Contacts of the helix formed by residues 289 - 299 (chain A) in PDB entry 4EWS
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 GLY 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A MET* 1.3 71.3 - - - +
290A ASP* 1.3 55.5 + - - -
292A PHE* 3.3 4.2 + - - +
293A LYS* 3.0 26.9 + - - +
316A PRO 3.1 28.2 - - - +
317A SER* 3.7 20.6 + - - -
318A GLN 5.0 0.2 - - - -
319A ALA 3.0 15.0 + - - -
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Residues in contact with ASP 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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288A MET 3.1 1.8 + - - -
289A GLY* 1.3 68.5 - - - -
291A GLU* 1.3 60.0 + - - +
293A LYS* 3.4 13.7 + - - +
294A ALA* 2.9 30.2 + - - +
317A SER* 3.1 23.5 + - - -
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Residues in contact with GLU 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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286A SER 3.6 11.1 - - - +
287A LEU* 3.6 16.3 - - + +
288A MET* 3.0 26.2 + - + +
290A ASP* 1.3 76.7 - - - +
292A PHE* 1.4 57.0 + - - +
294A ALA* 3.3 8.3 + - - +
295A VAL* 3.0 34.0 + - + +
424A ARG* 3.4 25.0 + - - +
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Residues in contact with PHE 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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287A LEU* 3.9 21.4 - - + +
288A MET 2.8 19.3 + - - +
289A GLY 3.5 8.5 - - - +
291A GLU* 1.4 72.2 - - - +
293A LYS* 1.3 61.6 + - + +
295A VAL* 3.4 3.1 + - - +
296A LEU* 3.3 40.4 + - + +
312A VAL* 4.2 9.0 - - + -
316A PRO 5.1 0.7 - - - -
319A ALA* 3.8 23.1 - - + +
320A GLN 5.6 0.7 - - - -
321A VAL* 3.4 30.3 - - + -
348A PHE* 4.5 3.6 - + - -
350A PHE* 3.9 28.5 - + - -
412A MET* 3.9 15.7 - - + -
502A 2OB 3.6 28.7 - - + -
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Residues in contact with LYS 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 GLY 3.0 17.3 + - - +
290A ASP* 3.7 14.1 + - - +
292A PHE* 1.3 74.3 - - + +
294A ALA* 1.3 64.2 + - - +
296A LEU* 3.4 15.0 + - + +
297A GLU* 3.3 22.4 + - - +
303A THR* 3.3 41.7 + - - +
312A VAL* 5.9 1.1 - - + +
316A PRO* 4.0 30.6 - - + +
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Residues in contact with ALA 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 ASP 2.9 17.3 + - - +
291A GLU* 3.3 9.8 + - - +
293A LYS* 1.3 77.0 - - - +
295A VAL* 1.4 50.1 + - + +
297A GLU* 3.2 8.9 + - - +
298A THR* 2.6 41.4 + - - +
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Residues in contact with VAL 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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287A LEU* 3.9 22.9 - - + -
291A GLU* 3.0 17.9 + - + +
292A PHE 3.6 8.1 - - - +
293A LYS 3.4 0.4 - - - -
294A ALA* 1.4 74.1 - - + +
296A LEU* 1.3 62.0 + - - +
298A THR* 3.4 12.0 + - - -
299A TRP* 3.2 26.0 - - - -
416A VAL* 3.9 8.1 - - + -
420A GLU* 3.8 39.5 - - + +
424A ARG* 4.3 4.5 - - - +
502A 2OB 3.9 28.0 - - + -
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Residues in contact with LEU 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 PHE* 3.3 43.5 + - + +
293A LYS* 3.6 14.4 - - + +
294A ALA 3.4 0.2 - - - -
295A VAL* 1.3 75.5 - - - +
297A GLU* 1.3 61.0 + - - +
299A TRP* 3.6 9.7 + - - +
301A PHE* 3.5 21.8 - - + +
303A THR* 6.2 1.8 - - - +
308A PHE* 3.7 33.0 - - + -
312A VAL* 4.5 10.8 - - + -
408A PHE* 5.8 1.6 - - + -
412A MET* 3.7 23.1 - - - -
416A VAL* 4.3 17.4 - - + +
502A 2OB 4.0 10.1 - - + -
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Residues in contact with GLU 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 LYS* 3.3 10.0 + - - +
294A ALA* 3.2 11.1 + - - +
296A LEU* 1.3 75.4 - - - +
298A THR* 1.4 57.2 + - - +
299A TRP 2.9 10.6 + - - -
300A GLY* 3.1 13.9 + - - -
301A PHE 3.2 14.8 + - - +
302A ASN* 3.0 37.8 - - - +
303A THR* 3.3 32.3 + - - +
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Residues in contact with THR 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 ALA* 2.6 26.0 + - - +
295A VAL* 3.4 10.6 + - - -
297A GLU* 1.4 74.2 - - - +
299A TRP* 1.4 78.2 + - + +
300A GLY 3.4 3.7 + - - -
420A GLU* 4.8 5.2 - - - +
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Residues in contact with TRP 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 VAL 3.2 24.3 + - - -
296A LEU 3.6 4.4 + - - +
297A GLU 2.9 1.8 + - - -
298A THR* 1.4 91.7 - - + +
300A GLY* 1.3 59.5 + - - +
301A PHE* 3.5 16.9 - - - -
415A ALA 4.3 9.8 - - - +
416A VAL* 3.5 30.5 - - + -
419A PRO* 3.5 49.8 - - + -
420A GLU* 3.0 27.1 + - + +
423A SER* 4.0 16.8 - - - -
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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