Contacts of the strand formed by residues 436 - 442 (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 TYR 436 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381F ALA* 6.4 0.2 - - + -
382F GLY* 3.4 16.4 - - - +
383F ARG* 3.6 43.1 + - + -
429F CME 3.5 7.1 + - - +
431F THR* 3.0 4.7 - - - -
432F ASP* 2.7 45.2 + - - +
434F ASP* 3.6 29.4 - - + -
435F GLY* 1.4 75.2 - - - +
437F TYR* 1.3 63.3 + - - +
522F ARG* 3.8 15.3 + - - -
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Residues in contact with TYR 437 (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* 4.0 13.1 - - - +
381F ALA* 3.4 5.3 + - - +
382F GLY 3.1 54.7 + - - +
383F ARG* 4.0 3.8 - - - -
384F VAL* 4.3 14.8 - - + -
397F VAL* 4.4 7.6 - - + -
429F CME 3.6 25.6 - - - -
431F THR* 4.1 12.1 - - + -
436F TYR* 1.3 77.3 - - - +
438F SER* 1.3 70.5 + - - +
439F PHE* 3.6 25.8 - + - -
463F PHE* 3.7 24.9 - + - -
523F PHE* 2.9 41.6 + - - +
525F ILE* 4.1 14.1 - - + -
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Residues in contact with SER 438 (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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361F HIS* 3.6 14.4 + - - +
379F ILE* 4.5 9.1 - - - +
380F VAL 3.6 4.5 - - - -
381F ALA* 3.7 17.0 - - - -
429F CME 3.2 38.6 - - - +
437F TYR* 1.3 81.6 - - - +
439F PHE* 1.3 68.2 + - - +
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Residues in contact with PHE 439 (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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361F HIS* 3.4 19.5 - - - +
363F LEU* 4.5 2.5 - - + -
379F ILE* 3.4 8.6 - - - +
380F VAL* 3.0 37.5 + - + +
397F VAL* 3.7 26.7 - - + -
399F MET* 3.5 51.6 - - + -
428F ARG 3.6 17.7 - - - -
429F CME 3.6 28.9 - - + -
437F TYR* 3.6 32.3 - + - -
438F SER* 1.3 75.8 - - - +
440F ARG* 1.3 63.2 + - - +
441F THR* 5.1 0.4 - - + -
463F PHE* 4.1 6.5 - + - -
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Residues in contact with ARG 440 (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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361F HIS* 3.1 9.3 + - - +
362F ASP* 2.9 45.1 + - + +
363F LEU* 2.7 32.9 + - - +
364F LEU* 3.4 29.4 - - + +
365F LEU* 4.2 12.7 - - - +
377F ARG* 3.7 22.8 - - - +
378F ILE 3.4 12.6 - - - +
379F ILE* 4.3 15.7 - - + +
439F PHE* 1.3 75.2 - - - +
441F THR* 1.3 62.9 + - - +
517F ASP* 5.0 5.3 + - - -
518F CYS* 5.4 7.8 - - + -
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Residues in contact with THR 441 (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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363F LEU* 3.6 19.7 - - - +
364F LEU* 3.5 19.5 - - - +
377F ARG* 3.8 0.9 - - - -
378F ILE* 2.7 47.5 + - + +
380F VAL* 4.0 14.8 - - + -
399F MET* 4.2 11.4 - - + -
401F GLN* 2.6 32.3 + - - +
423F PHE* 3.9 1.7 - - - -
439F PHE 5.1 0.2 - - - +
440F ARG* 1.3 78.5 - - - +
442F ILE* 1.3 70.1 + - - +
461F ILE* 4.3 2.0 - - + -
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Residues in contact with ILE 442 (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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364F LEU* 3.7 20.2 - - + +
373F PRO* 4.0 15.5 - - + +
374F ILE 4.1 5.4 - - - +
375F GLY* 4.0 20.6 - - - +
376F GLU 3.1 12.8 - - - +
377F ARG* 4.6 3.8 - - + -
378F ILE* 4.1 2.0 - - - -
401F GLN* 3.0 25.0 + - - +
403F ASN* 3.8 12.1 - - + -
404F ALA* 3.4 34.5 - - + +
420F ASP* 5.9 0.2 - - - +
423F PHE* 3.6 26.4 - - + -
441F THR* 1.3 80.3 + - - +
443F LYS* 1.3 67.5 + - - +
444F PRO* 3.4 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