Contacts of the helix formed by residues 445 - 450 (chain A) in PDB entry 1YC0
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 ALA 445 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A SER* 1.3 79.7 + - - +
446A ALA* 1.3 65.8 + - - +
447A HIS* 3.5 30.1 - - + -
448A CYS* 3.2 22.5 + - - +
449A PHE* 3.9 0.3 - - - -
497A ASP* 3.6 13.2 - - - +
499A VAL* 3.4 8.2 - - - +
599A GLY* 3.5 21.8 - - - +
615A ILE* 4.1 4.0 - - + -
616A ILE 4.0 5.4 - - - +
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Residues in contact with ALA 446 (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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445A ALA* 1.3 69.2 - - - +
447A HIS* 1.3 61.8 + - - +
449A PHE* 2.8 21.9 + - - +
450A SER* 3.0 10.2 + - - -
484A PRO* 4.4 5.7 - - + +
488A TYR* 3.4 38.3 - - + -
497A ASP* 2.9 9.5 + - - +
498A LEU 3.4 26.6 - - - +
499A VAL* 3.7 13.8 - - + +
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Residues in contact with HIS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA* 3.5 16.2 - - + -
446A ALA* 1.3 76.8 - - - +
448A CYS* 1.3 68.5 + - - +
450A SER* 2.8 21.4 + - - +
451A HIS* 4.1 8.7 - - - -
488A TYR* 3.4 11.5 + - - +
493A PRO 3.7 15.7 - - - +
497A ASP* 2.6 36.9 + - - -
598A SER* 2.7 33.2 + - - -
617A SER 3.3 16.4 - - - -
259I CYS* 3.4 33.1 - - + +
260I ARG 3.8 0.4 + - - -
261I GLY* 3.8 1.1 + - - -
263I PHE* 4.4 1.3 - + - -
281I GLY 4.0 8.5 - - - -
282I GLY* 4.2 5.0 - - - +
283I CYS* 4.4 7.6 - - + -
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Residues in contact with CYS 448 (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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427A ILE* 3.7 16.5 - - + +
432A CYS* 2.0 50.7 - - + -
444A SER* 4.5 1.6 - - - +
445A ALA* 3.2 22.1 + - - +
446A ALA 3.0 0.6 + - - -
447A HIS* 1.3 84.7 - - - +
449A PHE* 1.3 66.1 + - + +
450A SER 3.5 0.2 - - - -
451A HIS* 4.8 1.0 + - - -
453A PRO* 4.9 1.4 - - - +
598A SER* 3.8 18.6 - - - -
263I PHE* 3.3 25.9 - - - -
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Residues in contact with PHE 449 (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 ILE* 3.9 17.9 - - + -
427A ILE* 3.9 15.3 - - + -
444A SER* 4.3 6.1 - - - -
445A ALA 3.9 7.4 - - - -
446A ALA* 2.8 8.4 + - - +
448A CYS* 1.3 86.3 - - + +
450A SER* 1.3 56.6 + - - +
451A HIS 3.1 10.7 + - - -
452A SER* 3.1 14.8 + - - -
453A PRO* 3.6 18.0 - - + +
458A VAL* 4.1 20.6 - - + -
479A ILE* 4.8 0.9 - - + -
482A TYR* 3.6 49.9 - + + -
484A PRO* 6.1 2.5 - - + -
499A VAL* 3.9 17.5 - - + -
501A ILE* 3.3 34.5 - - + -
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Residues in contact with SER 450 (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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446A ALA 3.0 3.9 + - - -
447A HIS* 2.8 20.5 + - - +
448A CYS 3.5 0.2 - - - -
449A PHE* 1.3 76.4 - - - +
451A HIS* 1.3 74.6 + - - +
452A SER* 3.3 5.5 + - - -
488A TYR* 3.4 33.7 - - - -
490A VAL* 4.1 23.4 - - - +
493A PRO* 5.3 4.0 - - - +
282I GLY 4.1 3.6 + - - -
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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