Contacts of the helix formed by residues 286 - 301 (chain A) in PDB entry 4AD7
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 LEU 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A VAL* 4.5 2.7 - - + -
237A VAL* 3.6 28.7 - - + -
283A GLN 3.4 17.9 - - - +
284A ALA 3.1 0.6 - - - -
285A ASP* 1.3 77.2 - - - +
287A ASP* 1.3 64.7 + - - +
288A ALA 3.4 0.8 + - - -
289A GLU* 3.6 4.4 + - - +
290A TRP* 3.0 23.4 + - - +
393A TRP* 3.6 36.6 - - + +
453A ILE* 3.7 22.0 - - + +
456A GLN* 4.1 9.9 - - + -
457A ILE* 3.6 33.7 - - + +
460A LEU* 4.3 13.5 - - + +
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Residues in contact with ASP 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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284A ALA 3.4 17.9 + - - +
285A ASP 3.1 1.4 - - - -
286A LEU* 1.3 76.7 - - - +
288A ALA* 1.3 66.9 + - - +
290A TRP* 3.1 1.6 + - - +
291A ARG* 2.9 62.8 + - - +
390A GLN 4.3 3.1 - - - +
391A ASP 5.4 0.2 - - - +
393A TRP* 4.2 13.4 + - + +
394A ILE* 3.7 29.2 + - + +
299B LEU* 5.7 1.7 - - - +
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Residues in contact with ALA 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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285A ASP 4.4 4.8 + - - +
286A LEU 3.5 0.4 - - - -
287A ASP* 1.3 83.4 - - - +
289A GLU* 1.3 65.0 + - + +
291A ARG* 3.1 7.7 + - - +
292A ASN* 2.9 37.1 + - - +
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Residues in contact with GLU 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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285A ASP 5.3 1.5 + - - +
286A LEU 3.6 5.1 + - - +
287A ASP 3.5 0.2 - - - -
288A ALA* 1.3 81.3 - - + +
290A TRP* 1.3 61.2 + - - +
292A ASN* 3.3 26.1 + - - +
293A LEU* 2.9 31.0 + - - +
457A ILE* 3.7 26.9 - - + +
460A LEU* 3.7 26.6 - - + +
461A LYS* 3.4 41.3 + - + +
464A THR* 4.2 2.9 + - - +
468A ARG* 5.5 1.4 + - - -
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Residues in contact with TRP 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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96A LEU* 4.4 12.6 - - + -
100A LEU* 4.1 8.3 - - + -
230A ALA* 3.9 33.2 - - + -
233A VAL* 4.7 4.5 - - + -
234A VAL* 3.7 30.5 - - + -
286A LEU 3.0 20.6 + - - +
287A ASP* 3.3 4.5 - - - +
289A GLU* 1.3 77.2 - - - +
291A ARG* 1.3 63.5 + - - +
293A LEU* 3.3 4.0 + - + +
294A LEU* 2.9 48.7 + - + +
389A VAL* 3.1 32.3 + - + -
390A GLN* 3.8 19.7 - - - -
392A PHE* 4.4 2.2 - - + +
393A TRP* 3.2 36.5 - + + +
460A LEU* 3.7 20.2 - - + +
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Residues in contact with ARG 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 ASP* 2.9 40.5 + - - +
288A ALA* 3.5 7.2 - - - +
290A TRP* 1.3 75.5 - - + +
292A ASN* 1.3 58.4 + - - +
294A LEU* 3.4 7.0 + - - +
295A ASP* 2.8 43.4 + - - +
390A GLN* 3.3 33.8 + - + +
391A ASP* 3.6 11.5 - - - +
394A ILE* 3.5 24.7 - - - +
298B VAL* 5.3 4.8 + - - +
299B LEU* 4.2 8.3 - - - +
302B ASP* 2.5 45.3 + - - -
383B LYS* 4.6 12.1 - - - +
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Residues in contact with ASN 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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288A ALA* 2.9 21.7 + - - +
289A GLU* 3.4 35.3 + - - +
290A TRP 3.2 0.2 - - - -
291A ARG* 1.3 76.9 - - - +
293A LEU* 1.3 55.8 + - - +
295A ASP* 3.2 11.3 + - - +
296A SER* 2.9 29.1 + - - -
464A THR* 3.9 17.9 - - + +
468A ARG* 4.5 18.8 + - - +
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Residues in contact with LEU 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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226A GLY 4.1 8.1 - - - +
229A VAL* 4.3 5.6 - - + -
230A ALA* 4.1 23.3 - - + -
289A GLU 2.9 18.6 + - - +
