Contacts of the helix formed by residues 395 - 405 (chain A) in PDB entry 1YA8
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 LEU 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ILE* 3.8 14.1 - - + -
392A ALA* 3.0 37.4 + - + +
394A GLU* 1.3 90.1 - - + +
396A ILE* 1.3 65.6 + - - +
397A PRO* 3.3 1.1 - - - -
398A GLU* 3.0 21.5 + - - +
399A ALA* 3.1 12.2 + - - +
550A LEU* 3.7 43.0 - - + +
551A PHE* 4.6 12.6 - - + +
553A LYS* 4.4 25.1 - - + +
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Residues in contact with ILE 396 (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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379A MET* 3.4 33.0 - - + +
382A LEU* 3.5 40.2 - - + +
383A TRP* 4.1 6.7 - - + +
391A ILE* 4.0 17.7 - - + +
392A ALA 3.2 15.9 + - - +
393A LYS* 3.5 21.3 - - + +
395A LEU* 1.3 75.4 - - - +
397A PRO* 1.3 59.2 - - + +
399A ALA* 3.1 6.5 + - - -
400A THR* 2.6 54.6 + - - +
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Residues in contact with PRO 397 (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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379A MET* 3.6 30.6 - - + +
393A LYS 3.6 11.0 - - - +
394A GLU* 3.9 8.7 - - - +
395A LEU 3.4 4.7 - - - -
396A ILE* 1.3 94.0 - - + +
398A GLU* 1.3 56.5 + - - +
400A THR* 3.8 0.5 - - - -
401A GLU* 2.8 35.3 + - - +
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Residues in contact with GLU 398 (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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394A GLU 5.2 1.5 + - - +
395A LEU* 3.0 14.4 + - - +
397A PRO* 1.3 78.6 - - - +
399A ALA* 1.3 62.6 + - - +
401A GLU* 3.6 4.7 - - - +
402A LYS* 3.2 22.0 + - - +
546A PHE* 4.1 15.8 - - + -
550A LEU* 3.8 27.2 + - + +
553A LYS 5.8 0.2 - - - +
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Residues in contact with ALA 399 (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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382A LEU* 4.6 8.7 - - + -
391A ILE* 5.1 2.9 - - + -
395A LEU 3.1 7.1 + - - +
396A ILE* 3.5 10.1 - - - +
398A GLU* 1.3 77.0 - - - +
400A THR* 1.3 67.5 + - - +
402A LYS* 3.0 18.5 + - - +
403A TYR* 3.4 11.6 + - - -
420A LEU* 4.9 2.5 - - + -
546A PHE* 3.8 6.5 - - - -
547A TRP* 3.9 18.4 - - + -
550A LEU* 3.4 28.2 - - + +
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Residues in contact with THR 400 (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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375A GLN* 3.3 23.3 - - - +
378A ALA* 3.7 8.1 - - + -
379A MET* 3.2 29.7 - - + +
382A LEU* 3.5 12.4 - - - +
396A ILE* 2.6 33.4 + - - +
397A PRO* 3.8 2.2 - - - -
399A ALA* 1.3 73.1 - - - +
401A GLU* 1.3 57.9 + - - +
403A TYR* 3.4 1.5 + - - +
404A LEU* 2.9 50.8 + - + +
417A PHE* 6.0 0.7 - - + -
420A LEU* 5.6 3.1 - - - -
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Residues in contact with GLU 401 (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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375A GLN* 3.7 16.7 + - - +
379A MET* 5.9 1.6 - - - +
397A PRO 2.8 20.4 + - - +
398A GLU* 3.6 6.7 - - - +
400A THR* 1.3 78.0 - - - +
402A LYS* 1.3 59.5 + - - +
405A GLY* 2.6 56.8 + - - +
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Residues in contact with LYS 402 (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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398A GLU 3.2 5.5 + - - +
399A ALA 3.0 11.3 + - - +
401A GLU* 1.3 80.9 - - - +
403A TYR* 1.3 67.1 + - + +
405A GLY* 4.4 1.6 + - - -
406A GLY 5.0 1.6 + - - -
542A LYS* 5.7 14.7 - - - +
546A PHE* 3.6 57.6 - - + +
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Residues in contact with TYR 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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399A ALA 3.4 8.7 + - - +
400A THR* 4.2 3.6 - - - +
401A GLU 3.3 0.2 - - - -
402A LYS* 1.3 90.5 - - + +
404A LEU* 1.3 65.8 + - + +
405A GLY 3.2 2.6 + - - -
406A GLY* 3.7 4.3 + - - -
416A LEU* 2.9 58.2 - - + +
419A ASP* 3.8 12.1 - - + -
420A LEU* 3.3 45.1 - - + -
423A ASP* 3.1 24.4 + - - +
542A LYS* 6.2 0.9 - - - -
543A GLU* 3.7 10.2 - - + +
546A PHE* 4.3 10.5 - + - -
547A TRP* 2.9 32.7 + + - -
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Residues in contact with LEU 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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373A LEU* 5.2 1.3 - - + -
374A ASP 5.5 0.2 - - - -
375A GLN* 3.2 21.7 - - - +
378A ALA* 3.2 35.0 - - + -
400A THR* 2.9 27.2 + - + +
403A TYR* 1.3 71.1 - - + +
405A GLY* 1.3 56.7 + - - +
406A GLY 3.0 10.3 + - - -
407A THR 3.5 8.7 + - - +
413A LYS* 3.3 56.6 + - + +
416A LEU* 3.7 12.3 - - + +
417A PHE* 3.5 29.6 - - + +
420A LEU* 6.3 1.1 - - + -
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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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375A GLN* 3.5 6.0 + - - -
401A GLU* 2.6 47.1 + - - +
402A LYS 5.2 1.3 - - - -
403A TYR 3.2 0.6 - - - -
404A LEU* 1.3 71.3 - - - +
406A GLY* 1.3 65.3 + - - +
407A THR 4.6 1.6 - - - -
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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