Contacts of the strand formed by residues 436 - 442 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381L ALA* 6.2 1.3 - - + -
382L GLY* 3.5 16.2 - - - -
383L ARG* 3.5 41.5 + - + -
429L CME 3.6 6.3 + - - -
431L THR* 3.3 4.5 - - - -
432L ASP* 3.1 39.6 + - - +
434L ASP* 3.6 27.4 - - + -
435L GLY* 1.3 75.4 - - - +
437L TYR* 1.3 62.0 + - - +
522L ARG* 3.7 27.6 + - - -
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Residues in contact with TYR 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380L VAL* 3.9 12.4 - - - +
381L ALA* 3.4 4.4 + - - +
382L GLY 3.1 42.2 + - - +
383L ARG 4.1 1.6 - - - -
384L VAL* 4.2 17.7 - - + -
397L VAL* 4.4 7.9 - - + -
429L CME 3.5 25.8 - - - -
431L THR* 4.2 10.3 - - + -
436L TYR* 1.3 75.5 - - - +
438L SER* 1.4 67.4 + - - +
439L PHE* 3.6 28.7 - + - -
463L PHE* 3.9 17.4 - + - -
523L PHE* 2.6 45.9 + - - +
525L ILE* 4.1 14.1 - - + -
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Residues in contact with SER 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361L HIS* 3.7 10.8 + - - +
379L ILE* 4.6 7.0 - - - -
380L VAL 3.5 9.6 - - - -
381L ALA* 4.0 11.4 - - - -
429L CME 3.2 36.0 - - - +
437L TYR* 1.4 81.7 - - - +
439L PHE* 1.3 72.7 + - - +
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Residues in contact with PHE 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361L HIS* 3.3 27.8 - - + +
363L LEU* 4.5 1.6 - - + -
379L ILE* 3.2 10.4 - - - +
380L VAL* 2.9 35.4 + - + +
397L VAL* 3.7 35.2 - - + -
399L MET* 3.6 42.8 - - + -
427L GLY* 3.6 4.7 - - - -
428L ARG 3.3 32.1 - - - -
429L CME 3.7 12.3 - - + -
437L TYR* 3.6 33.0 - + - -
438L SER* 1.3 73.2 - - - +
440L ARG* 1.3 64.4 - - - +
441L THR* 5.3 0.4 - - + -
463L PHE* 4.2 5.8 - + - -
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Residues in contact with ARG 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361L HIS* 3.2 6.6 + - + +
362L ASP* 2.9 45.3 + - - +
363L LEU* 2.8 23.9 + - - +
364L LEU* 3.5 31.6 + - + +
365L LEU* 4.2 13.7 - - - +
372L LEU* 6.3 0.4 - - - +
377L ARG* 3.6 22.4 - - - +
378L ILE 3.4 11.2 - - - +
379L ILE* 4.4 14.1 - - + +
439L PHE* 1.3 77.9 - - - +
441L THR* 1.3 63.4 + - - +
514L ASN* 6.1 0.6 - - - +
517L ASP* 4.9 5.5 + - - -
518L CYS* 5.4 8.0 - - - -
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Residues in contact with THR 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363L LEU* 3.7 21.1 - - - +
364L LEU* 3.6 20.6 - - - +
377L ARG* 3.7 2.1 - - - -
378L ILE* 2.7 48.4 + - + +
380L VAL* 4.3 8.5 - - + -
399L MET* 4.4 8.3 - - + -
401L GLN* 2.5 34.4 + - - +
423L PHE* 3.8 2.4 - - - -
439L PHE* 5.3 0.2 - - + -
440L ARG* 1.3 76.6 - - - +
442L ILE* 1.4 67.8 + - - +
461L ILE* 4.3 9.6 - - + -
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Residues in contact with ILE 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364L LEU* 3.7 21.7 - - + +
373L PRO* 4.2 13.9 - - + +
374L ILE 3.5 16.4 - - - +
375L GLY* 3.8 25.1 - - - +
376L GLU 3.0 9.2 - - - +
377L ARG* 4.4 4.5 - - + +
378L ILE* 4.2 2.2 - - - -
401L GLN* 3.1 21.4 + - - +
403L ASN* 4.0 9.9 - - + -
404L ALA* 3.3 35.0 - - + +
420L ASP* 5.2 0.9 - - - +
423L PHE* 3.7 25.4 - - + -
441L THR* 1.4 79.6 + - - +
443L LYS* 1.3 65.5 + - - +
444L PRO* 3.5 1.7 - - - +
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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