Contacts of the helix formed by residues 342 - 347 (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 SER 342 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116K ASN* 4.0 18.4 - - - -
117K ALA* 4.4 7.9 - - - +
122K MET* 3.5 27.7 - - - +
142K ARG* 3.7 2.8 + - - -
157K VAL* 5.9 1.3 - - - -
304L ASP* 4.2 8.7 - - - -
340L PRO 4.6 3.4 - - - -
341L GLN* 1.3 71.0 - - - +
343L ILE* 1.3 65.3 + - - +
344L SER* 3.1 10.9 + - - -
345L GLU* 2.7 23.8 + - - -
346L THR* 3.1 23.5 + - - +
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Residues in contact with ILE 343 (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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79K TYR* 4.1 15.8 - - + -
114K VAL* 3.8 29.8 - - + -
115K ASN 4.0 13.0 + - - +
116K ASN 5.6 0.2 - - - -
117K ALA 5.5 0.2 - - - +
302L ALA 3.3 25.6 - - - +
303L GLN* 3.8 1.1 - - - -
304L ASP* 3.4 34.8 + - + +
342L SER* 1.3 74.2 - - - +
344L SER* 1.3 62.3 + - - +
345L GLU 3.5 0.3 + - - -
346L THR* 3.8 7.9 - - - -
347L THR* 2.8 44.2 + - + -
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Residues in contact with SER 344 (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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71K TRP* 3.5 13.3 + - - -
79K TYR* 2.6 31.5 + - - -
114K VAL* 4.1 3.8 - - - +
125K HIS* 2.7 27.1 + - - -
127K ASN* 3.6 6.7 + - - -
142K ARG* 3.7 0.9 - - - -
342L SER* 3.1 8.9 + - - -
343L ILE* 1.3 84.3 - - - +
345L GLU* 1.3 76.5 + - - +
470L ILE* 3.4 17.7 - - - +
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Residues in contact with GLU 345 (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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127K ASN* 3.8 4.6 - - - +
142K ARG* 2.8 33.7 + - - -
200K PHE* 3.4 49.4 - - + -
339L ILE* 4.0 12.7 - - - +
340L PRO 3.9 3.7 - - - +
341L GLN* 4.7 5.8 - - + -
342L SER* 2.7 41.2 + - - +
344L SER* 1.3 83.3 - - - +
346L THR* 1.3 64.1 + - + +
347L THR 3.4 1.1 - - - -
469L SER* 3.6 1.6 - - - -
470L ILE* 3.7 8.1 - - + +
471L ALA* 3.2 30.5 + - - +
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Residues in contact with THR 346 (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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303L GLN 5.1 0.2 + - - -
304L ASP* 3.2 22.3 + - - -
305L ASN 5.0 0.3 + - - -
306L SER* 3.4 29.2 + - - +
307L ARG* 3.6 4.0 - - - +
308L PHE* 3.8 16.6 - - + -
341L GLN* 3.5 39.7 - - + +
342L SER 3.1 10.3 + - - +
343L ILE* 3.8 5.2 - - - -
344L SER 3.5 0.2 - - - -
345L GLU* 1.3 78.8 - - - +
347L THR* 1.3 59.3 + - - +
468L PRO 4.6 1.2 - - - +
469L SER* 3.4 14.6 - - - -
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Residues in contact with THR 347 (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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71K TRP* 3.0 27.9 + - - -
79K TYR* 3.9 4.5 - - + -
302L ALA* 3.5 31.4 - - + -
303L GLN 3.7 15.9 - - - +
343L ILE* 2.8 42.0 + - + +
345L GLU 3.4 0.2 - - - -
346L THR* 1.3 81.2 - - - +
348L GLY* 1.3 59.8 + - - +
468L PRO 4.5 1.3 - - - -
469L SER* 3.6 5.8 - - - +
470L ILE* 3.0 21.3 + - - +
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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