Contacts of the helix formed by residues 220 - 240 (chain B) in PDB entry 5UNH
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 PHE 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ASN* 2.9 13.4 + - + +
219B GLY* 1.4 78.6 - - - +
221B ILE* 1.4 71.3 + - + +
223B PRO* 3.5 5.1 - - - +
224B LEU* 2.8 50.7 + - + +
265B PHE* 3.7 25.1 - + - -
266B ILE* 3.9 19.5 - - + -
269B TRP* 3.7 19.5 - - + -
270B LEU* 3.6 53.4 - - + -
273B HIS* 3.6 26.5 - + + +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN* 2.8 28.6 + - + +
217B ILE* 3.8 30.7 - - + +
220B PHE* 1.4 89.2 - - + +
222B ILE* 1.4 61.0 + - + +
224B LEU* 3.7 3.1 - - - +
225B ILE* 2.9 47.6 + - + +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.0 41.5 + - + +
218B LEU* 4.9 15.0 - - + +
221B ILE* 1.4 72.7 - - + +
223B PRO* 1.4 71.1 - - + +
225B ILE* 3.2 23.1 + - + +
226B PHE* 3.1 40.9 - - + -
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Residues in contact with PRO 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.6 30.1 - - + -
133B PHE* 5.1 5.2 - - + -
136B THR* 4.1 15.3 - - + +
217B ILE 3.7 0.7 - - - +
218B LEU 3.4 24.7 - - - +
219B GLY 3.8 6.1 - - - -
220B PHE 3.5 14.6 - - - +
222B ILE* 1.4 93.1 - - + +
224B LEU* 1.4 61.1 + - - +
226B PHE* 3.1 12.1 + - + +
227B ILE* 3.0 26.9 + - + +
265B PHE* 4.0 10.3 - - + -
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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
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220B PHE* 2.8 36.9 + - + +
221B ILE* 3.8 3.8 - - - +
223B PRO* 1.4 68.8 - - - +
225B ILE* 1.4 66.5 + - - +
227B ILE* 4.0 6.0 - - + +
228B ALA* 2.9 37.8 + - + +
262B VAL* 4.2 20.4 - - + +
265B PHE* 3.7 19.2 - - + -
266B ILE* 3.7 31.9 - - + -
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 2.9 38.6 + - + +
222B ILE* 3.2 17.5 + - + +
224B LEU* 1.4 72.9 - - - +
226B PHE* 1.4 60.5 + - + +
228B ALA* 3.7 4.0 - - - +
229B THR* 2.6 48.8 + - + +
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Residues in contact with PHE 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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119A VAL* 4.8 24.9 - - + -
136B THR* 3.5 30.7 - - + +
139B SER* 5.2 0.4 - - - -
140B VAL* 4.2 18.6 - - + -
222B ILE* 3.1 43.5 - - + -
223B PRO* 3.1 6.6 + - + +
225B ILE* 1.4 81.5 - - + +
227B ILE* 1.4 65.4 + - + +
229B THR* 3.0 8.5 + - - -
230B CYS* 3.0 32.5 + - - -
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Residues in contact with ILE 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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132B ILE 5.3 0.2 - - - +
135B ILE* 3.8 25.4 - - + -
136B THR* 3.7 29.8 - - - +
139B SER* 3.7 22.7 + - - +
223B PRO* 3.0 25.0 + - + +
224B LEU* 4.0 12.1 - - + +
226B PHE* 1.4 74.0 - - - +
228B ALA* 1.3 56.6 + - - +
230B CYS* 3.7 2.4 + - - +
231B TYR* 3.1 27.7 + - - +
261B VAL* 4.3 8.7 - - + +
262B VAL* 3.8 35.4 - - + +
265B PHE* 4.8 10.5 - - + -
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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 LEU* 2.9 29.9 + - + +
225B ILE* 3.7 3.6 - - - +
227B ILE* 1.3 75.6 - - - +
229B THR* 1.4 63.5 + - + +
231B TYR* 3.4 1.5 + - - +
232B PHE* 3.1 44.9 + - + -
262B VAL* 4.1 12.0 - - + +
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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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179A PHE* 6.5 0.7 - - + -
143B TYR* 5.1 1.1 - - - -
225B ILE* 2.6 38.0 + - + +
226B PHE* 3.0 17.7 + - - -
228B ALA* 1.4 71.6 - - + +
230B CYS* 1.4 52.2 + - - +
232B PHE* 3.8 3.9 - - - +
233B GLY* 2.8 31.9 + - - -
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Residues in contact with CYS 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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139B SER* 3.4 42.2 - - - +
140B VAL* 3.8 20.6 - - - -
143B TYR* 3.9 20.3 - - + -
226B PHE* 3.0 21.4 + - - +
227B ILE 3.9 3.6 - - - +
229B THR* 1.4 76.1 - - - +
231B TYR* 1.4 58.1 + - - +
233B GLY 3.3 0.7 + - - -
234B ILE* 3.0 38.5 + - + +
