Contacts of the strand formed by residues 426 - 430 (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 VAL 426 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.4 36.1 - - + +
20E GLY* 3.9 17.7 - - - +
23E LEU* 4.6 8.3 - - + -
28E ASN* 6.1 1.6 - - - +
31E ARG* 4.1 22.6 - - - +
363F LEU* 3.4 9.9 - - - +
366F ASN* 3.0 26.3 + - - -
399F MET 3.6 10.3 - - - +
424F GLY 3.7 8.0 - - - +
425F GLY* 1.3 82.3 - - - +
427F GLY* 1.4 62.3 + - - +
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Residues in contact with GLY 427 (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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31E ARG* 4.5 3.1 + - - -
360F ASP 3.0 14.4 - - - -
363F LEU* 3.8 12.1 - - - -
398F GLU* 3.6 3.3 - - - +
399F MET* 3.0 31.9 + - - +
426F VAL* 1.4 79.1 - - - +
428F ARG* 1.3 64.9 + - - +
439F PHE* 3.9 9.2 - - - -
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Residues in contact with ARG 428 (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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31E ARG* 3.2 55.4 - - - +
33E GLN* 2.6 33.3 + - - +
34E GLU* 3.9 5.1 + - - +
35E ILE* 5.0 5.3 - - - +
354F LEU* 4.0 19.7 - - - +
355F GLY 4.5 11.5 + - - -
356F PHE* 3.3 25.6 - - + +
357F GLY 4.8 1.0 - - - +
360F ASP* 3.1 50.7 + - + +
361F HIS* 3.7 4.5 + - - +
396F LEU* 4.4 3.0 - - + +
397F VAL 3.2 13.0 - - - +
398F GLU* 4.1 17.3 + - + -
427F GLY* 1.3 72.6 - - - +
429F CME 1.3 64.2 + - - +
439F PHE* 3.6 2.8 - - - -
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Residues in contact with CME 429 (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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356F PHE* 4.1 11.1 - - - -
361F HIS* 3.9 24.0 - - + +
396F LEU* 3.7 5.0 - - - +
397F VAL* 3.0 27.7 + - + -
428F ARG* 1.3 80.1 - - - +
430F LEU* 1.3 76.5 + - - -
432F ASP* 4.4 10.8 + - - +
436F TYR* 3.5 21.7 + - - -
437F TYR* 3.6 29.5 - - - -
438F SER* 3.2 45.8 - - - +
439F PHE* 3.6 18.6 - - + -
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Residues in contact with LEU 430 (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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351F PHE* 4.0 15.5 - - + +
352F SER* 4.1 24.2 - - - +
356F PHE* 3.7 34.5 - - + -
394F ASN* 4.1 32.5 - - - +
395F THR 3.3 20.4 - - - +
396F LEU* 4.3 4.7 - - - +
429F CME 1.3 97.7 + - - -
431F THR* 1.3 65.4 + - - +
432F ASP* 4.6 0.3 - - - -
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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