Contacts of the helix formed by residues 220 - 235 (chain B) in PDB entry 5HKE
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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208A THR 3.4 7.6 - - - -
209A GLY 3.8 15.2 + - - -
210A PHE* 4.3 12.1 - - - -
213A ILE* 4.1 11.2 - - - +
218B ASP* 2.7 22.6 + - - -
219B VAL* 1.4 79.3 - - - +
221B PRO* 1.3 75.3 - - - +
222B GLU* 3.9 4.8 + - - +
223B SER* 3.1 17.7 + - - -
224B ARG* 2.9 20.3 + - - +
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Residues in contact with PRO 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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206A ASP* 5.9 0.7 - - - +
207A GLY* 4.3 17.5 - - - -
208A THR* 3.3 18.4 - - - +
210A PHE* 4.6 4.5 - - + -
170B THR* 2.9 22.5 + - - +
171B ASN* 3.7 29.6 - - + +
172B ASN 3.3 21.5 - - - +
220B SER* 1.3 86.5 - - - +
222B GLU* 1.3 57.7 + - - +
224B ARG* 3.6 20.8 - - - +
225B PHE* 3.0 17.3 + - - +
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Residues in contact with GLU 222 (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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172B ASN 4.3 0.6 + - - -
173B PRO* 3.4 31.6 - - + +
177B TYR* 4.1 3.3 - - - +
178B GLN* 3.4 19.6 - - - +
181B ASN* 3.4 37.7 + - - +
220B SER* 3.3 5.4 + - - +
221B PRO* 1.3 79.0 - - - +
223B SER* 1.3 66.5 + - - +
225B PHE* 3.2 2.9 + - - +
226B VAL* 3.0 27.9 + - - +
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Residues in contact with SER 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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213A ILE* 4.8 3.3 - - - +
216B PRO* 3.5 25.8 - - - +
218B ASP* 2.7 47.1 + - - -
220B SER* 3.1 10.2 + - - -
222B GLU* 1.3 77.6 - - - +
224B ARG* 1.3 59.7 + - - +
226B VAL* 3.2 3.6 + - - +
227B ARG* 2.9 33.8 + - - +
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Residues in contact with ARG 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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208A THR* 5.5 1.4 + - - -
2B OCS 2.8 33.4 + - - -
3B THR* 3.1 14.4 + - - +
19B ASP* 4.0 1.5 + - - -
170B THR* 3.8 8.6 - - + -
171B ASN* 2.8 23.4 + - - -
219B VAL* 2.9 31.5 + - - +
220B SER 2.9 11.7 + - - +
221B PRO* 3.6 19.9 - - - +
223B SER* 1.3 77.3 - - - +
225B PHE* 1.3 55.8 + - - +
227B ARG* 3.9 19.3 - - - +
228B ALA* 2.8 35.2 + - - +
255B VAL* 3.4 35.2 - - + +
257B GLN* 3.5 20.4 - - - +
270B GLU* 4.5 3.6 + - - -
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Residues in contact with PHE 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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166B ILE* 3.8 26.5 - - + -
168B ILE* 3.6 29.7 - - + +
169B LEU* 4.0 5.2 - - + -
170B THR* 3.7 24.5 - - - +
175B PHE* 3.9 20.6 - + - -
178B GLN* 3.4 65.7 - - + +
179B MET* 4.0 4.9 - - - -
182B LEU* 4.2 9.6 - - + -
221B PRO 3.0 12.7 + - - +
222B GLU 3.4 4.7 - - - +
223B SER 3.2 0.2 - - - -
224B ARG* 1.3 76.4 - - - +
226B VAL* 1.3 62.4 + - + +
228B ALA 4.0 0.2 - - - -
229B THR* 2.8 33.2 + - - -
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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
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181B ASN* 3.4 24.0 - - - +
182B LEU* 4.1 20.6 - - + -
185B TYR* 3.7 41.5 - - + +
188B LEU* 5.2 0.4 - - + -
215B LEU* 4.1 8.5 - - + -
216B PRO* 4.0 17.9 - - + -
222B GLU 3.0 14.9 + - - +
223B SER* 3.2 5.8 + - - +
225B PHE* 1.3 76.4 - - + +
227B ARG* 1.3 58.2 + - - +
229B THR* 3.3 3.6 + - - -
230B PHE* 3.0 28.2 + - + +
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Residues in contact with ARG 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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217A GLY* 4.2 16.4 - - - -
227A ARG* 6.2 1.9 - - - +
215B LEU* 4.1 19.7 - - + -
216B PRO 2.9 38.5 + - - +
217B GLY* 3.3 16.9 + - - -
218B ASP 2.8 30.3 + - - -
