Contacts of the helix formed by residues 341 - 345 (chain B) in PDB entry 1KOJ
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 ASP 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 4.9 0.2 - - - -
187A ASP* 3.5 9.3 - - - +
189A THR* 5.3 1.9 + - - -
339B PRO 3.1 4.2 + - - +
340B TYR* 1.3 79.0 - - - +
342B GLN* 1.3 66.5 + - - +
343B TYR* 3.0 40.8 + - - +
344B LEU* 3.0 46.6 + - + +
382B PRO* 3.9 11.3 - - - +
383B GLY 4.0 2.8 + - - -
406B LEU 5.6 0.2 - - - +
408B PRO* 3.7 25.9 - - + +
412B GLN* 5.9 1.7 - - - +
481B LEU* 3.7 11.8 - - - +
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.1 30.6 + - - +
187A ASP* 2.8 21.7 + - + +
189A THR* 4.0 15.5 - - + -
190A HIS* 3.8 43.9 + - + +
193A LYS* 5.6 5.2 - - + +
341B ASP* 1.3 69.3 - - - +
343B TYR* 1.3 65.9 + - - +
345B HIS* 3.1 43.6 + - + +
382B PRO* 4.4 10.0 - - - +
385B ASN* 4.5 3.1 + - - -
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Residues in contact with TYR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 3.5 35.0 - - + +
193A LYS* 3.8 25.9 - - - +
165B MET 4.7 0.7 - - - +
168B GLU* 3.4 19.3 - - - +
169B ALA* 3.2 40.0 + - - +
171B LYS* 3.6 20.0 - - + +
172B PRO* 3.3 30.9 - - + +
341B ASP* 3.0 17.5 + - - +
342B GLN* 1.3 79.3 - - - +
344B LEU* 1.3 56.2 + - - +
345B HIS* 3.1 11.3 + + - -
346B ARG 4.8 0.3 + - - -
412B GLN* 4.0 11.9 - - + -
413B HIS* 2.6 31.3 + + - -
481B LEU* 4.7 2.9 - - + -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B MET* 4.8 3.1 - - - -
169B ALA* 3.7 23.8 - - + -
339B PRO* 3.9 29.7 - - + +
341B ASP* 3.0 34.6 + - + +
342B GLN 3.1 0.8 - - - -
343B TYR* 1.3 76.5 - - - +
345B HIS* 1.3 58.7 + - - +
346B ARG 3.0 7.7 + - - -
347B PHE* 3.0 46.9 + - + +
348B ALA 4.5 0.3 + - - -
382B PRO* 4.8 1.1 - - - +
406B LEU* 5.6 3.6 - - + -
478B PHE* 4.7 13.7 - - + -
481B LEU* 3.7 21.8 - - + -
486B LEU* 4.1 10.5 - - + -
489B LEU* 5.7 2.0 - - + -
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LYS* 5.6 3.5 + - - -
168B GLU* 2.6 36.3 + - + +
342B GLN* 3.1 38.0 + - + +
343B TYR* 3.1 13.1 + + - -
344B LEU* 1.3 76.5 - - - +
346B ARG* 1.3 100.8 + - + +
347B PHE 4.0 0.2 + - - -
348B ALA* 5.2 2.5 + - - +
349B ALA* 5.4 1.2 + - - +
381B GLU* 4.6 2.3 - - - +
382B PRO* 3.6 34.4 - - + +
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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