Contacts of the strand formed by residues 574 - 578 (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 ILE 574 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528C MET* 4.1 28.0 - - + -
529C ILE 3.7 5.6 - - - +
530C LEU* 3.9 10.5 - - + -
531C PRO* 3.7 19.1 - - + -
534C PHE* 3.7 17.0 - - + -
540C TYR* 3.7 22.7 - - + -
541C PRO 2.8 13.5 + - - +
542C LEU* 3.0 20.6 - - + +
543C LEU 2.8 29.6 + - - -
573C ILE* 1.3 69.8 - - - +
575C VAL* 1.3 57.4 + - - +
618C PHE* 3.7 31.2 - - + +
619C VAL* 4.7 4.5 - - + -
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Residues in contact with VAL 575 (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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527C GLN* 4.2 0.7 - - - +
528C MET* 3.7 0.3 - - - -
529C ILE* 2.9 55.4 + - + +
543C LEU* 3.1 25.8 - - + +
545C ASP* 3.7 27.6 - - + +
564C ALA* 3.5 37.5 - - + +
567C LEU* 5.1 4.3 - - + -
573C ILE* 3.4 6.5 + - + +
574C ILE* 1.3 72.3 - - - +
576C ALA* 1.3 60.4 + - - +
577C SER* 5.4 0.2 - - - +
627C TRP* 5.4 0.7 - - - +
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Residues in contact with ALA 576 (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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527C GLN 3.2 13.0 - - - +
528C MET* 3.9 15.5 - - + -
542C LEU* 4.4 18.8 - - + -
543C LEU 2.8 8.4 + - - +
544C LEU* 3.4 8.4 - - + +
545C ASP 2.7 32.5 + - - -
574C ILE* 3.9 0.4 + - + -
575C VAL* 1.3 75.2 - - - +
577C SER* 1.3 59.5 + - - +
613C PHE* 4.2 21.8 - - + -
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Residues in contact with SER 577 (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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526C TYR* 3.1 5.7 - - - +
527C GLN* 2.8 44.1 + - - +
544C LEU* 4.7 2.0 - - - -
545C ASP* 2.8 36.3 + - - +
554C LYS* 3.6 38.2 + - - +
555C ALA* 4.4 1.5 - - - +
575C VAL* 5.4 0.5 - - - +
576C ALA* 1.3 71.9 - - - +
578C PHE* 1.3 61.4 + - - +
613C PHE* 5.5 0.4 - - - -
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Residues in contact with PHE 578 (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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517C ILE* 3.7 25.6 - - + -
519C LEU* 4.3 10.1 - - + -
524C PHE* 3.4 39.5 - + + -
525C TRP 3.5 11.9 - - - -
526C TYR* 3.8 12.8 - - + +
544C LEU* 4.8 2.8 - - + +
545C ASP 4.6 1.6 + - - -
546C VAL* 6.1 0.3 - - - -
548C ALA* 5.5 2.8 - - - +
554C LYS* 5.0 2.6 - - - +
577C SER* 1.3 76.8 - - - +
579C ASP* 1.3 63.7 + - - +
580C GLY* 3.5 22.6 + - - -
605C ASP* 3.4 25.6 - - + -
606C GLN* 2.8 42.9 + - - +
609C ALA* 3.4 28.9 - - + -
613C PHE* 4.6 6.5 - + + -
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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