Contacts of the strand formed by residues 473 - 480 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B ARG* 3.5 50.6 + - + -
455B THR 3.3 15.0 - - - +
456B LEU* 3.6 17.5 - - + -
457B PHE* 4.0 5.2 - - - -
471B ALA* 3.2 21.1 - - + +
472B ASP* 1.3 89.1 - - + +
474B LEU* 1.4 69.9 + - - +
475B GLU* 3.9 13.1 + - + -
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ARG* 3.5 3.3 - - - +
455B THR* 2.8 62.8 + - + +
456B LEU 4.9 0.2 - - - -
457B PHE* 3.7 28.3 - - + -
468B TYR* 3.4 48.2 - - + +
471B ALA* 5.6 0.9 - - + -
473B TYR* 1.4 78.9 - - - +
475B GLU* 1.3 64.5 + - - +
476B GLU* 3.6 18.2 - - + +
511B ILE* 4.4 3.8 - - + -
525B TYR* 4.0 13.0 - - + +
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Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LYS* 3.4 36.1 + - + +
453B ARG 3.2 8.5 - - - +
454B ARG* 2.8 52.2 + - + +
473B TYR* 4.0 9.3 - - + -
474B LEU* 1.3 79.8 - - - +
476B GLU* 1.3 67.6 + - - +
530B LEU* 3.7 13.0 - - - +
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LYS* 3.2 6.4 - - - -
453B ARG 3.0 29.1 + - - -
455B THR* 5.2 1.3 + - - +
468B TYR* 2.8 30.3 + - - -
474B LEU* 3.6 18.0 - - + +
475B GLU* 1.3 80.1 - - - +
477B ARG* 1.3 60.7 + - - +
478B HIS* 3.2 6.5 - - - +
525B TYR* 3.4 42.6 - - + -
527B PRO* 3.3 26.9 - - - +
530B LEU* 3.5 17.9 - - - +
537B SER* 5.7 0.7 - - - -
538B PRO* 5.4 0.9 - - - +
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 4.2 7.9 - - - -
60B VAL* 2.9 52.9 + - + -
61B LEU* 3.2 7.8 + - - +
62B ASP* 2.8 39.4 + - - +
75B GLU* 4.4 0.6 + - - -
81B ARG* 3.5 10.3 - - - +
451B GLY 3.8 1.6 - - - -
452B LYS* 3.6 26.6 - - - +
476B GLU* 1.3 77.7 + - - +
478B HIS* 1.4 58.8 + - - +
525B TYR* 3.1 8.1 - - - +
526B HIS* 2.7 47.1 + - + +
529B PHE* 3.6 21.1 - - + +
530B LEU* 3.6 32.6 - - - +
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Residues in contact with HIS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 4.4 5.8 - - - +
449B ARG* 3.0 38.5 + - + +
450B LEU* 3.1 5.7 - - - +
451B GLY 2.7 35.4 + - - +
453B ARG* 3.5 33.3 + - + +
455B THR* 3.5 19.5 + - - -
476B GLU* 3.2 20.8 + - - +
477B ARG* 1.4 79.1 - - - +
479B ARG* 1.4 65.6 + - - +
480B HIS* 3.4 18.1 - + + -
510B GLU* 3.3 27.6 - - + -
525B TYR* 4.0 5.3 - - + +
526B HIS* 4.0 1.1 - - - -
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Residues in contact with ARG 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 2.9 31.8 + - - -
50B PHE 5.2 1.6 + - - -
58B VAL* 4.4 21.4 - - - +
60B VAL* 4.7 12.6 - - + +
66B GLU* 3.0 27.3 + - - +
373B PHE* 4.9 19.2 - - + -
399B CYS* 4.5 3.6 - - - -
448B MET* 3.9 20.2 - - - +
449B ARG 3.1 6.3 - - - -
450B LEU* 3.4 20.0 - - + +
478B HIS* 1.4 75.3 - - - +
480B HIS* 1.4 71.6 + - - +
526B HIS* 3.1 30.6 + - + +
529B PHE* 5.6 4.3 - - - -
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Residues in contact with HIS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B CYS* 4.0 14.8 - - - -
403B GLN* 5.0 2.2 - - - +
436B MET 5.6 0.2 - - - +
448B MET* 3.4 13.1 - - - +
449B ARG* 2.8 41.8 + - - +
478B HIS* 3.4 35.2 + + + -
479B ARG* 1.4 83.5 + - - +
481B ARG* 1.4 58.8 + - - +
482B PHE 4.8 0.7 - - - +
483B GLU* 3.3 24.7 - - - +
510B GLU* 2.9 28.2 + - - -
524B GLN* 3.5 46.7 + - + +
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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