Contacts of the helix formed by residues 281 - 295 (chain A) in PDB entry 4QYJ
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 ASP 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A ASP 3.6 2.6 + - - -
280A CYS* 1.3 79.8 - - - +
282A PRO* 1.3 65.8 - - - +
283A GLN* 2.9 15.8 + - - +
284A GLU* 2.9 37.0 + - + +
285A ALA* 2.8 30.3 + - - +
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Residues in contact with PRO 282 (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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280A CYS 3.4 8.9 - - - +
281A ASP* 1.3 89.3 - - - +
283A GLN* 1.3 65.2 + - - +
285A ALA* 3.9 1.2 - - + +
286A ALA* 3.1 26.0 + - - +
313A ILE* 5.0 12.3 - - + -
316A ASP* 3.8 26.5 - - + +
317A VAL* 4.0 23.6 - - + +
320A ARG* 3.9 25.2 - - - +
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Residues in contact with GLN 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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281A ASP* 2.9 13.5 + - - +
282A PRO* 1.3 76.3 - - - +
284A GLU* 1.3 62.6 + - - +
286A ALA* 4.1 2.3 - - - +
287A GLU* 3.1 25.6 + - - +
320A ARG* 4.0 24.9 - - - +
324A ILE* 5.7 0.3 - - - +
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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
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280A CYS* 5.0 4.9 - - - -
281A ASP* 2.9 26.6 + - + +
283A GLN* 1.3 78.1 - - - +
285A ALA* 1.3 56.1 + - - +
287A GLU* 3.6 4.8 + - - +
288A GLY* 2.8 26.5 + - - -
433A TRP* 4.0 13.2 - - + -
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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
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276A VAL* 3.3 41.8 - - + +
280A CYS* 3.7 5.6 - - - -
281A ASP 2.8 16.8 + - - +
282A PRO* 3.9 3.8 - - + +
283A GLN 3.3 0.4 - - - -
284A GLU* 1.3 76.8 - - - +
286A ALA* 1.3 52.6 + - - +
288A GLY* 3.1 2.8 + - - -
289A ALA* 2.7 35.6 + - - +
317A VAL* 4.2 13.2 - - + -
433A TRP* 4.8 7.3 - - + -
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Residues in contact with ALA 286 (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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282A PRO 3.1 17.1 + - - +
283A GLN 4.2 2.5 - - - +
285A ALA* 1.3 73.6 - - - +
287A GLU* 1.3 64.2 + - - +
289A ALA* 4.3 4.9 - - - +
290A ALA* 3.2 24.4 + - - +
317A VAL* 3.7 28.4 - - + +
320A ARG* 4.0 9.2 - - + -
321A LEU* 3.7 23.0 - - + +
324A ILE* 3.5 8.0 - - + +
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Residues in contact with GLU 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 GLN 3.1 18.1 + - - +
284A GLU* 3.9 4.9 - - - +
286A ALA* 1.3 77.0 - - - +
288A GLY* 1.3 62.7 + - - +
290A ALA* 4.0 2.5 - - - +
291A ALA* 3.2 24.3 + - - +
324A ILE* 3.9 14.9 - - + +
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Residues in contact with GLY 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 2.8 16.5 + - - -
285A ALA 3.2 5.2 - - - -
287A GLU* 1.3 74.4 - - - +
289A ALA* 1.3 58.5 + - - +
291A ALA* 3.5 6.4 + - - +
292A ALA* 3.0 27.1 + - - +
433A TRP* 3.5 32.9 - - - -
457A HIS* 5.4 0.5 - - - +
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Residues in contact with ALA 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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274A VAL* 4.8 5.8 - - + +
