Contacts of the helix formed by residues 419 - 428 (chain B) in PDB entry 4Y72
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 SER 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B ILE* 4.7 2.9 - - - +
415B PRO 4.1 0.8 + - - -
416B GLN* 3.0 22.5 + - - -
417B LEU 3.3 1.4 - - - -
418B ASN* 1.3 81.6 - - - +
420B ALA* 1.3 59.9 + - - +
421B LEU* 3.7 11.8 + - - +
422B VAL* 3.2 21.7 + - - +
423B GLN* 3.0 24.9 + - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ASN 3.9 0.2 + - - -
419B SER* 1.3 71.3 - - - +
421B LEU* 1.3 56.6 + - - +
423B GLN* 3.4 10.9 - - - +
424B ASP* 2.7 48.7 + - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 4.4 6.3 - - + -
353B LYS* 4.1 40.2 - - + +
354B ILE* 4.6 8.1 - - + -
419B SER* 3.8 10.4 - - - +
420B ALA* 1.3 79.5 - - - +
422B VAL* 1.3 62.3 + - - +
424B ASP* 4.2 4.4 - - - +
425B LEU* 3.2 50.1 + - + +
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 5.1 3.8 - - + -
354B ILE* 3.2 36.1 - - + -
383B ALA* 3.6 25.0 - - + +
386B VAL* 4.1 16.4 - - + -
387B VAL* 4.4 7.6 - - + -
416B GLN 4.2 1.3 - - - +
417B LEU* 3.4 27.4 - - + +
419B SER* 3.2 17.8 + - - +
420B ALA 3.2 0.2 - - - -
421B LEU* 1.3 77.8 - - + +
423B GLN* 1.3 66.9 + - - +
425B LEU* 3.5 1.2 + - - -
426B ALA* 3.0 22.5 + - - +
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B VAL* 4.0 13.9 - - - +
391B GLN* 2.9 32.9 + - - +
417B LEU 5.3 0.4 + - - -
418B ASN* 4.5 16.5 + - - +
419B SER 3.0 19.8 + - - +
420B ALA* 3.4 14.1 - - - +
422B VAL* 1.3 77.1 - - - +
424B ASP* 1.3 62.3 + - - +
426B ALA* 3.0 20.7 + - - +
427B LYS* 3.0 29.2 + - + +
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ALA* 2.7 31.0 + - - +
421B LEU* 4.3 3.9 - - - +
423B GLN* 1.3 74.5 - - - +
425B LEU* 1.3 67.4 + - - +
427B LYS* 3.4 13.8 + - - +
428B ALA* 3.3 21.0 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 3.7 30.3 - - + -
353B LYS* 5.0 2.7 - - + -
376B LEU* 3.8 29.6 - - + -
379B MET* 4.3 15.7 - - + +
380B GLN* 3.5 36.5 - - + +
383B ALA* 3.8 16.8 - - + -
421B LEU* 3.2 35.8 + - + +
422B VAL* 4.8 0.4 - - - -
424B ASP* 1.3 77.9 - - - +
426B ALA* 1.3 62.0 + - - +
428B ALA* 3.3 9.3 + - - +
429B VAL* 4.0 0.2 - - - +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B GLN 4.0 10.5 - - - -
383B ALA* 3.7 3.1 - - - +
384B LYS* 3.6 30.0 - - + +
387B VAL* 3.7 17.3 - - + -
422B VAL 3.0 14.9 + - - +
423B GLN 3.0 8.9 + - - +
425B LEU* 1.3 77.5 - - - +
427B LYS* 1.3 59.8 + - + +
428B ALA 3.3 0.2 - - - -
429B VAL* 3.0 21.8 - - - +
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Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLN* 3.0 26.5 + - + +
424B ASP* 4.0 15.0 - - - +
425B LEU 3.3 0.4 - - - -
426B ALA* 1.3 79.1 - - + +
428B ALA* 1.3 57.7 + - - +
429B VAL* 3.0 7.9 + - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLN* 3.1 36.3 + - - +
424B ASP 3.3 14.9 + - - +
425B LEU* 3.3 3.8 + - - +
426B ALA 3.3 1.2 - - - -
427B LYS* 1.3 75.3 - - - +
429B VAL* 1.3 58.6 + - - -
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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