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Residues in contact with TYR 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 ILE 3.1 18.8 + - - +
228B ALA* 3.4 4.0 + - - +
230B CYS* 1.4 75.6 - - - +
232B PHE* 1.3 88.8 + + - +
234B ILE* 3.2 8.7 + - - +
235B ARG* 2.8 56.9 + - - +
255B LEU* 4.0 21.7 + - + +
258B ALA* 3.6 27.6 - - + +
259B ALA* 3.7 28.2 - - + +
261B VAL* 6.3 0.4 - - + -
262B VAL* 4.2 20.9 - - + -
263B LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 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* 3.1 37.4 + - + +
229B THR* 3.8 3.6 - - - +
231B TYR* 1.3 93.8 - + - +
233B GLY* 1.3 58.7 + - - +
234B ILE 3.3 0.2 - - - -
235B ARG* 3.4 41.1 - - + +
236B LYS* 3.0 29.3 + - - +
262B VAL* 6.5 0.4 - - + -
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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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143B TYR* 3.4 30.0 - - - -
147B ILE* 3.7 12.3 - - - +
229B THR 2.8 19.0 + - - -
230B CYS 3.7 0.4 - - - -
231B TYR 3.2 0.2 - - - -
232B PHE* 1.3 75.6 - - - +
234B ILE* 1.4 59.8 + - - +
236B LYS* 4.3 3.4 - - - +
237B HIS* 3.8 9.4 + - - +
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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 SER* 4.6 3.1 - - - +
142B ARG* 4.0 13.5 - - + +
143B TYR* 3.7 37.0 - - + +
146B VAL* 3.9 30.3 - - + -
230B CYS* 3.0 28.5 + - + +
231B TYR* 3.6 7.4 - - - +
233B GLY* 1.4 77.0 - - - +
235B ARG* 1.3 64.4 + - - +
236B LYS 3.4 0.2 - - - -
237B HIS* 3.6 0.7 + - - +
238B LEU* 3.1 33.0 + - + +
254B VAL* 5.5 5.4 - - + -
255B LEU* 5.3 5.8 - - + -
258B ALA* 4.3 24.0 - - + -
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Residues in contact with ARG 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 TYR* 2.8 43.4 + - + +
232B PHE* 3.4 36.1 - - + -
234B ILE* 1.3 77.9 - - - +
236B LYS* 1.4 61.2 + - - +
238B LEU* 4.0 1.0 - - - +
239B LEU* 3.2 45.2 + - + +
255B LEU* 3.7 26.2 - - + +
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Residues in contact with LYS 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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232B PHE 3.0 20.1 + - - +
233B GLY* 4.7 4.0 - - - +
234B ILE 3.4 0.2 - - - -
235B ARG* 1.4 76.2 - - - +
237B HIS* 1.4 59.9 + - - +
239B LEU* 3.4 6.7 + - - +
240B LYS* 3.3 22.7 + - - +
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Residues in contact with HIS 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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146B VAL* 3.5 25.5 + - + -
147B ILE* 3.4 51.5 + - + +
233B GLY 3.8 7.9 + - - +
234B ILE 3.6 4.0 + - - +
235B ARG 3.4 0.2 - - - -
236B LYS* 1.4 78.4 - - - +
238B LEU* 1.3 70.4 + - + +
239B LEU 3.4 0.9 + - - -
240B LYS* 3.4 16.1 + - - +
241B THR* 3.5 15.6 - - + +
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Residues in contact with LEU 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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146B VAL* 3.7 34.8 - - + -
234B ILE* 3.1 32.2 + - + +
235B ARG 4.5 0.2 - - - +
237B HIS* 1.3 83.0 - - + +
239B LEU* 1.3 56.1 + - - +
240B LYS 3.5 0.2 - - - -
241B THR* 2.7 28.5 + - + -
242B ASN 4.7 0.2 + - - -
251B ARG* 4.2 21.0 - - + +
254B VAL* 5.1 8.7 - - + -
255B LEU* 3.8 24.5 - - + -
329B LEU* 4.5 13.5 - - + -
332B VAL* 3.8 32.1 - - + -
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Residues in contact with LEU 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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235B ARG* 3.2 48.2 + - + +
236B LYS* 3.7 6.7 - - - +
237B HIS 3.2 0.4 - - - -
238B LEU* 1.3 77.1 - - - +
240B LYS* 1.4 58.4 + - - +
241B THR 3.2 5.8 + - - -
242B ASN* 3.7 19.4 + - - +
251B ARG* 5.6 10.5 - - - +
255B LEU* 5.5 7.2 - - + -
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Residues in contact with LYS 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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236B LYS 3.3 16.1 + - - +
237B HIS* 3.4 9.4 + - - +
239B LEU* 1.4 74.1 - - - +
241B THR* 1.3 60.9 + - - +
242B ASN* 3.5 5.2 + - - +
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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