 - - + -
319A ILE* 5.2 9.0 - - + -
322A LEU* 4.5 20.0 - - + -
353A TYR* 2.6 37.6 + - + +
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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
------------------------------------------------------------
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