Contacts of the helix formed by residues 324 - 328 (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 324 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K THR* 3.3 21.0 + - + +
134K GLY* 2.9 28.5 + - - -
136K ASN* 3.2 29.8 - - - -
321L THR* 2.7 17.0 + - - +
322L PRO 3.5 2.7 - - - +
323L ASP* 1.3 76.5 - - - +
325L LYS* 1.3 52.9 + - - +
326L THR* 3.2 13.2 - - - -
327L SER* 2.9 44.3 + - - -
328L ILE 4.2 0.3 + - - -
449L TRP* 3.6 31.0 - + - -
451L ASN* 4.0 1.3 - - - -
490L PRO* 3.9 19.2 + - - +
491L ILE* 3.8 17.7 - - + -
494L SER* 5.2 0.7 - - - -
5550L DHB 2.2 33.6 + - - -
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Residues in contact with LYS 325 (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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199G ASP* 5.0 4.8 + - - +
335H ALA* 3.7 23.7 - - + +
336H LEU* 2.9 37.9 + - - +
338H SER* 3.1 13.5 + - - +
322L PRO 3.4 13.0 + - - +
323L ASP* 4.2 4.3 - - - +
324L TYR* 1.3 68.8 - - - +
326L THR* 1.4 63.1 + - - +
328L ILE* 3.1 23.5 + - - +
329L ALA 4.7 0.3 + - - -
450L ARG 5.4 0.4 - - - +
451L ASN* 2.8 52.4 + - - +
452L GLY* 4.0 6.9 - - - +
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Residues in contact with THR 326 (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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133K ARG* 3.9 36.4 + - + +
134K GLY* 3.7 21.3 - - - -
324L TYR* 3.0 17.2 + - - -
325L LYS* 1.4 78.0 - - - +
327L SER* 1.4 60.9 + - - +
328L ILE 3.2 1.1 + - - -
329L ALA* 4.0 2.4 + - - +
330L ARG* 3.7 36.0 + - - +
449L TRP* 5.3 1.6 - - - -
451L ASN* 4.7 0.5 + - - -
5550L DHB 4.3 4.3 + - - -
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Residues in contact with SER 327 (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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134K GLY* 3.1 24.4 + - - -
136K ASN* 4.3 1.6 - - - -
319L ALA 3.6 14.5 - - - +
320L LEU* 4.2 1.1 - - - +
321L THR* 3.1 33.6 + - - -
322L PRO 4.2 0.2 - - - -
324L TYR* 2.9 25.3 + - - -
326L THR* 1.4 61.2 - - - +
328L ILE* 1.3 58.9 + - - -
329L ALA 3.5 0.2 - - - -
330L ARG 3.8 1.1 - - - +
331L SER* 2.9 28.8 + - - -
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Residues in contact with ILE 328 (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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333H ARG* 3.4 25.8 - - + +
334H GLN* 4.7 13.7 - - - +
335H ALA* 3.8 26.5 - - + +
190K GLN* 2.8 21.2 + - - +
320L LEU* 4.2 10.8 - - + -
322L PRO* 3.8 40.8 - - + +
325L LYS 3.1 18.5 + - - +
327L SER* 1.3 76.0 - - - +
329L ALA* 1.3 60.3 + - + +
331L SER* 3.4 0.2 + - - -
333L ARG* 2.8 20.6 + - - +
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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