Contacts of the helix formed by residues 220 - 237 (chain B) in PDB entry 1YTB
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 ARG 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.2 26.8 - - + +
160B ILE* 3.6 13.4 - - + +
219B GLN* 1.3 71.4 - - - +
221B GLU* 1.3 77.7 + - - +
222B GLU 3.2 0.2 - - - -
223B ILE* 3.2 19.9 + - - +
224B TYR* 3.3 47.4 + - + -
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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 GLN* 3.0 25.0 + - + +
220B ARG* 1.3 92.9 + - + +
222B GLU* 1.3 54.7 + - + +
224B TYR* 3.2 13.2 + - + +
225B GLN* 2.8 48.8 + - + +
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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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200B PRO* 3.6 14.3 - - + +
201B LYS 5.6 0.8 - - - +
202B ILE* 3.9 17.2 - - + +
217B ALA* 3.4 5.2 - - + -
218B LYS* 2.8 34.2 + - - +
219B GLN* 3.0 33.2 + - + +
221B GLU* 1.3 75.8 - - + +
223B ILE* 1.3 59.2 + - - +
225B GLN* 3.7 16.4 - - - +
226B ALA* 2.9 31.5 + - - +
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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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65B PRO* 3.8 26.5 - - + -
67B LEU* 4.3 13.0 - - + -
160B ILE* 3.6 31.4 - - + +
162B GLY* 3.9 7.9 - - - +
202B ILE* 4.9 3.1 - - + -
214B LEU* 3.6 44.2 - - + +
215B THR 4.4 1.3 - - - +
217B ALA* 3.7 19.3 - - + -
219B GLN 4.6 0.7 - - - +
220B ARG* 3.2 11.5 + - - +
222B GLU* 1.3 76.6 - - - +
224B TYR* 1.3 64.7 + - + +
226B ALA* 3.5 6.1 + - - +
227B PHE* 3.1 19.8 + - - +
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Residues in contact with TYR 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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64B VAL* 3.8 16.1 - - + +
65B PRO* 3.6 43.3 + - + -
67B LEU* 4.3 21.3 - - + +
220B ARG* 3.3 54.5 + - + -
221B GLU* 3.2 11.1 + - + +
223B ILE* 1.3 75.7 - - + +
225B GLN* 1.3 65.5 + - + +
227B PHE* 3.2 3.8 + - - +
228B GLU* 3.0 29.8 + - + +
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Residues in contact with GLN 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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200B PRO* 3.6 34.7 - - + +
221B GLU* 2.8 30.1 + - + +
222B GLU* 3.7 15.2 - - - +
224B TYR* 1.3 71.0 - - + +
226B ALA* 1.3 65.9 + - - +
228B GLU* 2.9 20.5 + - - +
229B ALA* 3.0 14.6 + - - +
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Residues in contact with ALA 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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197B MET* 3.5 26.3 - - + +
200B PRO* 3.9 1.5 - - - +
202B ILE* 3.7 27.8 - - + -
204B LEU* 4.7 2.0 - - + -
214B LEU* 3.7 15.0 - - + -
222B GLU 2.9 19.1 + - - +
223B ILE 3.5 5.8 - - - +
225B GLN* 1.3 77.5 - - - +
227B PHE* 1.3 62.2 + - - +
229B ALA 3.2 0.9 + - - -
230B ILE* 3.1 19.9 + - - +
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Residues in contact with PHE 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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61B SER* 4.2 10.1 - - - -
63B ILE* 3.7 40.2 - - + -
65B PRO* 3.8 21.1 - - + -
164B CYS* 3.3 29.2 - - - -
166B VAL* 3.7 28.0 - - + -
212B ILE* 4.5 5.2 - - + -
214B LEU* 3.7 12.3 - - + +
223B ILE 3.1 10.8 + - - +
224B TYR 3.7 6.7 - - - +
225B GLN 3.2 0.4 - - - -
226B ALA* 1.3 79.2 - - - +
228B GLU* 1.3 70.1 + - - +
230B ILE* 4.0 9.6 - - + -
231B TYR* 3.2 31.5 + + - +
234B LEU* 4.2 11.9 - - + -
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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
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61B SER* 4.6 7.7 + - - -
63B ILE 4.6 6.1 - - - +
224B TYR* 3.0 20.4 + - + +
225B GLN* 2.9 12.2 + - - +
227B PHE* 1.3 89.6 - - - +
229B ALA* 1.3 62.4 + - - +
231B TYR* 3.7 4.2 + - - +
232B PRO* 3.1 19.9 - - - +
