Contacts of the helix formed by residues 540 - 551 (chain A) in PDB entry 1YA8
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 LYS 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ILE* 3.8 21.3 - - + -
352A LYS 5.3 6.8 + - - -
419A ASP* 5.9 1.0 - - - +
423A ASP* 3.0 40.3 + - - +
427A GLY* 4.2 22.4 - - - +
431A VAL* 4.0 9.9 - - + -
448A GLU* 4.8 6.2 + - - -
538A LYS 3.2 2.2 + - - -
539A LEU* 1.3 88.8 - - + +
541A ASP* 1.3 64.8 + - - +
542A LYS 3.2 3.1 - - - -
543A GLU* 3.0 22.9 + - + +
544A VAL* 2.9 26.3 + - + +
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Residues in contact with ASP 541 (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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435A ARG* 3.3 20.7 + - - +
524A GLU* 3.0 21.5 - - - +
538A LYS* 3.1 42.4 + - + +
539A LEU 2.8 6.0 + - - -
540A LYS* 1.3 76.6 - - - +
542A LYS* 1.3 64.2 + - - +
544A VAL* 3.6 3.5 + - - +
545A ALA* 3.3 22.0 + - - +
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Residues in contact with LYS 542 (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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402A LYS* 5.7 14.6 - - - +
403A TYR* 6.2 1.0 - - - -
540A LYS 3.2 0.6 - - - -
541A ASP* 1.3 79.9 + - - +
543A GLU* 1.3 88.7 + - - +
545A ALA* 3.4 8.3 - - - +
546A PHE* 3.1 20.8 + - + +
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Residues in contact with GLU 543 (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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403A TYR* 3.7 12.2 - - + +
423A ASP* 2.7 28.8 - - - +
428A VAL* 4.0 11.9 - - + -
540A LYS* 3.0 34.8 + - + +
542A LYS* 1.3 97.4 + - - +
544A VAL* 1.3 68.3 + - - +
545A ALA 3.0 1.8 - - - -
546A PHE* 3.0 7.0 + - - -
547A TRP* 2.8 34.8 + - + -
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Residues in contact with VAL 544 (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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428A VAL* 3.5 31.1 - - + +
431A VAL* 3.9 28.5 - - + -
432A ILE* 4.0 15.9 - - + -
435A ARG* 3.4 24.5 - - - +
540A LYS* 2.9 25.6 + - + +
541A ASP* 3.7 8.1 - - - +
543A GLU* 1.3 76.9 - - - +
545A ALA* 1.3 58.4 + - - +
547A TRP* 3.4 1.9 + - - +
548A THR* 2.6 37.2 + - - +
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Residues in contact with ALA 545 (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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541A ASP* 3.3 12.3 + - - +
542A LYS* 3.4 11.2 - - - +
543A GLU 3.0 0.2 - - - -
544A VAL* 1.3 77.2 - - - +
546A PHE* 1.3 68.2 + - - +
548A THR* 3.1 15.8 + - - -
549A ASN* 2.9 23.4 + - - +
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Residues in contact with PHE 546 (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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398A GLU* 4.1 19.5 - - + -
399A ALA* 3.8 9.6 - - - -
402A LYS* 3.6 59.9 - - + +
403A TYR* 4.3 4.9 - + - -
542A LYS* 3.1 10.7 + - + +
543A GLU* 3.0 9.7 + - - +
545A ALA* 1.3 80.2 - - - +
547A TRP* 1.3 88.4 + + - +
549A ASN* 3.4 9.2 + - - +
550A LEU* 3.1 54.7 + - + +
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Residues in contact with TRP 547 (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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391A ILE* 3.7 26.5 - - + -
399A ALA* 3.9 10.5 - - + -
403A TYR* 2.9 28.9 + + - -
420A LEU* 3.2 33.9 - - + -
423A ASP* 4.3 3.4 - - - +
424A VAL* 3.4 26.9 - - + -
428A VAL* 3.8 28.0 - - + -
543A GLU* 2.8 30.3 + - + +
544A VAL 3.8 2.7 - - - +
546A PHE* 1.3 84.1 - + - +
548A THR* 1.3 60.7 + - - +
549A ASN 3.4 0.2 - - - -
550A LEU* 3.7 25.4 - - + -
551A PHE* 3.1 62.5 + + + +
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Residues in contact with THR 548 (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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428A VAL* 5.4 0.3 - - - +
432A ILE* 5.1 6.9 - - - +
544A VAL* 2.6 31.5 + - - +
545A ALA* 3.1 8.6 + - - -
547A TRP* 1.3 77.2 - - - +
549A ASN* 1.3 67.4 + - - +
551A PHE* 4.1 2.9 - - - +
552A ALA* 3.3 21.7 + - + +
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Residues in contact with ASN 549 (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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545A ALA* 2.9 26.3 + - - +
546A PHE* 3.9 8.1 + - - +
548A THR* 1.3 81.5 - - - +
550A LEU* 1.3 59.7 + - - +
552A ALA* 2.7 34.4 + - - +
553A LYS 4.4 3.3 - - - -
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Residues in contact with LEU 550 (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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391A ILE* 5.2 0.7 - - + -
395A LEU* 3.7 48.1 - - + +
398A GLU* 3.8 30.3 + - - +
399A ALA* 3.4 32.8 - - + -
546A PHE* 3.1 35.3 + - + +
547A TRP* 3.7 22.4 - - + +
549A ASN* 1.3 79.5 - - - +
551A PHE* 1.3 61.7 + - + +
553A LYS* 3.4 11.0 + - - +
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Residues in contact with PHE 551 (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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389A VAL 4.3 5.2 - - - -
390A CYS 3.9 17.3 - - - -
391A ILE* 4.0 24.7 - - + -
395A LEU* 4.6 11.0 - - + +
424A VAL* 4.1 23.6 - - + -
547A TRP* 3.1 50.4 + + + +
548A THR* 4.2 3.4 - - - +
550A LEU* 1.3 74.8 - - + +
552A ALA* 1.3 57.0 + - - +
553A LYS* 2.9 15.8 + - - +
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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