Contacts of the helix formed by residues 405 - 412 (chain A) in PDB entry 7ACN
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 TYR 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A TYR* 3.2 47.1 + + - -
366A MET* 4.3 4.7 - - + +
367A GLY* 3.5 34.4 - - - -
370A ALA* 3.9 22.8 - - + +
400A ILE* 2.8 37.4 + - + +
403A ASP* 4.2 13.5 - - + -
404A GLY* 1.3 76.5 - - - +
406A ALA* 1.4 60.4 + - - +
408A VAL* 3.2 14.6 + - + +
409A LEU* 3.2 20.7 + - + +
502A ALA* 4.9 1.9 - - + +
503A ASP* 4.6 15.4 + - - +
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Residues in contact with ALA 406 (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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400A ILE* 3.1 26.2 + - + +
401A GLU* 3.6 18.8 - - - +
405A TYR* 1.4 76.9 - - - +
407A GLN* 1.3 56.5 + - - +
409A LEU* 3.3 11.9 + - - +
410A ARG* 2.8 54.8 + - - +
416A VAL* 4.7 9.9 - - + +
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Residues in contact with GLN 407 (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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401A GLU* 4.5 2.3 + - - +
404A GLY* 3.7 11.7 + - - +
405A TYR 3.3 0.6 - - - -
406A ALA* 1.3 78.7 - - - +
408A VAL* 1.3 50.4 + - + +
410A ARG* 2.6 46.3 + - - +
411A ASP* 2.8 71.9 + - - +
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Residues in contact with VAL 408 (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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370A ALA* 3.7 28.7 - - + +
373A ALA* 3.8 6.5 - - + -
374A LYS* 3.7 22.0 - - + +
377A LEU* 3.7 17.5 - - + +
404A GLY 3.5 17.0 + - - +
405A TYR* 3.2 10.4 + - + +
407A GLN* 1.3 73.7 - - - +
409A LEU* 1.3 59.3 + - - +
411A ASP* 3.2 5.8 + - - +
412A VAL* 3.0 27.5 + - - +
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Residues in contact with LEU 409 (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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355A ILE* 4.7 2.9 - - + -
366A MET* 4.5 22.9 - - + +
369A SER* 4.2 8.7 - - - +
370A ALA* 4.2 23.6 - - - +
373A ALA* 4.3 6.7 - - + -
387A PHE* 4.0 26.0 - - + -
389A ILE* 3.8 33.8 - - + +
400A ILE* 5.4 2.0 - - + -
405A TYR* 3.2 20.1 + - + +
406A ALA* 3.6 10.3 - - - +
408A VAL* 1.3 78.1 - - - +
410A ARG* 1.3 65.1 + - - +
412A VAL* 3.3 12.6 - - - +
414A GLY* 3.0 22.2 + - - -
416A VAL* 5.5 1.8 - - + -
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Residues in contact with ARG 410 (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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389A ILE* 5.2 0.2 - - - +
401A GLU* 2.7 44.1 + - - -
406A ALA* 2.8 22.1 + - - +
407A GLN* 2.6 57.6 + - - +
409A LEU* 1.3 75.5 - - - +
411A ASP* 1.3 63.1 + - - +
413A GLY* 3.0 16.1 + - - -
414A GLY 3.7 18.5 + - - +
416A VAL* 4.4 23.1 - - + +
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Residues in contact with ASP 411 (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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377A LEU* 3.7 19.7 - - + +
382A LYS* 2.6 38.0 + - - -
407A GLN* 2.8 55.7 + - - +
408A VAL* 3.2 6.9 + - - +
410A ARG* 1.3 75.5 - - - +
412A VAL* 1.3 48.8 + - - +
413A GLY 3.1 0.2 - - - -
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Residues in contact with VAL 412 (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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373A ALA* 3.7 31.6 - - + +
376A ALA* 4.2 8.1 - - + -
377A LEU* 3.6 27.6 - - + +
381A LEU 4.2 9.0 - - - +
382A LYS* 3.1 11.4 - - - +
383A CYS* 2.8 33.7 + - - +
387A PHE* 4.0 17.7 - - + -
408A VAL 3.0 11.8 + - - +
409A LEU* 3.3 18.6 - - - +
411A ASP* 1.3 74.5 - - - +
413A GLY* 1.3 55.2 + - - +
470A THR* 5.6 0.9 - - + -
474A ILE* 4.7 5.2 - - + -
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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
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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