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Residues in contact with ALA 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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197B MET* 3.7 21.1 - - + -
199B LYS 5.3 5.2 - - - +
200B PRO* 5.6 1.1 - - + -
225B GLN 3.0 11.2 + - - +
226B ALA 3.7 7.0 - - - +
228B GLU* 1.3 77.6 - - - +
230B ILE* 1.3 56.0 + - - +
232B PRO* 3.2 18.0 - - - +
233B VAL* 4.4 6.9 - - - +
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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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195B TYR* 3.6 48.7 - - + +
197B MET* 3.9 9.0 - - + -
204B LEU* 3.8 24.2 - - + -
206B ILE* 4.4 5.8 - - + -
212B ILE* 5.2 2.7 - - + -
226B ALA 3.1 12.6 + - - +
227B PHE* 3.6 20.2 - - + +
229B ALA* 1.3 75.6 - - - +
231B TYR* 1.3 69.4 + - - +
232B PRO* 3.1 2.9 - - - -
233B VAL* 2.8 27.5 + - + +
234B LEU* 2.9 41.6 + - + +
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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
----------------------------------------------------------
61B SER* 3.5 44.6 + - - +
63B ILE* 4.2 10.1 - - + +
166B VAL* 3.6 37.6 + - + -
168B PHE* 3.7 18.6 - + - -
227B PHE* 3.2 23.7 + + + +
228B GLU* 4.1 3.8 - - - +
230B ILE* 1.3 80.7 - - - +
232B PRO* 1.4 64.1 - - + +
234B LEU* 3.9 10.1 - - + -
235B SER* 2.8 56.1 + - - -
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Residues in contact with PRO 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 GLU 3.1 18.8 - - - +
229B ALA* 3.2 15.9 - - - +
231B TYR* 1.4 92.5 - - + +
233B VAL* 1.3 58.9 + - + +
235B SER* 3.9 5.2 - - - -
236B GLU* 3.1 28.7 + - - +
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Residues in contact with VAL 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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175B LEU* 3.5 27.8 - - + +
179B HIS* 3.4 35.7 - - + +
195B TYR* 4.7 8.5 - - + +
229B ALA 4.4 10.3 - - - +
230B ILE* 2.8 22.3 + - + +
232B PRO* 1.3 77.4 - - + +
234B LEU* 1.3 64.7 + - + +
236B GLU* 3.4 8.4 + - - +
237B PHE* 3.2 35.7 + - + +
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Residues in contact with LEU 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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166B VAL* 4.0 24.0 - - + -
168B PHE* 3.1 25.5 - - + -
170B ILE* 4.1 20.9 - - + +
175B LEU* 4.5 6.5 - - + -
206B ILE* 4.1 27.4 - - + -
212B ILE* 4.1 14.1 - - + -
227B PHE* 4.2 3.4 - - + -
230B ILE* 2.9 47.4 + - + +
231B TYR* 3.5 13.7 - - + +
233B VAL* 1.3 78.2 - - + +
235B SER* 1.3 64.7 + - - +
236B GLU 3.3 0.2 + - - -
237B PHE* 3.4 10.7 + - - +
238B ARG 3.5 4.3 + - - -
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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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168B PHE* 3.7 11.1 - - - -
231B TYR* 2.8 53.5 + - - -
232B PRO* 3.9 5.8 - - - -
234B LEU* 1.3 71.6 - - - +
236B GLU* 1.3 62.5 + - - +
238B ARG* 3.4 18.0 - - - +
240B MET* 6.0 0.3 - - - +
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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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171B ARG* 2.9 18.9 + - - +
178B SER* 5.6 0.7 - - - -
179B HIS* 5.1 4.2 + - - -
232B PRO 3.1 14.7 + - - +
233B VAL* 3.5 13.8 - - - +
234B LEU 3.2 0.2 - - - -
235B SER* 1.3 80.0 - - - +
237B PHE* 1.3 89.7 + - + +
238B ARG 3.3 0.9 + - - -
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Residues in contact with PHE 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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170B ILE* 3.5 11.3 - - + -
171B ARG* 2.8 72.2 + - + +
174B GLY* 3.2 24.7 - - - -
175B LEU* 3.6 26.7 - - + -
178B SER* 3.3 24.9 - - - -
179B HIS* 4.3 6.7 - - - -
233B VAL* 3.2 37.0 + - + +
234B LEU 3.4 4.9 + - - -
236B GLU* 1.3 106.8 - - + +
238B ARG* 1.3 56.5 + - - +
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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