Contacts of the strand formed by residues 436 - 442 (chain J) 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 TYR 436 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382J GLY* 3.4 17.5 - - - -
383J ARG* 3.5 45.6 + - + -
429J CME 3.9 4.3 + - - +
431J THR* 3.1 4.8 - - - -
432J ASP* 2.8 47.8 + - - +
434J ASP* 3.6 24.2 - - + -
435J GLY* 1.4 71.1 - - - +
437J TYR* 1.4 63.2 + - - +
522J ARG* 4.0 17.0 + - - -
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Residues in contact with TYR 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380J VAL* 4.0 11.9 - - - +
381J ALA* 3.5 7.2 + - - +
382J GLY 3.2 48.1 + - - +
383J ARG 4.2 1.3 - - - -
384J VAL* 3.9 19.1 - - + -
397J VAL* 4.4 8.7 - - + -
429J CME 3.6 26.7 - - - -
431J THR* 4.3 9.0 - - + -
436J TYR* 1.4 76.0 - - - +
438J SER* 1.4 70.6 + - - +
439J PHE* 3.6 29.8 - + - -
463J PHE* 3.9 18.2 - + - -
523J PHE* 2.7 48.2 + - - +
525J ILE* 3.9 16.4 - - + -
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Residues in contact with SER 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J HIS* 3.5 15.1 + - - +
379J ILE* 4.6 8.9 - - - +
380J VAL 3.5 10.1 - - - -
381J ALA* 3.9 10.8 - - - -
429J CME 3.0 39.9 - - - +
437J TYR* 1.4 81.3 - - - +
439J PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J HIS* 3.3 20.0 - - - -
363J LEU* 4.5 3.4 - - + -
379J ILE* 3.3 8.8 - - - +
380J VAL* 2.9 35.7 + - + +
397J VAL* 3.6 36.1 - - + -
399J MET* 3.6 43.7 - - + -
427J GLY 3.8 2.5 - - - -
428J ARG 3.4 32.5 - - - -
429J CME 3.6 13.9 - - + -
437J TYR* 3.6 33.9 - + - -
438J SER* 1.3 75.9 - - - +
440J ARG* 1.4 62.7 + - - +
441J THR* 5.3 0.2 - - - -
463J PHE* 4.0 5.4 - + - -
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Residues in contact with ARG 440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J HIS* 3.1 8.3 + - - +
362J ASP* 2.6 45.9 + - + +
363J LEU* 2.7 34.0 + - - +
364J LEU* 3.3 30.7 - - + +
365J LEU* 3.9 12.7 - - - +
377J ARG* 3.4 23.0 - - - +
378J ILE 3.4 10.8 - - - +
379J ILE* 4.3 15.9 - - + -
439J PHE* 1.4 73.6 - - - +
441J THR* 1.3 67.9 + - - +
517J ASP* 4.9 5.1 + - - -
518J CYS* 5.3 7.8 - - + -
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Residues in contact with THR 441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363J LEU* 3.6 20.5 - - - +
364J LEU* 3.7 14.3 - - - +
377J ARG* 3.6 4.0 - - - +
378J ILE* 2.7 60.7 + - + +
380J VAL* 4.1 13.5 - - + -
399J MET* 4.4 7.6 - - + -
401J GLN* 2.8 31.0 + - - +
423J PHE* 3.9 1.4 - - - -
439J PHE 5.4 0.2 - - - +
440J ARG* 1.3 81.5 - - - +
442J ILE* 1.3 68.5 + - - +
461J ILE* 4.7 2.2 - - + -
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Residues in contact with ILE 442 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J LEU* 3.9 14.6 - - + +
373J PRO* 4.4 12.1 - - + +
374J ILE 3.7 17.7 - - - +
375J GLY* 3.8 20.6 - - - +
376J GLU 2.9 13.7 - - - +
377J ARG* 4.2 5.8 - - + -
378J ILE* 4.2 2.9 - - - -
401J GLN* 2.8 26.3 + - - +
403J ASN* 4.1 9.2 - - + -
404J ALA* 3.7 24.5 - - + +
420J ASP* 5.8 0.2 - - - +
423J PHE* 3.5 27.6 - - + -
441J THR* 1.3 89.1 + - - +
443J LYS* 1.3 66.1 + - - +
444J PRO* 3.4 1.2 - - - +
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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