Contacts of the strand formed by residues 475 - 482 (chain C) in PDB entry 5Z58
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 MET 475 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C TYR* 4.3 2.5 - - + +
461C LEU* 4.1 15.9 - - + -
465C MET* 2.7 52.5 - - + -
473C PRO* 4.9 3.4 - - + -
474C LEU* 1.3 92.3 - - - +
476C CYS* 1.3 66.2 + - - +
496C VAL* 3.5 12.5 - - - +
497C LEU* 3.3 20.4 + - + -
498C SER* 2.9 24.6 + - - +
501C ILE* 5.4 0.2 - - - +
510C LEU* 5.4 0.2 - - + -
564C THR* 5.3 5.2 - - - +
565C ILE 3.5 16.2 - - - +
566C THR* 4.0 18.6 - - - +
572C GLU* 5.2 0.9 - - - +
574C ALA* 4.4 7.0 - - + -
575C GLN 4.2 18.4 - - - +
577C PHE* 5.0 4.9 - - + -
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Residues in contact with CYS 476 (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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475C MET* 1.3 77.0 - - - +
477C HIS* 1.3 74.6 + - - +
478C THR* 4.6 4.5 - - - -
494C GLY* 4.6 6.5 - - - -
495C ARG 4.1 8.3 - - - -
496C VAL* 4.1 24.0 - - - -
497C LEU* 4.2 6.8 - - - +
501C ILE* 4.2 13.9 - - + -
550C VAL* 4.7 5.6 - - - -
552C ILE* 5.2 4.7 - - - -
564C THR* 3.4 10.7 - - - +
565C ILE* 3.1 55.0 + - + +
577C PHE* 4.4 1.4 - - - -
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Residues in contact with HIS 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 3.0 34.8 + - + -
221C ILE* 5.1 1.0 - - + +
452C THR* 3.6 22.2 - - + -
476C CYS* 1.3 77.0 - - - +
478C THR* 1.3 80.4 + - - +
479C THR* 3.3 18.9 + - + +
494C GLY* 2.9 22.9 - - - -
495C ARG* 3.1 21.1 + - + +
497C LEU* 3.9 17.0 - - + -
562C THR* 3.6 22.2 - - + -
563C ALA 3.6 5.6 + - - -
564C THR* 4.1 2.7 - - + +
577C PHE* 3.8 21.1 - + + +
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Residues in contact with THR 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C CYS* 4.6 6.3 - - - -
477C HIS* 1.3 79.3 + - - +
479C THR* 1.3 60.5 + - - +
480C LYS 3.6 6.7 - - - -
481C MET* 5.7 1.3 - - - -
492C ALA* 4.5 16.2 - - + -
493C PHE 3.5 15.9 - - - +
552C ILE* 5.8 3.8 - - + -
555C VAL* 5.8 0.7 - - + -
559C ILE* 5.6 2.8 - - + +
561C LYS 4.6 3.1 + - - -
562C THR* 3.5 6.6 - - - -
563C ALA* 2.1 67.5 + - + +
565C ILE* 3.9 28.0 - - + -
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Residues in contact with THR 479 (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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217C ALA* 3.4 20.5 - - - +
220C ARG* 3.6 21.1 - - + -
221C ILE* 2.2 50.0 - - + +
477C HIS* 3.3 39.0 + - + +
478C THR* 1.3 72.7 - - - +
480C LYS* 1.3 67.1 + - - +
493C PHE 3.4 2.9 + - - -
561C LYS 5.5 2.7 - - - -
562C THR* 4.8 7.4 - - - +
580C LEU* 4.4 16.3 - - + +
615C PRO* 5.5 2.1 - - - +
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Residues in contact with LYS 480 (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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182C LYS* 6.2 0.4 - - - -
183C SER* 2.5 36.4 + - - -
203C MET* 5.4 1.7 - - + +
214C GLU* 2.9 30.8 + - - +
217C ALA* 4.5 9.1 - - + +
221C ILE* 5.2 3.4 - - + -
478C THR* 3.6 3.2 - - - -
479C THR* 1.3 86.0 + - - +
481C MET* 1.3 88.0 + - - +
482C TYR* 4.0 24.7 + - + +
492C ALA* 3.8 1.0 - - - +
493C PHE* 3.4 35.7 + - + +
561C LYS 5.1 4.7 + - - +
613C SER 4.8 10.1 - - - +
615C PRO* 4.7 11.9 - - + -
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Residues in contact with MET 481 (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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478C THR* 5.7 1.8 - - - -
480C LYS* 1.3 96.2 - - - +
482C TYR* 1.3 66.0 + - - +
483C SER* 3.4 4.2 + - - -
490C PHE* 3.7 42.8 - - + +
491C HIS 3.6 1.8 - - - -
492C ALA* 3.1 31.0 - - + +
556C ASP* 4.0 7.2 - - - -
559C ILE* 3.1 40.8 - - + -
561C LYS* 4.6 7.6 - - - +
612C LYS* 3.8 32.8 + - + +
613C SER* 4.5 13.5 - - - +
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Residues in contact with TYR 482 (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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183C SER 3.7 15.5 - - - -
185C PRO* 2.9 41.8 - - + +
203C MET* 3.2 22.0 - - - +
480C LYS* 4.0 23.3 + - + +
481C MET* 1.3 70.6 - - - +
483C SER* 1.3 65.7 + - - +
490C PHE* 3.0 11.1 - - - +
491C HIS* 2.8 30.8 + - + +
493C PHE* 2.8 48.3 - + + -
538C HIS* 6.1 2.9 - - + -
551C LEU* 3.5 17.9 - - + -
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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
------------------------------------------------------------
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