290A TRP* 3.7 5.6 - - + +
292A ASN* 1.3 72.2 - - - +
294A LEU* 1.3 61.8 + - + +
296A SER* 2.6 19.6 + - - -
297A MET* 2.9 30.8 + - + +
460A LEU* 3.6 28.5 - - + +
463A MET* 3.6 17.9 - - + -
464A THR* 3.4 19.6 + - - +
467A LEU* 3.6 27.1 - - + -
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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
----------------------------------------------------------
100A LEU* 6.1 0.4 - - + -
230A ALA* 5.2 1.8 - - + -
290A TRP* 2.9 60.5 + - + +
291A ARG* 3.8 4.5 - - - +
293A LEU* 1.3 81.6 - - + +
295A ASP* 1.3 59.1 + - - +
297A MET* 3.3 24.0 + - + +
298A VAL* 2.9 34.7 + - + +
386A LEU* 3.3 46.0 - - + +
389A VAL* 4.2 5.8 - - + -
390A GLN* 3.6 16.6 - - + +
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 2.8 36.2 + - - +
292A ASN* 3.5 12.2 + - - +
294A LEU* 1.3 77.5 - - - +
296A SER* 1.3 56.9 + - - +
298A VAL* 3.2 9.8 + - - +
299A LEU* 2.9 35.8 + - + +
468A ARG* 6.4 0.2 - - - +
383B LYS* 5.2 10.1 + - - -
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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
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292A ASN 2.9 11.8 + - - -
293A LEU* 2.6 26.5 + - - +
295A ASP* 1.3 75.0 - - - +
297A MET* 1.3 57.2 + - - +
299A LEU* 3.1 13.5 + - - +
300A ILE* 2.9 30.3 + - - +
464A THR* 4.1 14.2 - - - +
467A LEU* 3.4 35.2 - - - +
468A ARG* 4.7 10.5 - - - -
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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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223A PHE* 3.2 35.1 - - + +
226A GLY* 3.4 35.0 - - - +
227A LEU* 3.5 24.5 - - + -
230A ALA* 4.8 4.9 - - + -
293A LEU* 2.9 27.3 + - + +
294A LEU* 3.7 33.2 - - + +
295A ASP 3.2 0.2 - - - -
296A SER* 1.3 73.0 + - - +
298A VAL* 1.3 65.0 + - - +
300A ILE* 3.5 9.8 - - - +
301A THR* 3.4 8.3 - - - +
386A LEU* 4.1 13.0 - - + -
467A LEU* 3.8 20.2 - - + -
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Residues in contact with VAL 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 2.9 18.3 + - - +
295A ASP* 3.6 12.3 - - - +
297A MET* 1.3 76.4 - - - +
299A LEU* 1.3 61.8 + - + +
301A THR* 2.6 25.6 + - - -
302A ASP* 3.8 6.6 - - - +
383A LYS* 4.1 29.8 - - + +
386A LEU* 4.5 20.6 - - + -
387A ARG* 5.3 7.2 - - + -
376B GLU* 4.1 21.3 - - - +
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Residues in contact with LEU 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 ASP* 2.9 19.7 + - + +
296A SER* 3.1 15.7 + - - +
298A VAL* 1.3 78.8 - - + +
300A ILE* 1.3 58.3 + - - +
302A ASP* 3.0 29.6 + - - +
468A ARG* 6.2 3.6 - - + -
471A TYR* 3.2 50.4 - - + +
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Residues in contact with ILE 300 (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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219A ALA* 3.9 28.5 - - + +
222A SER* 4.7 0.4 - - - -
223A PHE* 3.6 26.0 - - + -
296A SER 2.9 12.0 + - - +
297A MET 3.5 13.7 - - - +
299A LEU* 1.3 76.0 - - - +
301A THR* 1.3 63.3 + - - +
302A ASP 3.2 0.2 - - - -
303A LYS* 3.3 20.7 + - + +
304A PHE* 3.6 8.7 - - + -
467A LEU* 3.8 29.6 - - + +
470A ALA* 3.9 11.4 - - + +
471A TYR* 3.6 40.8 - - + +
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Residues in contact with THR 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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223A PHE* 3.6 23.6 - - + -
297A MET 3.4 16.4 - - - +
298A VAL* 2.6 22.4 + - - -
300A ILE* 1.3 73.4 - - - +
302A ASP* 1.3 64.7 + - - +
303A LYS 3.1 2.2 - - - -
304A PHE* 3.1 38.1 + - + +
305A TRP* 3.1 16.8 + - - -
379A VAL* 3.8 21.1 - - + +
382A ALA* 6.2 0.4 - - + -
383A LYS* 3.7 18.0 - - + -
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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