285A ALA 2.7 17.6 + - - +
286A ALA* 4.2 5.4 - - - +
288A GLY* 1.3 73.1 - - - +
290A ALA* 1.3 60.2 + - - +
292A ALA* 2.9 24.1 + - - +
293A ILE* 3.1 18.3 + - - +
304A GLY 5.0 0.7 - - - +
307A LEU* 3.7 41.5 - - + -
317A VAL* 6.0 0.2 - - + -
321A LEU* 4.3 7.4 - - + -
406A LEU* 4.8 3.8 - - + -
433A TRP* 5.3 0.6 - - - -
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Residues in contact with ALA 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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286A ALA 3.2 17.7 + - - +
287A GLU 4.0 3.4 - - - +
289A ALA* 1.3 76.3 - - - +
291A ALA* 1.3 58.9 + - - +
293A ILE* 4.2 2.2 - - - -
294A PHE* 2.8 55.1 + - + +
321A LEU* 4.1 10.1 - - + +
324A ILE* 4.0 25.1 - - + -
328A ILE* 5.9 0.2 - - + -
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Residues in contact with ALA 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 GLU 3.2 15.9 + - - +
288A GLY* 3.7 5.2 - - - +
290A ALA* 1.3 78.3 - - - +
292A ALA* 1.3 62.2 + - - +
293A ILE 3.3 0.3 + - - -
295A PHE* 3.2 28.3 - - + +
457A HIS* 5.8 0.2 - - - -
458A ASN* 4.0 2.9 + - - +
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Residues in contact with ALA 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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274A VAL* 4.4 15.3 - - + -
288A GLY 3.0 13.8 + - - +
289A ALA* 2.9 17.1 + - - +
291A ALA* 1.3 76.9 - - - +
293A ILE* 1.3 54.9 + - - +
295A PHE* 5.1 0.7 - - - -
303A ALA* 3.5 2.3 - - - +
304A GLY* 2.9 20.8 + - - +
433A TRP* 5.8 1.1 - - + +
457A HIS* 3.8 31.7 - - + +
458A ASN* 3.3 20.1 + - - +
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Residues in contact with ILE 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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289A ALA 3.2 15.7 - - - +
290A ALA* 3.8 3.4 - - - +
292A ALA* 1.3 78.1 - - - +
294A PHE* 1.3 95.2 + - + +
295A PHE 3.5 3.4 - - - +
298A GLY* 3.2 18.9 - - - +
303A ALA* 4.0 17.0 - - + -
304A GLY 3.4 21.3 - - - +
305A SER* 3.9 11.0 - - - -
403A GLY 4.1 12.3 - - - +
404A PRO* 4.2 0.5 - - - +
405A VAL 3.7 26.7 - - - +
406A LEU* 4.1 17.5 - - + -
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Residues in contact with PHE 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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290A ALA* 2.8 38.2 + - + +
293A ILE* 1.3 94.3 - - + +
295A PHE* 1.3 63.1 + - - +
296A ASN 3.5 0.9 + - - -
297A HIS* 3.4 13.7 + - - -
298A GLY 4.4 0.4 - - - +
321A LEU* 5.0 2.9 - - + -
325A GLY* 4.4 10.3 - - - -
328A ILE* 3.7 29.6 - - + -
339A HIS 5.6 1.0 - - - +
340A MET* 3.8 20.8 - - + +
383A PRO* 4.0 13.2 - - + -
384A THR 4.4 3.4 - - - -
385A ILE* 3.9 35.0 - - + -
404A PRO* 3.7 36.3 - - + -
406A LEU* 5.0 1.8 - - + -
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Residues in contact with PHE 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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110A TYR* 5.8 6.3 - + - -
114A MET* 2.8 45.5 - - + -
170A PHE* 4.1 13.5 - + - -
290A ALA 4.2 0.4 + - - -
291A ALA* 3.2 23.8 + - - +
293A ILE* 3.5 1.7 - - - +
294A PHE* 1.3 72.8 - - - +
296A ASN* 1.3 73.5 + - + +
298A GLY* 3.3 9.7 + - - -
300A VAL* 3.4 31.4 - - + +
458A ASN* 3.4 39.9 - - + +
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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