Contacts of the strand formed by residues 473 - 480 (chain C) in PDB entry 5U03
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 473 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C ARG* 3.5 52.0 + - + -
455C THR 3.3 14.1 - - - +
456C LEU* 3.6 17.0 - - + -
457C PHE* 4.0 4.7 - - - -
471C ALA* 3.2 20.7 - - + +
472C ASP* 1.3 87.3 - - + +
474C LEU* 1.4 71.1 + - - +
475C GLU* 3.9 13.1 + - + -
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Residues in contact with LEU 474 (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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454C ARG* 3.5 3.3 - - - +
455C THR* 2.8 63.4 + - + +
456C LEU 4.7 0.2 - - - +
457C PHE* 3.7 29.4 - - + -
468C TYR* 3.4 48.5 - - + +
471C ALA* 5.6 0.9 - - + -
473C TYR* 1.4 77.6 - - - +
475C GLU* 1.4 64.1 + - - +
476C GLU* 3.6 18.6 - - + +
511C ILE* 4.4 4.0 - - + -
525C TYR* 4.0 13.2 - - + +
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Residues in contact with GLU 475 (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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452C LYS* 3.4 36.1 + - + +
453C ARG 3.2 7.4 - - - +
454C ARG* 2.8 52.9 + - + +
473C TYR* 4.0 9.6 - - + -
474C LEU* 1.4 77.7 - - - +
476C GLU* 1.4 66.5 + - - +
530C LEU* 3.7 12.8 - - - +
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Residues in contact with GLU 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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452C LYS* 3.2 6.7 - - - -
453C ARG 3.0 29.2 + - - -
455C THR* 5.2 0.9 + - - +
468C TYR* 2.8 30.3 + - - -
474C LEU* 3.6 18.0 - - + +
475C GLU* 1.4 79.4 - - - +
477C ARG* 1.3 60.1 + - - +
478C HIS* 3.2 6.8 - - - +
525C TYR* 3.4 42.0 - - + -
527C PRO* 3.3 27.9 - - - +
530C LEU* 3.5 17.5 - - - +
537C SER* 5.7 0.9 - - - -
538C PRO* 5.4 0.9 - - - +
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Residues in contact with ARG 477 (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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59C PHE* 4.2 8.6 - - - -
60C VAL* 2.9 52.0 + - + -
61C LEU* 3.2 7.4 + - - +
62C ASP* 2.8 39.2 + - - +
75C GLU* 4.4 0.8 + - - -
81C ARG* 3.5 10.1 - - - +
451C GLY 3.8 1.8 - - - -
452C LYS* 3.6 26.6 - - - +
476C GLU* 1.3 77.6 + - - +
478C HIS* 1.4 59.1 + - - +
525C TYR* 3.1 7.3 - - - +
526C HIS* 2.7 47.9 + - + +
529C PHE* 3.6 21.3 - - + +
530C LEU* 3.6 33.2 - - + +
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Residues in contact with HIS 478 (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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60C VAL* 4.4 5.5 - - - +
449C ARG* 3.0 37.7 + - + +
450C LEU* 3.1 5.4 - - - +
451C GLY 2.7 36.4 + - - +
453C ARG* 3.5 32.7 + - + +
455C THR* 3.5 18.2 + - - -
476C GLU* 3.2 20.2 + - - +
477C ARG* 1.4 78.9 - - - +
479C ARG* 1.4 65.4 + - - +
480C HIS* 3.4 18.3 - + + -
510C GLU* 3.3 28.0 - - + -
525C TYR* 4.0 5.6 - - + +
526C HIS* 4.0 1.1 - - - -
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Residues in contact with ARG 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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48C GLY* 2.9 31.4 + - - -
50C PHE 5.2 2.0 + - - -
58C VAL* 4.4 21.7 - - - +
60C VAL* 4.7 13.5 - - + +
66C GLU* 3.0 27.3 + - - +
373C PHE* 4.9 17.7 - - + -
399C CYS* 4.5 3.5 - - - -
448C MET* 3.9 20.4 - - - +
449C ARG 3.1 6.3 - - - -
450C LEU* 3.4 19.3 - - + +
478C HIS* 1.4 76.4 - - - +
480C HIS* 1.4 71.6 + - - +
526C HIS* 3.1 30.4 + - + +
529C PHE* 5.6 4.0 - - - -
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Residues in contact with HIS 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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399C CYS* 4.0 14.8 - - - -
403C GLN* 5.0 2.2 - - - +
436C MET 5.6 0.2 - - - +
448C MET* 3.4 12.4 - - - +
449C ARG* 2.8 42.7 + - - +
478C HIS* 3.4 36.4 + + + -
479C ARG* 1.4 82.2 + - - +
481C ARG* 1.4 59.2 + - - +
482C PHE 4.8 0.7 - - - +
483C GLU* 3.3 24.5 - - - +
510C GLU* 2.9 28.0 + - - -
524C GLN* 3.5 45.4 + - + +
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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