Contacts of the strand formed by residues 540 - 546 (chain C) in PDB entry 5Y7K
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 TYR 540 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531C PRO* 4.1 18.8 - - + -
532C PRO 5.2 1.0 + - - -
533C HIS 3.9 4.5 + - - -
534C PHE* 3.7 21.3 - + - -
535C ASP* 3.0 43.0 + - - +
538C LYS* 3.2 40.9 + - - -
539C LYS* 1.3 77.0 - - - +
541C PRO* 1.3 70.3 - - + +
542C LEU 3.7 0.9 + - - -
572C ASN* 3.5 26.0 - - + +
574C ILE* 3.7 30.7 - - + +
618C PHE 2.9 17.4 + - - -
619C VAL* 3.5 7.4 - - - +
620C ASP* 2.9 23.4 + - - -
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Residues in contact with PRO 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C LYS 4.6 0.4 - - - +
540C TYR* 1.3 89.0 - - + +
542C LEU* 1.3 60.4 + - - +
571C GLU 5.5 1.1 - - - +
572C ASN 3.7 13.2 - - - +
573C ILE* 3.6 7.4 - - + +
574C ILE* 2.8 27.5 + - - +
620C ASP* 4.9 0.7 - - + -
623C ARG* 3.3 49.6 - - + +
763C PHE* 3.5 35.9 - - + -
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Residues in contact with LEU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C MET* 4.6 2.7 - - + -
540C TYR 3.7 0.6 + - - -
541C PRO* 1.3 74.9 - - - +
543C LEU* 1.3 67.0 + - - +
544C LEU* 4.0 11.0 - - + +
574C ILE* 3.0 24.7 - - + +
576C ALA* 4.4 10.8 - - + -
610C ALA* 5.5 2.0 - - + -
613C PHE* 3.8 32.5 - - + -
619C VAL* 3.8 40.2 - - + -
623C ARG 3.1 7.5 + - - +
624C ILE* 3.2 22.3 - - + -
625C ALA 2.8 31.4 + - - +
763C PHE* 3.8 4.5 - - - -
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Residues in contact with LEU 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542C LEU* 1.3 77.5 - - - +
544C LEU* 1.3 56.6 + - - +
545C ASP 3.5 0.5 + - - -
563C TRP* 4.1 6.7 - - + -
567C LEU* 3.5 32.1 - - + -
573C ILE* 4.1 15.0 - - + +
574C ILE 2.8 9.2 + - - +
575C VAL* 3.1 12.1 - - + -
576C ALA 2.8 31.5 + - - -
625C ALA* 3.3 32.3 - - + +
626C ILE* 3.7 6.3 - - - +
627C TRP* 3.6 38.8 - - + +
759C ILE* 4.2 12.6 - - + -
763C PHE* 4.8 2.7 - - + -
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Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542C LEU* 4.0 6.3 - - + +
543C LEU* 1.3 71.6 - - - +
545C ASP* 1.3 59.1 + - - +
546C VAL* 3.5 2.9 + - + -
576C ALA* 3.4 20.6 - - + +
577C SER* 4.7 4.7 - - - -
578C PHE* 4.8 4.0 - - + +
606C GLN* 3.4 42.4 - - + +
610C ALA* 4.4 2.9 - - + +
613C PHE* 4.5 22.7 - - + -
625C ALA 2.7 17.9 + - - +
626C ILE* 3.5 20.6 - - + +
627C TRP 3.1 26.7 + - - +
647C PHE* 3.8 29.2 - - + -
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Residues in contact with ASP 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C LEU 3.5 2.8 + - - -
544C LEU* 1.3 70.8 - - - +
546C VAL* 1.3 62.7 + - - +
554C LYS* 2.7 31.9 + - - +
562C ASN* 5.7 2.4 + - - -
564C ALA* 4.8 7.4 - - - +
575C VAL* 3.7 24.6 - - + +
576C ALA 2.7 8.5 + - - +
577C SER* 2.8 40.6 + - - +
578C PHE 4.6 1.4 + - - -
606C GLN* 5.1 0.2 - - - +
627C TRP* 3.7 34.3 + - - +
628C GLY* 5.4 0.9 - - - -
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Residues in contact with VAL 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C LEU* 4.3 1.8 - - + +
545C ASP* 1.3 79.2 + - - +
547C TYR* 1.3 66.3 + - - +
548C ALA* 3.9 7.9 - - + -
554C LYS* 4.3 4.3 + - - -
578C PHE 6.1 0.2 - - - -
606C GLN* 3.5 30.1 - - - +
626C ILE* 3.8 17.5 - - + -
627C TRP 3.2 8.5 + - - +
628C GLY* 3.5 9.4 - - - -
629C TRP 4.3 1.2 + - - -
632C GLY* 3.3 14.8 - - - +
635C VAL* 3.6 26.5 - - + -
636C THR* 3.2 28.7 - - - +
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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