Contacts of the helix formed by residues 284 - 303 (chain A) in PDB entry 1A16
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 GLN 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A THR* 1.3 72.8 - - - +
285A ALA* 1.3 58.0 + - - +
287A ARG* 3.3 6.3 + - - +
288A GLU* 2.9 57.4 + - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 3.3 6.3 + - - +
284A GLN* 1.3 79.0 - - - +
286A GLN* 1.3 61.2 + - - +
288A GLU* 3.6 11.2 + - - -
289A ILE* 3.4 27.0 + - - +
397A GLN* 3.3 48.5 - - + +
398A TYR* 3.8 8.2 - - + -
401A ILE* 4.1 3.0 - - + +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY 2.8 31.9 + - - +
255A ASP* 4.0 0.6 - - - +
256A LEU* 3.6 46.8 - - + +
277A PRO* 4.5 1.9 - - - +
281A LYS 4.2 3.1 - - - +
282A PHE* 3.7 11.8 - - + -
283A THR* 3.0 41.4 + - - +
285A ALA* 1.3 73.0 - - - +
287A ARG* 1.3 61.1 + - - +
289A ILE 3.4 1.4 + - - -
290A TYR* 3.0 29.5 + - - +
401A ILE* 4.2 21.0 - - + +
403A ILE* 3.8 6.1 - - - +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 5.6 3.0 - - - +
282A PHE* 4.0 14.5 - - + +
283A THR 2.8 17.9 + - - +
284A GLN* 3.5 7.2 - - - +
286A GLN* 1.3 78.2 - - - +
288A GLU* 1.3 57.8 + - + +
290A TYR* 4.2 4.0 - - - -
291A ASP* 3.1 61.6 + - - +
427A PRO* 3.4 38.6 - - - +
428A GLU* 4.2 18.4 + - - +
431A GLU* 4.8 10.1 + - - -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLN* 2.9 53.9 + - + +
285A ALA* 3.8 7.5 - - - +
286A GLN 3.3 0.4 - - - -
287A ARG* 1.3 78.5 - - + +
289A ILE* 1.3 58.8 + - - +
291A ASP* 4.0 7.7 + - - +
292A ILE* 3.5 22.2 + - - +
328A LEU* 3.7 29.3 - - + +
397A GLN* 5.3 1.0 + - - +
398A TYR* 2.6 35.2 + - + -
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.4 15.5 - - - +
286A GLN 3.4 2.4 + - - +
287A ARG 3.3 0.2 - - - -
288A GLU* 1.3 75.1 - - - +
290A TYR* 1.3 67.4 + - - +
291A ASP 3.2 0.2 - - - -
292A ILE* 3.2 16.4 + - + +
293A VAL* 3.2 13.1 + - + +
325A LEU* 4.8 4.3 - - + -
328A LEU* 3.9 11.4 - - + -
330A ILE* 3.5 32.1 - - + -
386A LEU* 3.8 29.2 - - + +
388A ILE* 3.8 18.2 - - + -
398A TYR* 3.9 10.8 - - + -
401A ILE* 4.3 14.6 - - + -
403A ILE* 3.8 19.5 - - + -
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Residues in contact with TYR 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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274A ARG* 5.3 1.0 - - - -
275A THR* 3.3 22.5 + - - -
282A PHE* 3.7 21.8 - + + -
286A GLN 3.0 18.3 + - - +
287A ARG* 3.4 6.3 + - - +
289A ILE* 1.3 78.0 - - - +
291A ASP* 1.3 58.2 + - - +
293A VAL* 3.3 2.4 + - - +
294A LEU* 2.9 31.2 + - + +
403A ILE* 3.5 27.3 - - + +
405A ILE* 3.5 32.4 - - + +
425A LYS* 2.5 36.8 + - - +
427A PRO* 3.6 32.3 - - + -
430A ILE* 3.5 12.2 - - + +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 3.1 53.6 + - - +
288A GLU* 4.0 9.4 - - - +
289A ILE 3.2 0.4 - - - -
290A TYR* 1.3 77.5 - - - +
292A ILE* 1.3 57.6 + - + +
294A LEU* 3.4 7.3 + - - +
295A GLU* 3.0 32.0 + - - +
427A PRO* 4.2 8.5 - - - +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU 3.5 10.3 - - - +
289A ILE* 3.2 7.9 + - - +
291A ASP* 1.3 77.1 - - + +
293A VAL* 1.3 61.3 + - - +
295A GLU* 4.8 3.1 - - - -
296A SER* 3.0 28.2 + - - -
320A ILE* 3.8 13.1 - - + +
321A MET* 3.7 33.0 - - + +
324A GLY* 3.5 37.5 - - - +
325A LEU* 3.9 12.1 - - + +
328A LEU* 3.7 20.9 - - + -
386A LEU* 3.7 16.2 - - + -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE 3.2 15.1 + - - +
290A TYR 3.8 5.4 - - - +
292A ILE* 1.3 77.3 - - - +
294A LEU* 1.3 56.5 + - - +
296A SER* 3.3 7.7 + - - -
297A LEU* 3.0 22.9 + - - +
321A MET* 5.3 1.6 - - - -
384A PRO* 3.2 38.0 - - + +
385A GLY* 3.9 2.5 - - - -
386A LEU* 3.8 36.3 - - + +
403A ILE* 3.9 19.1 - - + -
405A ILE* 3.8 20.9 - - + +
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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
----------------------------------------------------------
