Contacts of the strand formed by residues 474 - 480 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G GLU* 4.2 11.0 - - - +
8G THR* 3.6 42.2 - - + +
10G SER* 3.9 33.7 - - - +
137G ILE* 5.9 0.2 - - + -
138G HIS* 4.5 6.7 - - + -
311H ARG* 4.4 5.8 - - - +
316H HIS* 4.2 8.7 - - + -
464H GLY* 3.4 2.4 - - - -
465H ILE* 2.8 49.1 + - + +
472H THR 3.8 8.3 - - - +
473H LYS* 1.3 77.8 - - - +
475H ILE* 1.3 69.6 + - - +
476H THR* 4.6 2.2 - - + -
525H ILE* 4.9 0.7 - - + -
526H VAL 4.7 1.3 - - - +
527H LEU* 4.4 18.2 - - + -
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Residues in contact with ILE 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G SER* 3.5 10.0 + - - -
11G GLN 3.2 27.2 + - - +
12G THR 4.3 0.9 - - - +
13G ALA* 3.7 35.2 - - + -
17G VAL* 4.9 0.2 - - + -
21G LEU* 4.0 26.2 - - + -
67G PHE* 4.8 0.4 - - + -
131G PHE* 3.6 41.5 - - + -
138G HIS* 5.1 2.2 + - - -
400H TRP* 4.4 9.9 - - + -
462H HIS* 5.4 0.7 - - - +
463H PHE 3.3 12.1 - - - +
464H GLY* 4.1 5.8 - - - -
473H LYS* 4.0 10.1 - - - -
474H LEU* 1.3 80.2 - - - +
476H THR* 1.3 70.5 + - - +
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Residues in contact with THR 476 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G THR* 3.8 20.6 - - + -
9G PRO 2.8 26.7 + - - -
10G SER* 4.4 0.2 - - - -
11G GLN* 3.9 11.7 - - - +
462H HIS* 3.4 4.3 - - - +
463H PHE* 2.9 48.2 + - + +
465H ILE* 4.4 11.0 - - + -
474H LEU* 4.6 2.9 - - + -
475H ILE* 1.3 78.5 - - - +
477H GLN* 1.4 74.9 + - - +
504H LEU* 3.5 11.1 - - - +
523H PHE* 4.3 14.6 - - + -
525H ILE* 5.5 0.2 - - + -
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Residues in contact with GLN 477 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLN* 3.8 14.6 - - + +
12G THR* 3.2 24.9 + - - +
457H ARG* 2.7 30.7 + - - +
460H HIS* 3.0 14.2 - - + -
461H ILE 3.5 5.2 - - - +
462H HIS* 3.4 22.4 - - + +
476H THR* 1.4 95.1 + - - +
478H LEU* 1.3 60.9 + - - +
479H TYR* 3.5 22.3 + - + +
491H ILE* 4.2 3.8 - - - +
504H LEU* 3.6 24.9 - - - +
523H PHE* 4.3 1.2 - - - -
3550H DHB 3.0 22.2 + - - -
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Residues in contact with LEU 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380H VAL* 3.5 26.5 - - + -
460H HIS* 3.1 27.4 - - - +
461H ILE* 2.9 21.1 + - + +
463H PHE* 3.4 30.4 - - + -
477H GLN* 1.3 73.8 - - - +
479H TYR* 1.3 72.0 + - - +
480H PHE* 3.7 30.7 - - + -
504H LEU 3.6 4.3 - - - -
506H ALA* 3.9 15.9 - - + -
523H PHE* 3.7 27.6 - - + -
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Residues in contact with TYR 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLN* 2.6 28.5 + - - -
457H ARG* 3.0 30.5 + - - -
458H PRO* 3.9 15.9 - - + -
459H ALA 3.8 9.4 - - - +
460H HIS* 3.7 21.8 - - + -
477H GLN* 3.5 25.3 + - + +
478H LEU* 1.3 73.1 - - - +
480H PHE* 1.3 61.0 + - - +
486H ILE* 3.9 22.2 - - + -
492H VAL* 3.4 24.9 - - + +
501H VAL* 5.6 1.1 - - + -
504H LEU* 2.7 36.1 + - + +
505H ILE* 3.4 4.9 - - + -
506H ALA* 2.7 34.1 + - - +
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Residues in contact with PHE 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378H ILE* 3.7 24.9 - - + -
380H VAL* 5.1 1.1 - - + -
443H LYS* 3.8 25.4 - - + +
444H PRO* 3.7 38.6 - - + -
458H PRO* 6.2 0.2 - - - +
459H ALA* 3.6 29.1 + - + -
460H HIS* 4.3 2.0 - - - -
461H ILE* 4.0 7.6 - - + -
478H LEU* 3.7 25.6 - - + -
479H TYR* 1.3 75.0 - - - +
481H GLU* 1.3 70.6 + - - +
482H GLY 3.1 0.7 + - - -
483H ASP* 3.0 26.6 + - + +
486H ILE* 3.6 6.0 - - - +
505H ILE* 4.0 3.4 - - - -
506H ALA* 4.1 0.9 - - + -
521H TYR* 3.9 32.3 - + + +
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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