Contacts of the helix formed by residues 541 - 552 (chain A) in PDB entry 5Y36
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A PHE 3.6 2.5 + - - -
540A LEU* 1.3 72.4 - - - +
542A GLY* 1.4 60.9 + - - +
543A GLU* 4.1 5.5 + - - +
544A GLN* 2.8 39.9 + - - +
545A LYS* 2.9 29.8 + - - +
684A LYS 4.4 0.9 - - - -
685A SER* 5.8 0.7 - - - -
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Residues in contact with GLY 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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521A TYR* 5.3 1.0 - - - -
541A SER* 1.4 72.5 - - - +
543A GLU* 1.3 56.3 + - - +
545A LYS* 3.4 4.5 + - - +
546A LYS* 3.0 28.6 + - - +
684A LYS* 3.0 35.0 + - - +
685A SER* 4.1 15.0 + - - +
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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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541A SER* 3.4 5.5 + - - +
542A GLY* 1.3 73.4 - - - +
544A GLN* 1.4 58.0 + - + +
546A LYS* 3.6 10.3 + - + +
547A ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 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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529A TYR* 3.0 38.9 + - - -
539A PHE 4.5 0.2 - - - +
540A LEU* 3.8 12.1 - - + +
541A SER* 2.8 43.5 + - - +
543A GLU* 1.4 74.6 - - + +
545A LYS* 1.4 58.9 + - - +
547A ALA* 3.4 3.1 + - - -
548A ILE* 3.0 36.0 + - - +
568A TYR* 3.3 19.6 + - - +
569A PHE* 5.3 0.2 - - - -
573A GLU* 2.8 24.3 + - - +
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Residues in contact with LYS 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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521A TYR* 3.8 26.2 - - + +
524A LEU* 3.6 24.7 - - + +
525A THR* 2.8 46.2 + - - +
540A LEU* 3.3 35.7 + - + -
541A SER 2.9 12.8 + - - +
542A GLY* 3.6 7.4 - - - +
544A GLN* 1.4 74.9 - - - +
546A LYS* 1.3 61.4 + - - +
548A ILE* 3.5 2.9 + - - +
549A VAL* 3.1 28.1 + - - +
683A LEU 3.7 12.8 + - - +
684A LYS 3.9 18.0 + - - +
685A SER* 5.6 0.6 - - - +
686A ASP* 6.0 0.2 + - - -
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Residues in contact with LYS 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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521A TYR* 4.1 18.9 - - - +
542A GLY 3.0 17.7 + - - +
543A GLU* 3.7 9.4 - - + +
545A LYS* 1.3 74.9 - - - +
547A ALA* 1.4 52.1 + - - +
549A VAL* 3.3 5.1 + - + +
550A ASP* 2.8 66.6 + - - +
684A LYS* 6.2 5.4 - - + +
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Residues in contact with ALA 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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543A GLU 2.9 19.4 + - - +
544A GLN* 3.4 8.0 + - - +
546A LYS* 1.4 75.3 - - - +
548A ILE* 1.4 55.0 + - - +
550A ASP* 3.4 8.2 + - - +
551A LEU* 2.9 32.9 + - - +
568A TYR* 3.8 18.2 - - + +
572A ILE* 4.2 17.1 - - + +
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Residues in contact with ILE 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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524A LEU* 3.9 13.0 - - + -
540A LEU* 3.5 35.2 - - + -
544A GLN 3.0 16.9 + - - +
545A LYS* 3.8 4.7 - - - +
546A LYS 3.4 0.2 - - - -
547A ALA* 1.4 73.8 - - - +
549A VAL* 1.4 58.1 + - - +
552A LEU* 2.8 43.3 + - + +
553A PHE* 3.3 27.6 + - + -
559A VAL* 5.0 2.7 - - + -
564A LEU* 3.9 20.9 - - + -
568A TYR* 3.4 31.0 - - + -
587A PHE* 6.2 0.2 - - + -
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Residues in contact with VAL 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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517A TYR* 4.0 29.8 - - + -
520A VAL* 3.8 29.2 - - + -
521A TYR* 4.2 18.2 - - + +
524A LEU* 4.0 6.3 - - + -
545A LYS 3.1 15.4 + - - +
546A LYS* 3.3 10.3 + - + +
548A ILE* 1.4 74.3 - - - +
550A ASP* 1.3 65.6 + - - +
553A PHE* 3.6 12.7 - - + +
554A LYS* 3.2 34.4 + - + +
591A LEU* 5.0 1.3 - - + -
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Residues in contact with ASP 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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546A LYS* 2.8 58.4 + - - +
547A ALA* 3.7 7.9 + - - +
549A VAL* 1.3 75.6 - - - +
551A LEU* 1.3 59.1 + - - +
554A LYS* 2.9 45.4 + - - +
555A THR* 5.3 1.0 - - - +
608A ASP* 5.5 4.1 - - - +
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Residues in contact with LEU 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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547A ALA 2.9 17.7 + - - +
548A ILE 4.2 0.2 - - - +
550A ASP* 1.3 76.3 - - - +
552A LEU* 1.3 68.7 + - + +
554A LYS 4.3 0.2 - - - -
555A THR* 2.7 46.2 + - + +
567A ASP* 4.3 9.4 - - + +
568A TYR* 3.7 32.5 - - + +
571A LYS* 5.5 9.4 - - + +
572A ILE* 3.6 28.3 - - + -
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Residues in contact with LEU 552 (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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548A ILE* 2.8 21.1 + - + +
551A LEU* 1.3 94.5 - - + +
553A PHE* 1.4 58.0 + - - +
555A THR* 3.2 6.8 + - - +
556A ASN* 3.0 31.4 + - - +
559A VAL* 3.7 29.5 - - + +
563A GLN* 4.0 30.2 - - + +
564A LEU* 3.6 40.2 - - + +
567A ASP* 4.2 11.4 - - + +
568A TYR* 4.0 8.7 - - + -
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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