Contacts of the helix formed by residues 222 - 235 (chain B) in PDB entry 2KHW
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 THR 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B SER 4.3 7.0 - - - +
221B ASP* 1.3 82.0 + - - +
223B ILE* 1.3 67.2 + - - +
224B GLU* 3.3 29.0 - - - +
225B ASN* 2.8 36.2 + - - +
226B VAL* 3.3 5.9 + - - +
252B ASP 5.1 4.0 - - - -
254B ARG 3.3 13.5 - - - +
255B THR* 4.5 7.0 - - + -
256B LEU* 4.5 1.1 - - - -
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Residues in contact with ILE 223 (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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222B THR* 1.3 71.6 - - - +
224B GLU* 1.3 63.3 + - - +
225B ASN 3.1 0.2 + - - -
226B VAL* 3.3 8.4 + - + +
227B LYS* 3.1 38.5 + - - +
243B LEU* 4.7 6.1 - - + -
250B LEU* 3.6 44.9 - - + +
251B GLU 3.0 31.0 - - - +
252B ASP* 4.6 2.9 + - - +
254B ARG 3.1 12.7 + - - +
256B LEU* 3.7 22.0 - - + +
259B TYR* 3.8 21.3 - - + -
261B ILE* 5.0 0.7 - - + -
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Residues in contact with GLU 224 (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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222B THR* 3.0 19.7 + - - +
223B ILE* 1.3 79.0 - - - +
225B ASN* 1.3 74.4 + - - +
227B LYS* 3.7 10.1 - - - +
228B ALA* 3.3 19.2 + - - +
238B PRO* 5.9 1.0 - - - +
252B ASP* 3.9 31.2 - - + +
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Residues in contact with ASN 225 (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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221B ASP* 3.1 32.1 + - - +
222B THR* 2.8 25.4 + - - +
224B GLU* 1.3 88.4 - - - +
226B VAL* 1.3 67.1 + - - +
228B ALA* 2.8 19.6 + - - +
229B LYS* 3.1 15.8 + - + +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.2 23.6 - - + -
215B LEU* 4.8 0.7 - - + -
217B VAL* 4.0 10.8 - - + -
221B ASP* 3.7 15.2 + - - +
222B THR 3.9 4.0 - - - +
223B ILE* 3.3 8.0 + - + +
225B ASN* 1.3 75.2 - - - +
227B LYS* 1.3 66.0 + - - +
229B LYS* 2.8 33.7 + - + +
230B ILE* 3.1 21.1 - - + +
243B LEU* 4.2 14.1 - - + -
256B LEU* 3.8 29.4 - - + -
267B LEU* 5.5 4.3 - - + -
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Residues in contact with LYS 227 (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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223B ILE* 3.1 22.2 + - + +
224B GLU* 3.7 9.4 - - - +
226B VAL* 1.3 78.0 - - - +
228B ALA* 1.3 64.4 + - - +
229B LYS 3.2 0.3 + - - -
230B ILE* 3.2 4.6 + - - -
231B GLN 3.1 15.6 + - - -
238B PRO* 3.8 32.4 + - + +
241B GLN* 3.4 54.6 + - + +
242B ARG* 4.7 4.4 - - - +
243B LEU* 4.1 33.2 - - + +
250B LEU 5.0 4.6 + - - -
252B ASP* 3.6 27.7 + - - +
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Residues in contact with ALA 228 (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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224B GLU 3.3 11.2 + - - +
225B ASN* 2.8 15.3 + - - +
227B LYS* 1.3 79.4 - - - +
229B LYS* 1.3 64.0 + - + +
231B GLN* 3.0 26.3 + - + +
232B ASP* 3.0 19.0 + - - +
238B PRO* 5.8 2.4 - - - +
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Residues in contact with LYS 229 (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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215B LEU* 3.3 44.1 - - + +
216B GLU 3.2 27.5 - - - +
217B VAL* 3.7 16.4 - - + -
221B ASP* 4.9 2.5 - - - +
225B ASN* 3.1 13.9 + - + +
226B VAL* 2.8 17.0 + - - +
228B ALA* 1.3 78.6 - - + +
230B ILE* 1.3 64.1 + - - +
231B GLN 3.1 1.0 + - - -
232B ASP* 3.1 5.8 + - - +
233B LYS* 3.1 31.1 + - - +
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Residues in contact with ILE 230 (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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205B VAL* 4.2 24.9 - - + -
213B ILE* 4.8 6.1 - - + -
215B LEU* 3.7 21.5 - - + -
226B VAL* 3.1 37.2 - - + +
227B LYS* 3.2 5.6 + - - +
229B LYS* 1.3 79.0 - - - +
231B GLN* 1.3 55.7 + - - +
233B LYS* 4.6 3.6 - - - -
234B GLU* 2.5 57.3 + - + +
236B ILE* 4.0 10.5 - - + -
241B GLN* 3.3 21.3 - - - +
243B LEU* 4.4 9.4 - - + -
269B LEU* 4.0 10.8 - - + -
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Residues in contact with GLN 231 (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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227B LYS 3.1 10.8 + - - +
228B ALA* 3.0 19.6 + - - +
230B ILE* 1.3 77.6 - - - +
232B ASP* 1.3 63.8 + - - +
235B GLY* 2.7 31.2 + - - -
236B ILE 3.1 27.8 + - - +
237B PRO* 3.8 5.6 - - + +
238B PRO* 3.2 30.7 - - - +
241B GLN* 4.2 1.1 - - - +
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Residues in contact with ASP 232 (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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228B ALA* 3.0 14.8 + - - +
229B LYS* 3.1 8.3 + - - +
231B GLN* 1.3 83.4 - - - +
233B LYS* 1.3 67.0 + - + +
235B GLY 4.4 0.6 + - - -
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Residues in contact with LYS 233 (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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213B ILE* 4.2 13.2 - - + -
214B THR 5.1 2.7 - - - -
215B LEU* 3.7 27.4 - - + -
229B LYS* 3.1 22.8 + - - +
230B ILE* 4.0 3.8 - - - +
232B ASP* 1.3 86.6 + - + +
234B GLU* 1.3 77.6 + - + +
235B GLY 3.3 1.7 + - - -
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Residues in contact with GLU 234 (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 THR* 4.5 6.5 - - + +
211B LYS* 3.3 38.0 + - - +
213B ILE* 3.1 33.5 - - + +
230B ILE* 2.5 27.7 + - + +
233B LYS* 1.3 80.6 - - - +
235B GLY* 1.3 61.3 + - - -
236B ILE* 3.2 28.5 + - + +
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Residues in contact with GLY 235 (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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231B GLN* 2.7 28.2 + - - -
232B ASP 4.4 0.6 - - - -
233B LYS 3.3 2.2 + - - -
234B GLU* 1.3 73.6 - - - +
236B ILE* 1.3 59.8 + - - +
237B PRO* 3.9 5.9 - - - +
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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