Contacts of the strand formed by residues 474 - 480 (chain F) in PDB entry 1YKN
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 LEU 474 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E GLU* 4.2 15.0 - - - +
8E THR* 3.6 42.6 - - + +
10E SER* 4.0 28.0 - - - +
137E ILE* 5.6 0.4 - - + -
138E HIS* 4.5 7.2 - - + -
311F ARG* 4.2 8.1 - - - +
316F HIS* 4.2 4.0 - - + -
464F GLY* 3.6 1.4 - - - -
465F ILE* 2.9 44.4 + - + +
472F THR 3.9 7.0 - - - +
473F LYS* 1.3 79.5 - - - +
475F ILE* 1.3 70.8 + - - +
476F THR* 4.6 2.9 - - - -
525F ILE* 5.0 0.2 - - + -
526F VAL 4.9 0.9 - - - +
527F LEU* 4.3 19.1 - - + -
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Residues in contact with ILE 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E SER* 3.4 10.6 + - - -
11E GLN 3.2 31.3 + - - +
12E THR 4.5 0.9 - - - +
13E ALA* 3.9 29.2 - - + -
21E LEU* 3.9 26.2 - - + -
67E PHE* 4.6 2.2 - - + -
131E PHE* 3.4 43.8 - - + -
138E HIS* 5.3 1.6 + - - -
400F TRP* 4.4 9.0 - - + -
462F HIS* 5.4 0.7 - - - +
463F PHE 3.1 9.6 - - - +
464F GLY* 4.0 11.2 - - - -
473F LYS* 3.9 9.9 - - - +
474F LEU* 1.3 76.4 - - - +
476F THR* 1.3 68.6 + - - +
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Residues in contact with THR 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E THR* 4.0 19.5 - - + -
9E PRO 2.7 27.0 + - - -
11E GLN* 3.7 10.6 - - - +
462F HIS* 3.6 3.3 + - - +
463F PHE* 2.9 43.4 + - + +
465F ILE* 4.5 9.6 - - + -
474F LEU* 4.6 3.1 - - + -
475F ILE* 1.3 78.1 - - - +
477F GLN* 1.3 77.3 + - - +
504F LEU* 3.5 10.2 - - - +
523F PHE* 4.2 16.4 - - + -
525F ILE* 5.4 0.2 - - + -
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Residues in contact with GLN 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLN* 3.8 14.1 - - + +
12E THR* 2.9 31.4 + - - +
457F ARG* 2.8 30.7 + - - +
460F HIS* 2.9 16.0 - - + -
461F ILE 3.7 5.2 - - - +
462F HIS* 3.4 20.1 - - + +
476F THR* 1.3 97.8 + - - +
478F LEU* 1.3 60.1 + - - +
479F TYR* 3.6 23.7 + - + +
491F ILE* 4.3 2.8 - - - +
504F LEU* 3.8 20.4 - - - +
523F PHE* 4.4 0.2 - - - -
2550F DHB 3.2 16.2 + - - -
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Residues in contact with LEU 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F VAL* 3.7 29.6 - - + -
460F HIS* 3.2 7.1 - - - +
461F ILE* 3.1 36.3 + - + +
463F PHE* 3.7 20.5 - - + -
477F GLN* 1.3 73.9 - - - +
479F TYR* 1.4 73.0 + - - +
480F PHE* 3.7 30.7 - - + -
504F LEU 3.7 4.9 - - - -
506F ALA* 3.9 15.3 - - + -
523F PHE* 3.7 35.9 - - + -
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Residues in contact with TYR 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLN* 2.7 28.7 + - - -
457F ARG* 3.2 27.5 + - - -
458F PRO* 3.9 16.4 - - + -
459F ALA 3.8 9.0 - - - +
460F HIS* 3.6 27.4 - - + -
477F GLN* 3.6 24.5 + - + +
478F LEU* 1.4 75.7 - - - +
480F PHE* 1.4 58.3 + - - +
486F ILE* 3.8 23.6 - - + -
492F VAL* 3.5 22.9 - - + +
501F VAL* 5.9 1.3 - - + -
504F LEU* 2.9 34.2 + - + +
505F ILE* 3.4 6.1 - - + -
506F ALA* 2.7 33.6 + - - +
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Residues in contact with PHE 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F ILE* 3.8 15.9 - - + -
380F VAL* 4.9 1.6 - - + -
443F LYS* 3.8 31.6 - - + +
444F PRO* 3.8 36.1 - - + -
459F ALA* 3.7 21.9 + - + -
460F HIS* 4.3 1.6 - - - -
461F ILE* 4.0 7.6 - - + -
478F LEU* 3.7 26.0 - - + -
479F TYR* 1.4 75.7 - - - +
481F GLU* 1.3 70.1 + - - +
482F GLY 3.3 0.5 + - - -
483F ASP* 3.2 25.1 + - + +
486F ILE* 3.6 5.9 - - - +
505F ILE* 4.1 3.6 - - - -
506F ALA 4.0 0.9 - - - -
521F TYR* 3.6 49.6 - + + +
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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