Contacts of the helix formed by residues 342 - 347 (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 SER 342 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASN* 3.9 29.8 - - - -
117E ALA 4.4 4.3 - - - +
122E MET* 3.7 14.0 - - - +
142E ARG* 3.7 2.9 + - - -
157E VAL* 6.3 0.7 - - - -
304F ASP* 4.1 5.8 - - - -
340F PRO 3.5 2.7 + - - -
341F GLN* 1.3 75.8 - - - +
343F ILE* 1.3 64.4 + - - +
344F SER* 3.1 15.4 + - - -
345F GLU* 2.6 28.7 + - - -
346F THR* 3.0 24.7 + - - +
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Residues in contact with ILE 343 (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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79E TYR* 4.2 21.1 - - + +
114E VAL* 4.2 22.7 - - + -
115E ASN 3.7 21.4 + - - +
116E ASN 5.6 0.2 - - - -
117E ALA 5.6 0.2 - - - +
122E MET* 4.8 0.2 - - + -
302F ALA 3.6 22.7 - - - +
303F GLN* 4.6 0.4 - - - -
304F ASP* 3.8 28.9 + - + +
342F SER* 1.3 72.5 - - - +
344F SER* 1.3 63.0 + - - +
345F GLU 3.3 0.3 + - - -
346F THR* 3.6 9.0 - - - -
347F THR* 2.9 43.7 + - + -
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Residues in contact with SER 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E TRP* 3.4 24.4 + - - -
79E TYR* 2.5 34.8 + - - -
114E VAL* 4.1 3.8 - - - +
122E MET* 4.2 0.7 - - - +
125E HIS* 2.5 26.3 + - - -
127E ASN* 3.6 10.3 + - - -
142E ARG* 3.6 9.8 + - - -
342F SER* 3.1 14.0 + - - -
343F ILE* 1.3 80.7 - - - +
345F GLU* 1.3 62.0 + - - +
470F ILE* 3.5 8.4 - - - +
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Residues in contact with GLU 345 (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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127E ASN* 4.1 4.0 - - - +
142E ARG* 2.9 28.5 + - - -
200E PHE* 3.3 48.0 - - + -
339F ILE* 3.9 13.6 - - - +
340F PRO 3.8 4.1 - - - +
341F GLN* 3.7 7.4 - - + -
342F SER* 2.6 49.2 + - - +
344F SER* 1.3 81.4 - - - +
346F THR* 1.3 64.1 + - + +
347F THR 3.4 2.1 + - - -
469F SER* 3.4 2.9 + - - -
470F ILE* 3.9 7.1 - - + +
471F ALA* 3.4 27.5 + - + +
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Residues in contact with THR 346 (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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304F ASP* 2.9 24.9 + - - -
306F SER* 3.4 29.1 + - - +
307F ARG* 3.7 2.7 - - - +
308F PHE* 3.7 21.1 - - + -
341F GLN* 3.6 29.6 - - + +
342F SER 3.0 15.0 + - - +
343F ILE* 3.6 5.7 - - - -
344F SER 3.5 0.2 - - - -
345F GLU* 1.3 81.5 - - - +
347F THR* 1.4 59.4 + - - +
468F PRO 4.5 1.6 - - - +
469F SER* 3.4 12.8 - - - -
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Residues in contact with THR 347 (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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71E TRP* 3.0 26.4 + - - -
79E TYR* 4.1 5.4 - - - -
302F ALA* 3.7 26.5 - - + -
303F GLN 3.5 25.4 - - - +
343F ILE* 2.9 32.4 + - + +
345F GLU 3.4 0.4 - - - -
346F THR* 1.4 83.4 - - - +
348F GLY* 1.3 60.0 + - - +
468F PRO 4.3 2.0 - - - -
469F SER* 3.6 5.2 - - - -
470F ILE* 2.9 23.2 + - - +
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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