Contacts of the helix formed by residues 248 - 256 (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 ASN 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B LYS 4.3 1.3 - - - +
211B THR* 3.5 29.0 + - - +
212B PHE* 4.5 0.2 - - + -
213B THR* 5.0 2.4 - - - +
246B SER* 2.9 6.4 + - - +
247B THR* 1.3 78.9 - - - +
249B THR* 1.3 63.2 + - - +
250B ALA* 3.2 13.6 + - - +
251B LYS* 2.9 34.9 + - + +
252B VAL* 3.3 24.4 + - - +
262B MET* 4.4 0.7 - - - -
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Residues in contact with THR 249 (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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247B THR 3.8 4.6 + - - -
248B ASN* 1.3 73.3 + - - +
250B ALA* 1.3 64.7 + - - +
252B VAL* 3.5 1.9 + - - +
253B LYS* 3.2 23.5 + - + +
259B PRO* 5.6 13.5 - - + -
262B MET* 3.1 35.7 - - + +
264B GLU* 5.0 2.4 + - - -
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Residues in contact with ALA 250 (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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248B ASN* 3.2 10.5 + - - +
249B THR* 1.3 78.0 - - - +
251B LYS* 1.3 67.4 + - + +
253B LYS* 3.1 21.3 + - - +
254B GLU* 3.2 7.8 + - - +
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Residues in contact with LYS 251 (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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212B PHE* 3.8 28.0 - - + +
213B THR* 3.9 28.7 - - + +
248B ASN* 2.9 32.5 + - - +
250B ALA* 1.3 72.5 - - + +
252B VAL* 1.3 65.8 + - - +
254B GLU* 3.1 15.7 + - + +
255B PHE* 3.1 22.0 + - - +
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Residues in contact with VAL 252 (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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212B PHE* 3.8 33.7 - - + -
244B ALA* 3.8 13.0 - - + -
246B SER* 3.9 7.2 - - - -
248B ASN 3.3 15.7 + - - +
249B THR 3.8 7.0 - - - +
251B LYS* 1.3 77.3 - - - +
253B LYS* 1.3 61.8 + - - +
255B PHE* 3.4 7.8 + - - +
256B GLY 3.5 0.5 + - - -
257B ILE* 3.2 50.5 + - + +
258B ASP 5.6 0.2 - - - -
262B MET* 3.8 27.4 - - + -
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Residues in contact with LYS 253 (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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249B THR* 3.2 15.7 + - + +
250B ALA* 3.1 12.9 + - - +
251B LYS 3.1 0.2 - - - -
252B VAL* 1.3 78.0 - - - +
254B GLU* 1.3 63.8 + - - +
256B GLY* 3.0 16.3 + - - -
257B ILE 3.8 11.5 + - - +
258B ASP* 5.6 5.6 - - - +
259B PRO* 5.3 13.0 - - + +
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Residues in contact with GLU 254 (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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250B ALA 3.2 7.4 + - - +
251B LYS* 3.1 19.0 + - + +
253B LYS* 1.3 79.8 - - - +
255B PHE* 1.3 60.9 + - - +
256B GLY* 3.5 0.7 + - - -
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Residues in contact with PHE 255 (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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207B ILE* 4.5 3.8 - - + -
212B PHE* 3.8 23.8 - + + -
218B ILE* 4.9 10.8 - - + -
221B ALA* 3.7 35.7 - - + -
222B LYS* 3.6 35.2 - - + -
225B LYS* 2.6 52.6 + - + -
242B PHE* 4.5 13.2 - + - -
251B LYS 3.1 6.9 + - - +
252B VAL 3.7 8.3 - - - +
253B LYS 3.1 0.6 - - - -
254B GLU* 1.3 77.3 - - - +
256B GLY* 1.3 54.1 + - - +
257B ILE* 3.5 34.5 - - + -
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Residues in contact with GLY 256 (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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225B LYS* 4.6 2.9 - - - +
238B VAL* 3.8 23.0 - - - +
239B ALA* 5.8 0.9 - - - -
253B LYS 3.0 10.2 + - - -
254B GLU 3.2 1.3 - - - -
255B PHE* 1.3 80.3 - - - +
257B ILE* 1.3 68.8 + - - +
258B ASP 4.1 1.1 + - - -
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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