Contacts of the helix formed by residues 287 - 294 (chain A) in PDB entry 4B92
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 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A HIS* 3.1 25.8 + - + +
286A GLN* 1.3 76.4 - - - +
288A TRP* 1.3 69.5 + - - +
289A SER* 3.3 28.7 + - - -
290A HIS* 3.5 12.7 + - + +
291A ALA* 3.2 15.9 + - - +
424A PHE* 4.4 5.9 - - - -
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Residues in contact with TRP 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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212A GLY* 4.4 6.5 - - - -
213A PRO* 3.4 31.1 - - + +
285A HIS 5.2 0.4 - - - -
286A GLN 3.4 4.6 + - - +
287A ASP* 1.3 73.1 + - - +
289A SER* 1.3 72.4 + - - +
291A ALA* 3.3 6.7 + - - +
292A ALA* 2.9 42.9 + - + -
331A THR* 4.5 5.2 - - + -
334A LYS* 3.6 26.0 - - + -
335A ALA* 3.6 23.3 - - + -
337A GLY 3.4 23.6 + - - -
338A LYS* 3.4 51.0 + - + +
344A ILE* 3.9 12.8 - - + +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 3.3 19.4 + - - -
288A TRP* 1.3 88.5 - - - +
290A HIS* 1.3 57.9 + - - +
292A ALA* 3.3 3.1 + - - +
293A ALA* 3.1 27.2 + - - +
331A THR* 3.1 30.6 - - - +
334A LYS* 6.0 0.2 - - - +
338A LYS* 5.3 4.7 + - - -
424A PHE* 3.9 16.3 - - - -
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Residues in contact with HIS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A HIS* 3.4 7.9 + + - -
285A HIS* 3.6 34.2 + + + +
287A ASP* 3.5 18.4 + - + +
289A SER* 1.3 79.1 - - - +
291A ALA* 1.3 65.3 + - - +
293A ALA* 3.2 5.9 + - - +
294A TYR* 3.0 45.0 - + - -
424A PHE* 4.0 25.5 - + + -
425A ASN 6.0 1.1 - - - -
428A GLU* 6.4 2.5 - - + -
1484A ZN 2.2 37.0 - - - -
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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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213A PRO* 3.5 27.1 - - + -
282A HIS 3.4 23.3 - - - +
283A TYR* 3.5 32.8 - - - +
285A HIS 4.3 6.1 - - - +
287A ASP 3.2 10.6 + - - +
288A TRP* 3.3 4.7 + - - +
290A HIS* 1.3 79.2 - - - +
292A ALA* 1.3 61.0 + - - +
294A TYR* 3.4 9.5 + - - +
295A VAL* 3.7 2.1 - - - +
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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
----------------------------------------------------------
213A PRO* 4.2 2.9 - - + -
288A TRP* 2.9 52.0 + - + +
289A SER 3.6 4.0 - - - +
290A HIS 3.1 0.2 - - - -
291A ALA* 1.3 73.4 - - - +
293A ALA* 1.3 63.3 + - - +
294A TYR 3.1 2.5 - - - -
295A VAL* 3.2 23.2 + - - +
331A THR* 6.0 0.4 - - + -
334A LYS* 3.3 28.9 + - + +
344A ILE* 4.6 4.7 - - + -
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Residues in contact with ALA 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 SER 3.1 12.7 + - - +
290A HIS 3.2 12.0 + - - +
292A ALA* 1.3 77.4 - - - +
294A TYR* 1.3 65.6 + - + +
295A VAL 3.7 0.2 + - - -
334A LYS* 4.4 8.5 - - - +
347A GLY 3.9 5.7 - - - +
348A VAL* 3.7 13.3 - - - +
349A SER 5.3 0.2 + - - -
424A PHE* 3.8 36.3 - - + -
426A LEU* 3.5 14.7 - - + +
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Residues in contact with TYR 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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278A LEU* 3.6 24.0 - - + -
282A HIS* 3.5 38.2 + + + -
283A TYR* 2.6 43.5 + - + -
290A HIS* 3.0 52.3 + + - -
291A ALA 3.4 2.2 + - - +
292A ALA 3.1 0.8 - - - -
293A ALA* 1.3 81.6 - - + +
295A VAL* 1.3 58.2 + - - +
296A THR* 3.2 7.6 + - - +
300A LEU* 3.7 24.1 - - + +
348A VAL* 4.1 6.5 - - - +
424A PHE* 5.8 1.6 - + - -
425A ASN 4.3 2.2 + - - -
426A LEU* 2.9 45.6 + - + -
428A GLU* 6.1 0.2 - - - +
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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
------------------------------------------------------------
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