219B VAL* 4.1 7.9 - - - +
223B SER 2.9 23.5 + - - +
224B ARG* 3.9 8.2 - - - +
226B VAL* 1.3 73.2 - - - +
228B ALA* 1.3 66.3 + - - +
230B PHE* 3.5 1.7 + - - +
231B SER* 2.9 37.2 + - - +
254B THR* 2.7 31.1 + - - +
255B VAL* 3.9 20.3 - - + +
256B GLU 5.1 1.0 + - - -
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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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3B THR* 3.9 25.1 - - + -
5B ILE* 4.8 3.8 - - + -
168B ILE* 3.9 14.1 - - + -
224B ARG 2.8 22.5 + - - +
225B PHE 4.1 2.5 - - - +
227B ARG* 1.3 72.3 - - - +
229B THR* 1.3 59.1 + - - +
231B SER* 4.0 0.8 - - - -
232B LYS* 2.8 33.6 + - - +
251B ILE* 4.5 5.5 - - + +
254B THR* 4.5 5.2 - - - -
255B VAL* 3.7 13.8 - - + +
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Residues in contact with THR 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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166B ILE* 3.4 33.0 - - + +
168B ILE* 3.5 14.7 - - - +
182B LEU* 4.2 18.6 - - + -
225B PHE* 2.8 26.9 + - - -
226B VAL 3.5 4.0 - - - -
227B ARG 3.2 0.2 - - - -
228B ALA* 1.3 77.3 - - - +
230B PHE* 1.3 64.3 + - - +
232B LYS* 3.9 0.6 - - - +
233B LEU* 2.9 48.7 + - + +
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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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261A VAL* 4.1 28.7 - - + -
188B LEU* 4.0 30.5 - - + -
189B SER* 3.9 26.2 - - - -
190B ILE* 4.0 8.1 - - + -
212B GLY* 4.8 7.9 - - - -
215B LEU* 3.9 32.8 - - + -
226B VAL* 3.0 16.7 + - + +
227B ARG 3.9 2.9 - - - +
229B THR* 1.3 77.7 - - - +
231B SER* 1.3 66.0 + - - +
233B LEU* 5.1 1.3 - - - -
234B ASN* 3.0 53.1 + - - +
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Residues in contact with SER 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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258A ILE* 3.7 22.2 - - - +
261A VAL* 4.0 14.5 - - - +
215B LEU* 5.4 1.2 - - - +
227B ARG* 2.9 22.8 + - - +
228B ALA* 4.0 2.2 - - - -
230B PHE* 1.3 79.0 - - - +
232B LYS* 1.3 58.3 + - - +
234B ASN 3.8 0.7 - - - -
235B SER* 3.0 30.7 + - - -
251B ILE* 4.6 4.5 - - - -
254B THR* 3.4 28.5 + - - +
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.6 3.8 - - + -
6B THR* 2.8 43.2 + - - +
7B LEU* 4.2 22.4 - - + +
8B ASN* 5.4 3.2 + - - +
166B ILE 2.8 30.4 + - - +
167B GLY 3.9 0.8 + - - +
168B ILE* 3.8 16.4 - - + -
228B ALA 2.8 18.3 + - - +
229B THR 4.0 2.0 - - - +
231B SER* 1.3 75.6 - - - +
233B LEU* 1.3 80.7 + - + +
235B SER* 2.9 20.3 + - - +
251B ILE* 4.1 22.5 - - + +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ILE* 4.1 26.5 - - + +
168B ILE* 6.1 0.2 - - + -
229B THR* 2.9 39.8 + - + +
230B PHE* 4.6 1.8 - - - +
232B LYS* 1.3 100.1 - - + +
234B ASN* 1.3 64.9 + - - +
235B SER 3.7 1.9 + - - +
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Residues in contact with ASN 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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260A GLY* 3.2 32.2 - - - +
261A VAL* 4.4 4.9 - - + -
190B ILE* 3.5 23.1 - - + +
230B PHE* 3.0 54.4 + - - +
231B SER 3.8 0.4 - - - -
232B LYS 3.2 0.4 - - - -
233B LEU* 1.3 83.3 - - - +
235B SER* 1.3 66.5 + - - +
236B SER* 4.3 0.5 - - - -
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Residues in contact with SER 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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258A ILE* 4.3 2.5 - - - -
259A LYS 3.5 6.3 - - - -
260A GLY* 4.4 0.7 - - - -
7B LEU* 4.3 8.0 - - - +
231B SER 3.0 17.3 + - - -
232B LYS 2.9 15.1 + - - +
233B LEU 3.4 2.1 - - - +
234B ASN* 1.3 79.0 - - - +
236B SER* 1.3 65.9 + - - +
237B LYS* 3.6 9.2 + - - +
247B GLN* 3.3 23.7 - - - +
251B ILE* 3.6 19.9 - - - +
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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