Contacts of the helix formed by residues 391 - 406 (chain A) in PDB entry 5YBD
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 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A ASN* 3.2 36.3 - - - +
377A ILE 2.9 17.0 + - - +
378A MET* 4.2 5.4 - - - +
379A THR* 5.4 8.6 - - + +
389A LYS 3.6 1.4 + - - +
390A PHE* 1.3 69.0 - - - +
392A PHE* 1.3 57.9 + - - +
393A HIS* 3.6 13.7 + - - +
394A GLY* 2.8 27.7 + - - -
395A ILE* 2.9 16.8 + - - +
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Residues in contact with PHE 392 (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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318A LEU* 4.5 13.5 - - + -
332A TRP* 4.2 19.7 - + - -
336A ASN* 3.2 33.7 - - - -
337A GLY* 3.6 18.2 - - - -
390A PHE* 3.4 33.8 + + + -
391A ASP* 1.3 73.1 + - - +
393A HIS* 1.3 53.4 + - - +
395A ILE* 3.6 14.4 - - + +
396A ALA* 2.7 37.1 + - - +
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Residues in contact with HIS 393 (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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391A ASP* 3.1 12.4 + - - +
392A PHE* 1.3 77.9 - - - +
394A GLY* 1.3 59.0 + - - +
396A ALA* 3.3 6.7 + - - +
397A GLN* 2.9 35.5 + - + +
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Residues in contact with GLY 394 (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 LYS 5.5 1.0 - - - +
376A ASN* 3.2 29.8 - - - -
377A ILE* 5.3 2.1 - - - +
391A ASP* 2.8 12.7 + - - -
393A HIS* 1.3 81.5 - - - +
395A ILE* 1.3 62.3 + - - +
397A GLN* 3.3 12.8 - - - +
398A ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 395 (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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314A TRP* 3.9 37.2 - - + -
318A LEU* 5.4 1.3 - - + -
377A ILE* 4.0 31.2 - - + +
390A PHE* 3.9 28.5 - - + -
391A ASP 2.9 19.7 + - - +
392A PHE* 3.7 22.2 - - + +
394A GLY* 1.3 75.5 - - - +
396A ALA* 1.3 63.5 + - - +
398A ALA* 3.1 6.7 + - + +
399A LEU* 3.0 37.0 + - + +
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Residues in contact with ALA 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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392A PHE 2.7 21.9 + - - +
393A HIS* 3.6 7.4 - - - +
395A ILE* 1.3 74.1 - - - +
397A GLN* 1.3 63.8 + - - +
398A ALA 3.1 0.2 + - - -
399A LEU* 3.3 8.2 + - - +
400A LEU* 3.1 33.7 + - + +
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Residues in contact with GLN 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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376A ASN* 6.4 0.4 - - - +
393A HIS* 2.9 20.7 + - + +
394A GLY* 3.3 15.9 - - - +
396A ALA* 1.3 75.6 - - - +
398A ALA* 1.3 62.3 + - + +
400A LEU* 3.8 7.4 - - - +
401A GLU* 3.0 58.2 + - - +
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Residues in contact with ALA 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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377A ILE* 6.0 6.7 - - + -
394A GLY 3.1 15.8 + - - +
395A ILE* 3.6 6.5 - - - +
396A ALA 3.1 0.4 - - - -
397A GLN* 1.3 81.2 - - + +
399A LEU* 1.3 64.9 + - + +
400A LEU 3.0 4.5 - - - -
401A GLU* 3.9 2.5 - - - +
402A HIS* 2.9 27.1 + - - +
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Residues in contact with LEU 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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314A TRP* 4.2 24.9 - - + -
315A GLN* 5.9 1.3 - - - +
395A ILE* 3.0 36.1 + - + +
396A ALA* 4.0 6.7 - - - +
398A ALA* 1.3 77.2 - - + +
400A LEU* 1.3 58.1 + - + +
402A HIS* 4.2 5.6 - - + +
403A HIS* 2.4 45.5 + - + -
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Residues in contact with LEU 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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396A ALA* 3.1 22.1 + - + +
397A GLN* 3.8 6.3 - - - +
398A ALA 3.0 0.4 - - - -
399A LEU* 1.3 78.0 - - + +
401A GLU* 1.3 60.1 + - - +
402A HIS 3.1 1.3 + - - -
403A HIS* 3.3 4.6 + - - +
404A HIS* 3.0 29.5 + - - +
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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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397A GLN* 3.0 40.9 + - - +
398A ALA* 4.1 3.3 - - - +
400A LEU* 1.3 76.8 - - - +
402A HIS* 1.3 65.1 + - - +
404A HIS* 4.4 5.2 - - + -
405A HIS* 3.0 68.1 + - + +
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Residues in contact with HIS 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 ALA 2.9 19.4 + - - +
399A LEU* 3.6 11.6 - - + +
401A GLU* 1.3 79.7 - - - +
403A HIS* 1.3 75.6 + + - +
405A HIS* 3.6 2.5 - - - +
406A HIS* 2.8 72.0 + + - -
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Residues in contact with HIS 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 LEU* 2.4 42.0 + - + +
400A LEU* 3.3 4.8 + - - +
402A HIS* 1.3 91.9 - + + +
404A HIS* 1.3 68.9 + - - +
406A HIS* 3.5 22.0 + - - +
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Residues in contact with HIS 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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400A LEU 3.0 17.5 + - - +
401A GLU* 3.9 7.6 - - - +
403A HIS* 1.3 78.4 - - - +
405A HIS* 1.3 77.2 + + + +
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Residues in contact with HIS 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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401A GLU* 3.0 48.6 + - + +
402A HIS* 3.6 4.0 - - - +
404A HIS* 1.3 93.9 - + + +
406A HIS* 1.3 76.9 + + + +
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Residues in contact with HIS 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 HIS* 2.8 61.5 + + - -
403A HIS* 3.5 20.0 + - - +
404A HIS 4.7 0.2 - - - -
405A HIS* 1.3 91.1 - + + +
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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