Contacts of the helix formed by residues 324 - 328 (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 324 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.3 15.9 - - + +
134E GLY* 2.7 30.5 + - - -
136E ASN* 3.2 31.0 - - - -
321F THR* 2.8 14.4 + - - +
322F PRO 3.6 2.3 - - - +
323F ASP* 1.4 72.0 - - - +
325F LYS* 1.4 56.5 + - - +
326F THR* 4.1 11.4 - - - -
327F SER* 2.8 45.1 + - - -
328F ILE 4.1 0.2 + - - -
449F TRP* 3.6 24.5 - + - -
451F ASN* 3.9 3.6 - - - +
490F PRO* 4.3 17.8 + - - +
491F ILE* 3.8 22.4 - - + -
494F SER* 5.2 0.7 - - - -
2550F DHB 2.2 41.6 + - - -
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Residues in contact with LYS 325 (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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199A ASP* 4.8 5.7 + - - -
335B ALA* 3.6 28.0 - - + +
336B LEU* 3.0 33.4 + - - +
338B SER* 3.4 12.9 + - - +
322F PRO 3.7 10.3 - - - +
323F ASP* 4.2 5.8 - - - +
324F TYR* 1.4 69.1 - - - +
326F THR* 1.4 64.4 + - - +
328F ILE* 2.9 27.8 + - - +
329F ALA 4.6 0.5 + - - -
450F ARG 5.4 0.9 - - - +
451F ASN* 2.9 52.7 + - - +
452F GLY* 4.1 6.2 - - - +
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Residues in contact with THR 326 (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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133E ARG* 3.7 31.6 + - - +
134E GLY* 3.7 22.2 - - - +
324F TYR* 3.3 14.2 + - - -
325F LYS* 1.4 78.2 - - - +
327F SER* 1.4 60.0 + - - +
328F ILE 3.4 0.5 + - - -
329F ALA* 3.9 3.5 + - - +
330F ARG* 3.6 41.2 + - + +
449F TRP* 5.4 1.0 - - - -
451F ASN* 4.6 0.4 + - - -
2550F DHB 4.2 3.9 + - - -
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Residues in contact with SER 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLY* 3.3 23.9 - - - -
136E ASN* 4.2 1.8 - - - -
319F ALA 3.6 15.3 - - - -
320F LEU* 4.4 0.9 - - - -
321F THR* 3.1 34.6 + - - -
324F TYR* 2.8 34.8 + - - -
326F THR* 1.4 70.0 - - - +
328F ILE* 1.4 59.9 + - - -
330F ARG 3.2 6.1 + - - +
331F SER* 2.8 25.0 + - - -
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Residues in contact with ILE 328 (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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333B ARG 3.5 23.1 - - - +
334B GLN* 4.7 11.7 - - - +
335B ALA* 3.7 31.2 - - + +
190E GLN* 2.8 22.9 + - - +
320F LEU* 3.9 11.0 - - + -
322F PRO* 3.7 41.1 - - + +
325F LYS 2.9 17.0 + - - +
327F SER* 1.4 76.5 + - - +
329F ALA* 1.3 58.3 + - + +
331F SER* 3.4 0.2 + - - -
333F ARG* 3.0 16.9 + - - +
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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