Contacts of the helix formed by residues 453 - 457 (chain A) in PDB entry 3MYV
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 PHE 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.8 26.7 - + - -
156A TYR* 4.1 0.9 - - - -
446A ASP* 3.8 23.1 - - + -
448A GLU 5.3 3.6 - - - +
449A VAL* 3.9 31.2 - - + -
450A ASP* 3.1 24.4 + - - +
452A ASP* 1.3 76.7 - - - +
454A TYR* 1.3 74.8 + + - +
455A LYS* 3.8 29.2 - - + -
456A CYS* 2.9 41.1 + - - +
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Residues in contact with TYR 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 3.6 12.9 + - - +
452A ASP 3.5 5.8 + - - +
453A PHE* 1.3 83.5 - + - +
455A LYS* 1.3 98.1 + - + +
456A CYS 3.3 1.7 + - - -
457A VAL* 3.6 14.0 - - - +
475A PRO* 3.5 18.4 - - + +
476A GLY* 3.5 41.8 + - - -
477A TYR* 3.6 30.9 - + - -
478A PRO* 5.8 0.4 - - + -
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 5.1 1.2 + - - -
70A LYS* 4.6 2.6 + - - -
88A MSE 4.7 2.6 + - - -
89A PHE* 3.0 54.4 + - + +
90A ASN* 5.0 1.6 - - - +
91A HIS* 4.6 8.2 + - + +
446A ASP* 5.1 3.3 + - - -
453A PHE* 3.0 31.3 + - + -
454A TYR* 1.3 115.7 + - + +
456A CYS* 1.3 57.2 + - - +
457A VAL 3.0 11.3 + - - +
477A TYR* 3.4 27.0 + - + +
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Residues in contact with CYS 456 (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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66A TYR* 4.0 6.9 + - - -
89A PHE* 4.4 3.4 - - - -
152A ARG 4.8 4.3 - - - +
153A CYS 4.8 0.3 - - - +
156A TYR* 3.4 32.8 - - - -
157A PRO* 4.7 5.2 - - - +
424A PHE* 3.7 22.7 - - + -
428A LEU* 3.4 26.3 - - + +
449A VAL* 4.8 2.0 - - + -
450A ASP 3.9 5.8 - - - +
451A TRP* 3.9 16.6 - - - -
453A PHE* 2.9 26.3 + - + +
455A LYS* 1.3 76.3 - - - +
457A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 457 (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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66A TYR* 4.2 2.2 - - - -
152A ARG 5.2 0.2 - - - +
153A CYS 3.5 9.4 - - - +
154A PHE 3.8 1.6 - - - +
155A GLY* 3.1 42.0 - - - +
156A TYR* 3.6 25.1 - - + +
454A TYR 3.6 13.0 - - - +
455A LYS 3.4 7.0 - - - +
456A CYS* 1.3 83.6 - - - +
458A LEU* 1.3 54.2 + - - +
474A ASN* 3.4 35.7 - - + +
477A TYR* 2.7 28.4 + - - -
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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