Contacts of the helix formed by residues 423 - 429 (chain A) in PDB entry 5HAN
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 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A CYS* 4.3 0.4 - - - -
421A GLY 4.2 0.6 + - - -
422A ALA* 1.4 69.0 - - - +
424A PRO* 1.3 76.6 - - - +
425A VAL* 3.6 14.2 + - - +
426A GLU* 3.0 44.2 + - + +
427A PHE* 2.8 22.0 + - - +
449A TYR* 5.3 2.8 - - - -
455A LYS* 5.6 0.3 + - - -
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Residues in contact with PRO 424 (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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378A PRO* 4.1 19.3 - - + -
417A CYS* 3.7 15.7 - - - -
422A ALA 3.4 7.8 - - - +
423A ASP* 1.3 89.5 - - - +
425A VAL* 1.3 56.1 + - - +
428A ALA* 2.9 30.5 + - - +
434A PHE* 3.3 20.9 - - + -
438A PHE* 4.4 2.0 - - + -
449A TYR* 3.5 42.4 - - + +
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Residues in contact with VAL 425 (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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423A ASP* 3.2 13.3 + - - +
424A PRO* 1.3 75.1 - - - +
426A GLU* 1.3 68.1 + - - +
428A ALA* 3.2 19.7 + - - +
429A LYS* 3.4 0.3 + - - +
438A PHE* 3.9 9.9 - - + -
449A TYR* 3.6 38.8 - - + -
450A PRO 5.9 0.9 - - - +
452A TRP* 4.4 9.2 - - + -
455A LYS* 3.5 36.6 - - + -
456A LEU* 3.3 20.2 - - + +
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Residues in contact with GLU 426 (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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423A ASP* 3.0 32.6 + - + +
425A VAL* 1.3 74.4 - - - +
427A PHE* 1.4 64.3 + - - +
429A LYS* 3.0 53.5 + - - +
430A ASP* 4.0 6.6 - - - +
455A LYS* 2.5 36.1 + - - +
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Residues in contact with PHE 427 (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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413A GLN* 3.4 30.3 - - + -
416A GLN* 4.3 6.1 - - + -
417A CYS* 3.5 35.7 - - + -
420A GLN* 3.5 28.3 - - - -
422A ALA* 3.9 13.2 - - + +
423A ASP 2.8 18.9 + - - +
424A PRO 3.9 0.7 - - - +
426A GLU* 1.4 71.5 - - - +
428A ALA* 1.3 61.3 + - - +
430A ASP* 3.2 9.9 + - - +
431A HIS* 2.8 74.5 + + + -
434A PHE* 3.7 16.8 - + - -
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Residues in contact with ALA 428 (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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424A PRO 2.9 19.4 + - - +
425A VAL 3.2 8.7 + - - +
427A PHE* 1.3 73.8 - - - +
429A LYS* 1.3 62.3 + - - +
430A ASP 3.1 0.2 + - - -
431A HIS 3.0 22.5 + - - +
434A PHE* 3.7 20.9 - - + -
435A ALA* 3.3 14.2 - - + +
438A PHE* 3.9 7.4 - - + -
456A LEU* 3.6 24.7 - - + -
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Residues in contact with LYS 429 (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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425A VAL 3.4 1.7 + - - +
426A GLU* 3.0 54.5 + - - +
428A ALA* 1.3 77.2 - - - +
430A ASP* 1.3 65.8 + - - +
431A HIS 5.5 0.2 - - - -
455A LYS* 3.8 38.9 + - - +
456A LEU* 3.7 17.9 - - + -
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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