Contacts of the helix formed by residues 324 - 328 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G THR* 3.2 25.5 - - + +
134G GLY* 2.9 28.5 + - - -
136G ASN* 3.3 27.8 - - - -
321H THR* 3.0 16.0 + - - +
322H PRO 3.5 1.9 - - - +
323H ASP* 1.3 74.6 - - - +
325H LYS* 1.4 59.2 + - - +
326H THR* 4.0 12.1 - - - -
327H SER* 2.8 35.5 + - - -
328H ILE 4.2 0.2 + - - -
449H TRP* 3.6 30.5 - + - -
451H ASN* 4.0 3.8 - - - +
490H PRO* 4.0 16.6 + - - +
491H ILE* 4.0 14.8 - - + -
494H SER* 5.3 0.7 - - - -
3550H DHB 2.4 32.5 + - - -
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Residues in contact with LYS 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322H PRO 3.6 15.5 - - - +
323H ASP* 4.0 5.8 - - - +
324H TYR* 1.4 71.4 - - - +
326H THR* 1.3 63.8 + - - +
328H ILE* 3.0 26.2 + - + +
329H ALA 4.6 0.7 + - - -
450H ARG 5.5 0.7 - - - +
451H ASN* 2.9 51.2 + - - +
452H GLY* 4.1 5.9 - - - +
199I ASP* 4.9 4.8 + - - +
335J ALA* 3.7 21.2 - - + +
336J LEU* 2.8 42.0 + - - +
338J SER* 3.5 11.5 + - - +
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Residues in contact with THR 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ARG* 3.3 43.6 + - + +
134G GLY* 3.7 22.2 - - - +
324H TYR* 3.2 15.4 + - - -
325H LYS* 1.3 78.1 - - - +
327H SER* 1.3 61.8 + - - +
328H ILE 3.2 0.7 + - - -
329H ALA* 4.0 2.8 + - - +
330H ARG* 3.6 29.9 + - + +
449H TRP* 5.5 1.6 - - - -
451H ASN* 4.8 0.9 + - - -
3550H DHB 4.5 4.0 + - - -
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Residues in contact with SER 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G GLY* 3.3 25.1 - - - -
136G ASN* 4.5 1.3 - - - -
319H ALA 3.6 16.2 - - - -
320H LEU* 4.1 0.9 - - - +
321H THR* 3.1 31.0 + - - -
324H TYR* 2.8 28.2 + - - -
326H THR* 1.3 79.0 - - - +
328H ILE* 1.3 58.7 + - - +
329H ALA 3.5 0.2 - - - -
330H ARG 3.4 3.4 + - - +
331H SER* 2.9 25.8 + - - -
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Residues in contact with ILE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G GLN* 2.9 20.6 + - - +
320H LEU* 3.8 10.1 - - + -
322H PRO* 3.6 43.3 - - + +
325H LYS* 3.0 20.3 + - + +
327H SER* 1.3 76.4 + - - +
329H ALA* 1.4 58.8 + - + +
331H SER* 3.2 2.6 + - - -
333H ARG* 2.9 21.1 + - - +
333J ARG 3.3 24.7 - - - +
334J GLN* 4.7 11.0 - - - +
335J ALA* 3.7 29.6 - - + +
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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
------------------------------------------------------------
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