Contacts of the helix formed by residues 220 - 241 (chain B) in PDB entry 1KNY
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B THR* 4.2 22.6 - - - +
162B LEU* 4.0 21.8 - - - +
217B LEU 5.6 0.2 + - - -
218B SER 3.4 9.2 + - - -
219B ASP* 1.3 71.8 + - - +
221B GLU* 1.3 67.6 + - - +
223B LEU* 2.8 16.0 + - - +
224B LEU* 3.1 20.1 + - - +
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Residues in contact with GLU 221 (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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219B ASP* 4.0 8.3 - - - +
220B SER* 1.3 79.7 - - - +
222B LYS* 1.3 58.7 + - - +
224B LEU* 4.1 7.5 - - - +
225B GLU* 3.1 28.8 + - - +
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B HIS* 6.3 1.7 - - + -
211B PHE* 4.2 22.8 - - + -
219B ASP* 3.5 40.3 + - + +
220B SER 3.1 0.6 - - - -
221B GLU* 1.3 77.8 - - - +
223B LEU* 1.3 58.6 + - - +
225B GLU* 4.0 8.5 - - + +
226B SER* 2.3 33.6 + - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 4.0 26.0 - - + -
163B PRO 5.0 1.6 - - - -
166B THR* 4.4 18.6 - - + +
208B LEU* 5.3 2.3 - - + +
211B PHE* 3.6 44.2 - - + -
216B GLN 4.6 3.1 - - - +
217B LEU* 3.3 36.6 - - + +
219B ASP 2.7 23.1 - - - +
220B SER* 2.8 7.2 + - - +
222B LYS* 1.3 77.3 - - - +
224B LEU* 1.3 60.5 + - - +
225B GLU 2.9 1.6 - - - -
226B SER* 2.6 22.4 + - - -
227B LEU* 2.8 18.7 + - + +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 2.9 52.0 - - + +
153B ILE* 5.1 1.3 - - + -
154B ARG* 3.1 47.3 - - + +
162B LEU* 4.0 18.2 - - + -
220B SER* 3.1 16.0 + - - +
221B GLU* 4.1 6.5 - - - +
223B LEU* 1.3 79.9 - - - +
225B GLU* 1.3 56.8 + - - +
227B LEU* 3.2 8.5 - - + +
228B GLU* 2.9 38.1 + - - +
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Residues in contact with GLU 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 GLU 3.1 18.5 + - - +
222B LYS* 4.1 5.8 - - + +
223B LEU 2.9 0.2 - - - -
224B LEU* 1.3 81.3 - - - +
226B SER* 1.3 63.8 + - - +
228B GLU* 4.1 5.1 - - - +
229B ASN* 3.1 39.2 + - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY 4.4 7.4 - - - +
207B HIS* 4.2 18.6 + - - -
208B LEU* 4.4 15.4 - - - +
211B PHE* 3.9 25.1 - - - -
222B LYS* 2.3 29.0 + - - +
223B LEU* 2.6 11.0 + - - -
225B GLU* 1.3 77.5 - - - +
227B LEU* 1.3 58.9 + - - +
229B ASN* 3.9 7.8 - - - +
230B PHE* 3.4 21.1 + - - +
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Residues in contact with LEU 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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150B TRP* 3.6 50.2 - - + -
162B LEU* 4.1 7.2 - - + -
165B LEU* 5.6 0.9 - - + -
166B THR* 3.8 23.1 - - + +
169B VAL* 3.8 28.3 - - + -
208B LEU* 3.8 22.0 - - + -
223B LEU* 2.8 17.0 + - - +
224B LEU* 3.2 18.6 - - - +
226B SER* 1.3 74.4 - - - +
228B GLU* 1.3 60.1 + - - +
229B ASN 3.2 1.3 - - - -
230B PHE* 3.1 7.2 + - + +
231B TRP* 2.9 27.2 + - - +
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 3.3 22.1 + - - -
151B ARG* 2.8 44.2 + - - +
154B ARG* 3.3 24.0 + - - -
224B LEU 2.9 18.3 + - - +
225B GLU* 4.6 2.9 - - - +
226B SER 3.5 0.2 - - - -
227B LEU* 1.3 78.8 - - - +
229B ASN* 1.3 65.4 + - - +
231B TRP* 3.0 11.5 + - + +
232B ASN* 2.9 37.8 + - - +
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Residues in contact with ASN 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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203B SER* 3.3 9.4 + - - +
204B GLY* 4.8 6.1 - - - -
225B GLU* 3.1 36.0 + - - +
226B SER* 3.9 9.5 - - - +
228B GLU* 1.3 81.4 - - - +
230B PHE* 1.3 68.2 + - - +
232B ASN* 3.3 12.1 + - - +
233B GLY 2.8 17.7 + - - -
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Residues in contact with PHE 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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143B LEU* 3.8 19.3 - - + -
150B TRP* 5.2 3.1 - + - -
169B VAL* 3.9 23.1 - - + -
173B GLY* 3.9 24.2 - - - -
176B LEU* 5.5 0.7 - - + -
202B PRO* 4.3 13.9 - - + -
203B SER 3.7 8.1 - - - -
204B GLY* 4.3 4.2 - - - -
205B TYR* 3.6 44.9 - + + -
208B LEU* 4.1 9.0 - - + -
226B SER 3.4 14.0 + - - +
227B LEU* 3.1 13.1 + - + +
229B ASN* 1.3 80.8 - - - +
231B TRP* 1.3 55.9 + - - +
233B GLY* 2.8 20.3 + - - -
234B ILE* 2.8 40.0 + - + +
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Residues in contact with TRP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 18.5 + - + -
2A ASN 3.8 0.8 + - - -
3A GLY* 3.5 36.8 - - - +
139B ILE* 4.8 3.6 - - + -
143B LEU* 4.0 31.0 - - + -
144B PHE* 3.7 30.5 - + + -
147B ALA* 4.3 11.7 - - + -
150B TRP* 3.9 15.7 - + + -
151B ARG* 3.6 21.0 - - - +
227B LEU 2.9 11.9 + - - +
228B GLU* 3.0 11.7 - - + +
