Contacts of the helix formed by residues 446 - 455 (chain A) in PDB entry 1Y0P
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 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ALA* 3.2 5.0 - - - +
445A ASP* 1.3 83.5 + - - +
447A LEU* 1.3 59.5 + - - +
448A VAL* 3.7 8.5 + - - +
449A LYS* 3.1 32.4 + - - +
450A LEU* 3.1 26.7 + - - +
494A TYR* 4.0 11.7 - - - -
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Residues in contact with LEU 447 (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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420A ILE* 4.2 15.9 - - + -
446A SER* 1.3 71.9 - - - +
448A VAL* 1.3 60.2 + - - +
450A LEU* 4.2 6.1 - - + -
451A GLY* 2.8 26.5 + - - -
458A GLY* 4.1 2.8 - - - -
461A LEU* 3.7 32.0 - - + +
462A THR* 3.6 28.7 - - + +
465A VAL* 3.6 36.1 - - + -
494A TYR* 3.6 45.4 - - + +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 3.3 7.4 + - - +
447A LEU* 1.3 77.0 - - - +
449A LYS* 1.3 62.1 + - + +
451A GLY* 3.9 0.5 - - - -
452A LYS* 3.0 30.0 + - + +
458A GLY* 3.7 29.7 - - - +
459A LYS* 4.3 5.6 - - + +
462A THR* 3.7 9.7 + - + +
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Residues in contact with LYS 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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444A ALA* 3.8 11.7 - - + -
445A ASP* 2.8 37.1 + - - +
446A SER* 3.1 22.6 + - - +
448A VAL* 1.3 79.4 - - + +
450A LEU* 1.3 64.8 + - - +
452A LYS* 3.2 7.6 + - - +
453A MET* 3.0 31.3 + - - +
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Residues in contact with LEU 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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420A ILE* 4.7 4.7 - - + -
442A PRO 3.6 29.8 - - - +
443A THR* 4.1 10.8 - - - -
444A ALA* 3.7 6.8 - - + +
446A SER 3.1 17.0 + - - +
447A LEU* 3.8 14.1 - - + +
449A LYS* 1.3 74.5 - - - +
451A GLY* 1.3 64.1 + - - +
453A MET* 3.2 11.4 + - + +
454A GLU* 3.1 32.6 + - + +
456A ILE* 5.6 1.1 - - + -
461A LEU* 4.9 3.6 - - + -
494A TYR* 3.7 23.3 - - + -
495A TYR 3.7 26.7 - - - +
496A ALA* 3.9 16.6 - - + +
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Residues in contact with GLY 451 (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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447A LEU 2.8 18.5 + - - -
448A VAL 3.9 1.1 - - - -
450A LEU* 1.3 77.6 - - - +
452A LYS* 1.3 56.5 + - - +
455A GLY* 2.9 28.6 + - - -
456A ILE* 2.9 39.1 + - - +
458A GLY* 4.4 2.2 - - - -
461A LEU* 4.3 6.2 - - - +
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Residues in contact with LYS 452 (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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448A VAL* 3.0 16.8 + - + +
449A LYS* 3.2 9.8 + - - +
451A GLY* 1.3 76.2 - - - +
453A MET* 1.3 64.3 + - + +
454A GLU 3.4 0.5 + - - -
455A GLY* 3.8 5.6 + - - -
458A GLY* 5.2 1.0 - - - +
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Residues in contact with MET 453 (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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442A PRO* 4.2 22.2 - - + -
443A THR 3.5 26.0 - - - +
444A ALA* 3.9 14.1 - - - -
449A LYS* 3.0 21.0 + - - +
450A LEU* 3.2 10.7 + - + +
452A LYS* 1.3 78.6 - - + +
454A GLU* 1.3 70.4 + - - +
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Residues in contact with GLU 454 (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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390A ARG* 5.4 0.7 + - - -
418A TYR* 3.1 41.4 + - + -
442A PRO* 3.3 33.5 - - + +
450A LEU* 3.1 20.0 + - + +
453A MET* 1.3 92.3 - - + +
455A GLY* 1.3 61.4 + - - +
456A ILE* 4.1 10.1 - - + -
496A ALA* 4.1 21.5 - - + -
498A GLU* 5.6 1.6 + - - +
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Residues in contact with GLY 455 (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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390A ARG* 3.9 24.9 + - - +
451A GLY 2.9 6.0 + - - -
452A LYS* 3.8 4.6 + - - -
453A MET 3.6 2.2 - - - -
454A GLU* 1.3 80.3 - - - +
456A ILE* 1.3 60.7 + - - +
457A ASP 4.3 0.2 + - - -
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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