Contacts of the helix formed by residues 402 - 412 (chain A) in PDB entry 1ASZ
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 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A THR* 1.3 71.6 - - - +
403A LYS* 1.3 57.8 + - - +
405A GLY* 3.1 2.1 + - - -
406A ILE* 2.9 50.3 + - + +
418A ASP 4.3 1.6 - - - -
420A GLU 2.6 29.2 + - - -
421A ASP* 3.5 3.6 + - - -
422A LEU* 3.4 36.5 + - + +
445A LEU* 3.4 28.4 - - + +
446A ASP 2.8 10.9 + - - +
447A LYS 2.9 24.7 + - - +
448A PHE* 3.2 31.2 - + - -
449A PRO* 3.2 31.0 - - + -
452A ILE* 4.6 0.7 - - + -
466A TYR* 4.8 4.0 - + + -
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Residues in contact with LYS 403 (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 THR* 3.0 8.9 + - - +
402A TYR* 1.3 77.4 - - - +
404A GLU* 1.3 66.7 + - + +
406A ILE* 3.2 11.5 + - + +
407A GLU* 3.1 39.7 + - - +
410A ARG* 3.6 20.2 - - - +
418A ASP* 2.6 28.6 + - - +
447A LYS* 5.9 0.2 - - - +
466A TYR* 4.1 28.9 - - + +
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Residues in contact with GLU 404 (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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399A ARG 4.5 2.4 - - - +
400A LEU* 4.0 21.1 - - + +
401A THR* 2.8 46.7 + - - +
403A LYS* 1.3 76.5 - - + +
405A GLY* 1.3 62.8 + - - +
407A GLU* 3.0 36.0 - - - +
408A MET* 3.3 14.0 + - - +
438A TYR* 5.3 2.3 + - - -
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Residues in contact with GLY 405 (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 LEU* 5.0 3.0 - - - +
401A THR 2.8 13.2 + - - -
402A TYR 3.5 4.0 - - - -
404A GLU* 1.3 76.4 - - - +
406A ILE* 1.3 63.8 + - - +
407A GLU 3.3 0.3 + - - -
408A MET* 3.4 8.6 + - - +
409A LEU* 3.3 23.3 + - - +
422A LEU* 6.4 0.7 - - - -
430A LEU* 4.1 27.0 - - - +
445A LEU* 4.8 6.1 - - - -
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Residues in contact with ILE 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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402A TYR* 2.9 38.8 + - + +
403A LYS* 3.2 12.3 + - + +
405A GLY* 1.3 72.3 - - - +
407A GLU* 1.3 70.6 + - - +
409A LEU* 3.3 4.1 + - - +
410A ARG* 3.0 52.5 + - - +
416A ILE* 3.5 27.8 - - + -
417A GLY 2.9 24.2 - - - +
418A ASP* 3.2 23.6 - - - +
422A LEU* 5.5 1.6 - - + -
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Residues in contact with GLU 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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403A LYS* 3.1 36.5 + - - +
404A GLU* 3.0 21.7 + - - +
406A ILE* 1.3 83.4 - - - +
408A MET* 1.3 66.6 + - + +
410A ARG* 2.9 7.4 + - - +
411A ALA* 2.7 26.4 + - + -
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Residues in contact with MET 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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400A LEU* 4.0 20.2 - - + -
404A GLU* 3.3 13.2 + - - +
405A GLY* 3.4 7.2 + - - +
407A GLU* 1.3 74.1 - - + +
409A LEU* 1.3 67.4 + - - +
411A ALA* 3.6 6.8 - - - +
412A ALA* 3.0 21.8 + - - +
430A LEU* 4.0 15.9 - - + -
433A LEU* 3.9 31.1 - - + +
434A VAL* 4.8 0.7 - - - -
437A LYS* 4.1 20.6 - - + -
438A TYR* 3.8 33.7 - - + +
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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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405A GLY 3.3 11.3 + - - +
406A ILE* 3.3 7.1 + - - +
407A GLU 2.9 4.4 + - - -
408A MET* 1.3 79.3 - - - +
410A ARG* 1.3 64.0 + - - +
412A ALA* 2.9 9.9 + - - +
414A LYS* 2.9 39.4 + - + +
416A ILE* 3.9 19.1 - - + -
422A LEU* 3.8 20.2 - - + -
426A ASN* 3.7 35.9 - - + +
429A PHE* 4.3 2.2 - - + -
430A LEU* 3.8 36.6 - - + +
433A LEU* 4.0 9.2 - - + -
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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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403A LYS* 3.6 12.9 - - - +
406A ILE* 3.0 31.6 + - - +
407A GLU* 2.9 13.4 + - - +
409A LEU* 1.3 74.7 - - - +
411A ALA* 1.3 55.0 + - - +
413A GLY* 2.7 25.6 + - - -
414A LYS 2.8 16.6 + - - +
415A GLU* 5.2 2.0 - - - +
416A ILE* 3.0 33.9 + - + +
417A GLY* 4.5 0.6 - - - -
418A ASP* 3.2 38.0 + - - +
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Residues in contact with ALA 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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407A GLU* 2.7 23.0 + - + +
408A MET* 3.6 8.5 - - - +
410A ARG* 1.3 73.2 - - - +
412A ALA* 1.3 58.1 + - - +
413A GLY 3.1 3.0 + - - -
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Residues in contact with ALA 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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408A MET 3.0 12.6 + - - +
409A LEU 2.9 6.2 + - - +
411A ALA* 1.3 75.2 - - + +
413A GLY* 1.3 57.9 + - - +
414A LYS* 3.4 3.5 + - - +
429A PHE* 4.4 27.8 - - + -
433A LEU* 4.7 9.2 - - + -
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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