230B PHE* 1.3 78.8 - + - +
232B ASN* 1.3 75.1 + - - +
234B ILE* 3.1 20.0 + - + +
235B GLN* 2.8 63.1 + - - -
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Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.8 2.0 + - - -
2A ASN* 5.9 1.8 + - - +
151B ARG* 5.7 0.2 - - - +
228B GLU* 2.9 29.7 + - - +
229B ASN* 3.8 12.6 + - - +
230B PHE 3.1 0.2 - - - -
231B TRP* 1.3 89.8 - - - +
233B GLY* 1.3 65.2 + - - +
234B ILE 3.1 0.2 - - - -
235B GLN* 3.2 13.6 + - + +
236B GLU* 3.1 28.4 + - - +
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Residues in contact with GLY 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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202B PRO* 4.0 7.7 - - - +
203B SER* 3.1 40.2 + - - -
229B ASN 2.8 7.6 + - - -
230B PHE 2.8 4.9 + - - -
232B ASN* 1.3 76.6 - - - +
234B ILE* 1.3 62.4 + - - +
236B GLU* 3.5 5.6 + - - +
237B TRP* 3.1 25.3 + - - +
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Residues in contact with ILE 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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139B ILE* 4.8 12.8 - - + -
143B LEU* 4.5 15.9 - - + -
176B LEU* 4.1 20.2 - - + -
202B PRO* 4.5 6.5 - - + -
230B PHE* 2.8 57.7 + - + +
231B TRP* 3.2 18.4 - - + +
233B GLY* 1.3 75.7 - - - +
235B GLN* 1.3 79.8 + - - +
236B GLU 3.1 0.2 + - - -
237B TRP* 3.6 6.0 - - + +
238B THR* 2.7 48.1 + - + +
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Residues in contact with GLN 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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1A MET* 2.8 58.4 + - - +
139B ILE* 5.5 1.2 - - - +
231B TRP* 2.8 61.9 + - + +
232B ASN* 3.2 16.1 + - - +
234B ILE* 1.3 88.8 - - - +
236B GLU* 1.3 60.9 + - + +
238B THR* 3.0 17.4 + - - -
239B GLU* 3.7 20.9 - - - +
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Residues in contact with GLU 236 (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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203B SER* 5.2 10.6 + - - -
232B ASN* 3.1 14.3 + - - +
233B GLY* 3.6 11.7 - - - +
234B ILE 3.1 0.4 - - - -
235B GLN* 1.3 76.0 - - + +
237B TRP* 1.3 56.0 + - - +
239B GLU* 2.9 30.6 + - - +
240B ARG* 2.9 28.9 + - - +
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Residues in contact with TRP 237 (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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135B ILE* 4.5 4.5 - - + -
176B LEU* 4.1 32.8 - - + -
177B ILE* 5.3 3.8 - - + -
180B HIS* 3.3 54.7 - + + -
200B ASP 2.3 30.1 + - - -
202B PRO* 3.7 29.6 - - + +
203B SER 5.4 0.2 - - - +
233B GLY 3.1 16.2 - - - +
234B ILE* 3.6 4.5 - - - +
236B GLU* 1.3 76.2 - - - +
238B THR* 1.3 69.7 + - + +
240B ARG* 3.0 30.1 + - - +
241B HIS* 2.7 54.8 + + - -
243B TYR* 3.6 21.8 - + - -
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Residues in contact with THR 238 (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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139B ILE* 3.5 23.3 - - + -
176B LEU* 5.7 0.4 - - + -
234B ILE* 2.7 31.4 + - + +
235B GLN* 3.0 18.4 + - - -
237B TRP* 1.3 86.7 - - + +
239B GLU* 1.3 52.6 + - - +
242B GLY* 2.6 29.3 + - - -
243B TYR* 2.7 53.1 + - + +
244B ILE* 3.9 2.0 - - - +
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Residues in contact with GLU 239 (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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1A MET 5.8 1.6 + - - -
235B GLN* 3.7 16.9 - - - +
236B GLU* 2.9 15.7 + - - +
238B THR* 1.3 81.7 + - - +
240B ARG* 1.3 60.4 + - - +
242B GLY* 4.0 4.0 + - - -
244B ILE* 4.0 25.3 - - + +
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Residues in contact with ARG 240 (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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200B ASP* 3.4 22.0 + - - +
201B LEU 4.0 10.9 + - - -
203B SER* 5.9 4.2 - - - +
236B GLU* 2.9 25.1 + - - +
237B TRP* 3.0 44.3 - - - +
239B GLU* 1.3 80.1 - - - +
241B HIS* 1.3 72.3 + - + +
242B GLY 3.6 0.2 + - - -
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Residues in contact with HIS 241 (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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132B HIS* 5.3 1.2 - - - -
180B HIS* 3.4 23.5 + + - -
200B ASP* 3.2 25.1 + - - -
237B TRP* 2.7 59.3 + + - -
240B ARG* 1.3 102.8 + - + +
242B GLY* 1.3 59.3 + - - +
243B TYR* 3.1 35.1 - + + -
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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
------------------------------------------------------------
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