Contacts of the strand formed by residues 436 - 442 (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 TYR 436 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381H ALA* 6.3 0.7 - - + -
382H GLY* 3.3 18.2 - - - +
383H ARG* 3.7 44.3 + - + -
429H CME 3.4 7.2 + - - +
431H THR* 3.2 4.8 - - - -
432H ASP* 3.0 39.0 + - - +
434H ASP* 3.7 25.4 - - + -
435H GLY* 1.4 73.7 - - - +
437H TYR* 1.3 62.6 + - - +
522H ARG* 3.9 22.3 + - - -
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Residues in contact with TYR 437 (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* 3.9 13.1 - - - +
381H ALA* 3.4 5.7 - - - +
382H GLY* 3.0 44.2 + - - +
383H ARG* 3.9 2.2 - - - -
384H VAL* 4.0 18.2 - - + -
397H VAL* 4.5 7.6 - - + -
429H CME 3.6 26.5 - - - -
431H THR* 4.4 8.1 - - + -
436H TYR* 1.3 78.6 - - - +
438H SER* 1.3 67.9 + - - +
439H PHE* 3.6 25.6 - + - -
463H PHE* 3.8 22.9 - + - -
523H PHE* 2.7 42.8 + - - +
525H ILE* 4.2 14.6 - - + -
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Residues in contact with SER 438 (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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534D HIS* 5.8 6.2 - - - +
535D PHE* 3.9 21.8 - - - -
361H HIS* 3.7 7.1 - - - +
379H ILE* 4.5 4.7 - - - -
380H VAL 3.5 5.4 - - - -
381H ALA* 3.8 15.5 - - - -
429H CME 3.2 36.3 - - - +
437H TYR* 1.3 80.8 - - - +
439H PHE* 1.3 70.3 + - - +
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Residues in contact with PHE 439 (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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535D PHE* 4.2 4.9 - - - -
361H HIS* 3.2 21.1 - - - +
363H LEU* 4.3 2.9 - - + -
379H ILE* 3.2 8.5 - - - +
380H VAL* 2.8 37.3 + - + +
397H VAL* 3.6 34.8 - - + -
399H MET* 3.7 46.4 - - + -
428H ARG 3.5 32.8 - - - -
429H CME 3.9 11.0 - - + -
437H TYR* 3.6 32.5 - + - -
438H SER* 1.3 74.7 - - - +
440H ARG* 1.3 63.2 + - - +
441H THR* 5.3 0.7 - - + -
463H PHE* 4.1 8.1 - + - -
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Residues in contact with ARG 440 (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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535D PHE* 3.5 44.8 + - + +
538D CYS* 3.3 47.8 + - - -
361H HIS 3.2 5.9 + - - -
362H ASP* 2.8 40.8 + - - +
363H LEU* 2.7 32.4 + - - +
364H LEU* 3.2 27.4 - - + +
365H LEU* 3.9 10.1 - - - +
377H ARG* 3.9 15.1 - - - +
378H ILE 3.5 10.1 - - - +
379H ILE* 4.4 10.3 - - + +
439H PHE* 1.3 75.3 - - - +
441H THR* 1.3 69.1 - - - +
517H ASP* 4.8 2.2 + - - -
518H CYS* 5.5 6.3 - - + +
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Residues in contact with THR 441 (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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363H LEU* 3.6 18.7 - - - +
364H LEU* 3.6 19.9 - - - +
377H ARG* 3.7 1.2 - - - -
378H ILE* 2.8 53.9 + - + +
380H VAL* 4.1 14.4 - - + -
399H MET* 4.4 9.4 - - + -
401H GLN* 2.5 32.9 + - - +
423H PHE* 3.9 1.6 - - - -
439H PHE 5.2 0.2 - - - +
440H ARG* 1.3 82.1 - - - +
442H ILE* 1.4 64.7 + - - +
461H ILE* 4.4 2.0 - - + -
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Residues in contact with ILE 442 (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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364H LEU* 3.7 21.3 - - + +
373H PRO* 4.2 15.7 - - + +
374H ILE 3.5 15.9 - - - +
375H GLY* 4.1 15.7 - - - +
376H GLU 3.1 14.4 - - - +
377H ARG* 4.6 4.5 - - + -
378H ILE* 4.4 0.2 - - - -
401H GLN* 2.8 29.8 + - - +
403H ASN* 4.0 7.9 - - + -
404H ALA* 3.4 36.8 - - + +
420H ASP* 5.5 0.7 - - - +
423H PHE* 3.6 25.7 - - + -
441H THR* 1.4 78.9 + - - +
443H LYS* 1.3 58.2 + - - +
444H PRO* 3.2 1.9 - - - +
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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