290A TYR* 2.9 20.1 + - + +
291A ASP* 3.8 9.0 - - - +
292A ILE 3.3 0.2 - - - -
293A VAL* 1.3 73.3 - - - +
295A GLU* 1.3 55.0 + - - +
297A LEU* 3.1 5.3 + - + +
298A GLU* 2.8 60.4 + - + +
405A ILE* 3.7 14.1 - - + +
425A LYS* 3.7 42.2 - - + +
426A LYS* 4.1 9.0 - - + +
427A PRO* 3.7 28.9 - - + -
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASP 3.0 18.1 + - - +
292A ILE* 4.0 4.5 - - - +
294A LEU* 1.3 75.7 - - - +
296A SER* 1.3 57.1 + - - +
298A GLU* 4.3 10.5 + - + +
299A THR* 2.9 45.7 + - - +
302A ARG* 5.6 2.5 - - - +
320A ILE* 3.8 29.3 - - + +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE 3.0 17.5 + - - -
293A VAL* 3.3 11.0 - - - -
295A GLU* 1.3 76.2 - - - +
297A LEU* 1.3 60.2 + - - +
299A THR* 4.0 0.9 - - - -
300A SER* 2.9 30.0 + - - -
317A VAL* 3.4 31.8 - - - +
320A ILE* 3.5 22.7 - - - +
321A MET* 3.7 10.0 - - - +
384A PRO* 3.6 12.6 - - - -
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Residues in contact with LEU 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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293A VAL 3.0 13.4 + - - +
294A LEU* 3.5 9.2 - - + +
296A SER* 1.3 76.5 - - - +
298A GLU* 1.3 57.2 + - - +
300A SER* 3.1 5.1 + - - -
301A LEU* 2.9 49.8 + - + +
382A VAL* 3.5 39.3 - - + +
384A PRO* 3.7 10.5 - - + +
405A ILE* 3.5 41.1 - - + +
406A GLU 4.4 0.9 - - - +
407A ASP* 3.9 11.7 - - - +
425A LYS* 3.6 20.2 - - + -
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Residues in contact with GLU 298 (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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294A LEU* 2.8 53.9 + - + +
295A GLU* 4.0 8.8 - - + +
297A LEU* 1.3 70.6 - - - +
299A THR* 1.3 62.9 + - - +
301A LEU* 3.1 11.3 + - + +
302A ARG* 3.0 40.5 + - - +
425A LYS* 5.0 11.2 - - - -
426A LYS* 2.9 32.9 + - - +
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Residues in contact with THR 299 (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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295A GLU* 2.9 29.4 + - - +
296A SER 4.0 1.3 - - - +
298A GLU* 1.3 72.0 - - - +
300A SER* 1.3 63.1 + - - +
302A ARG* 2.8 32.6 + - - +
303A LEU* 3.0 48.4 + - + +
316A GLU* 4.5 14.6 - - + +
317A VAL* 6.0 0.4 - - + -
320A ILE* 3.4 24.9 - - + +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER 2.9 21.9 + - - -
297A LEU 3.1 5.9 + - - -
299A THR* 1.3 76.6 - - - +
301A LEU* 1.3 57.1 + - - +
303A LEU* 3.9 0.4 - - - +
304A TYR* 2.9 37.6 + - - -
313A VAL* 3.4 21.6 - - - +
317A VAL* 3.2 22.3 - - - +
352A LEU* 3.7 4.0 - - - +
382A VAL* 3.6 23.2 - - - +
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Residues in contact with LEU 301 (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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297A LEU* 2.9 28.2 + - + +
298A GLU* 3.1 11.9 + - + +
300A SER* 1.3 76.5 - - - +
302A ARG* 1.3 60.1 + - + +
304A TYR* 5.1 0.4 - - - -
382A VAL* 4.3 12.3 - - + -
407A ASP* 4.0 11.0 - - + +
409A ILE* 3.5 32.5 - - + -
416A ASN* 2.9 30.5 + - - +
418A ASN* 3.4 26.0 - - + +
425A LYS* 4.0 16.8 - - - +
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 5.6 2.2 - - - +
298A GLU* 3.0 31.4 + - - +
299A THR* 2.8 41.9 + - - +
301A LEU* 1.3 79.3 - - + +
303A LEU* 1.3 66.3 + - + +
304A TYR 4.6 2.3 - - - +
305A ARG* 5.3 3.1 - - - -
416A ASN* 5.1 0.2 + - - -
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Residues in contact with LEU 303 (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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299A THR* 3.0 35.6 + - + +
300A SER 3.3 2.4 + - - +
302A ARG* 1.3 82.9 - - + +
304A TYR* 1.3 65.9 + - - +
305A ARG* 2.8 42.7 + - - +
308A THR* 3.9 2.2 - - - +
313A VAL* 4.1 20.9 - - + -
316A GLU* 3.6 39.7 - - + +
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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