Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 1BMO
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 TYR 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B PHE* 2.9 37.5 + + - +
204B GLU* 3.6 10.8 + - - +
206B ASN* 1.3 76.9 - - - +
208B ASN* 1.3 66.9 + - + +
210B TYR* 2.9 20.5 + - - +
211B ILE* 3.5 25.2 + - + +
274B GLY 3.8 19.1 - - - -
275B ILE* 3.6 14.7 - - + +
276B LYS* 2.8 35.6 + - + +
279B ASP* 2.7 35.1 + - - +
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Residues in contact with ASN 208 (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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182B ILE* 5.6 1.8 - - - +
206B ASN 3.3 0.6 - - - -
207B TYR* 1.3 81.7 - - + +
209B MET* 1.3 63.5 + - - +
210B TYR 3.1 1.2 + - - -
211B ILE* 3.5 30.5 + - + +
212B PHE* 4.6 2.4 + - - +
213B PRO* 5.4 0.2 - - - +
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Residues in contact with MET 209 (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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155B LYS* 4.3 13.1 - - + +
182B ILE* 3.7 32.9 - - + +
185B ASN* 3.5 31.0 - - + +
188B ARG* 3.6 43.3 - - + +
189B LEU 4.8 0.7 - - - -
202B ASP* 5.6 0.9 - - - +
206B ASN* 2.7 49.6 + - + +
208B ASN* 1.3 79.5 - - - +
210B TYR* 1.3 64.6 + - + +
213B PRO* 3.4 21.4 - - - +
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.9 34.3 - - + -
152B ASP* 4.3 12.7 + - - +
155B LYS* 3.7 34.0 - - + -
189B LEU* 5.3 1.4 - - - +
199B LEU* 4.7 5.4 + - - +
202B ASP* 2.8 34.4 + - - +
203B PHE* 3.4 46.7 + + + -
206B ASN* 3.2 25.8 - - + -
207B TYR 2.9 8.0 + - - +
209B MET* 1.3 84.1 - - + +
211B ILE* 1.3 64.5 + - - +
212B PHE 3.3 2.5 - - - -
213B PRO* 3.3 5.2 - - + +
214B VAL* 3.0 32.0 + - + +
275B ILE* 4.3 4.5 - - + -
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Residues in contact with ILE 211 (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 TYR* 3.5 48.2 - - + +
208B ASN* 3.5 22.3 + - - +
210B TYR* 1.3 77.0 - - - +
212B PHE* 1.3 60.2 + - - +
214B VAL* 3.9 1.0 - - - +
215B HIS* 2.6 42.8 + - + +
275B ILE* 4.2 12.1 - - + -
279B ASP* 3.5 40.8 - - + +
284B LEU* 4.5 9.4 - - + -
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Residues in contact with PHE 212 (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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158B LEU* 3.6 26.7 - - + -
175B GLN* 3.9 26.2 - - + -
178B ARG* 3.5 44.9 - - + -
179B VAL* 3.7 18.6 - - + -
182B ILE* 4.7 7.9 - - + -
208B ASN 4.6 2.8 + - - +
211B ILE* 1.3 77.3 - - - +
213B PRO* 1.4 62.5 - - + +
215B HIS* 2.9 2.6 + - - +
216B TRP* 2.7 53.8 + + + +
284B LEU* 3.5 42.4 - - + +
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Residues in contact with PRO 213 (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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154B LEU* 4.0 10.9 - - + +
155B LYS* 3.9 32.8 - - + +
158B LEU* 3.5 23.3 - - + -
182B ILE* 3.8 15.5 - - + -
209B MET 3.4 23.6 - - - +
210B TYR* 3.3 12.1 - - + +
212B PHE* 1.4 93.3 - - + +
214B VAL* 1.3 61.9 + - + +
216B TRP* 3.6 2.8 - - + +
217B GLN* 3.1 26.5 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 4.2 17.0 - - + -
154B LEU* 4.0 13.2 - - + -
210B TYR* 3.0 23.5 + - + +
211B ILE 3.9 2.7 - - - +
213B PRO* 1.3 76.8 - - + +
215B HIS* 1.3 63.3 + - - +
217B GLN 3.9 0.5 + - - -
218B PHE 3.7 5.4 + - - -
269B TRP* 2.8 45.2 + - + +
270B ALA* 4.2 10.1 - - + -
273B PHE* 4.2 19.1 - - + -
275B ILE* 3.5 35.0 - - + -
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Residues in contact with HIS 215 (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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211B ILE* 2.6 30.2 + - + +
212B PHE 2.9 7.0 + - - +
214B VAL* 1.3 80.0 - - + +
216B TRP* 1.3 66.5 + - - +
218B PHE* 3.4 5.5 + - - +
219B GLY 3.3 13.5 + - - -
266B LEU* 4.2 12.8 - - + +
269B TRP* 5.0 0.2 - - - +
270B ALA* 5.1 3.7 - - + +
275B ILE* 4.4 9.2 - - + +
279B ASP 3.2 25.4 - - - -
280B ILE* 3.3 12.8 - - - +
281B ASP* 2.9 39.9 + - + -
284B LEU* 3.7 26.8 - - + +
285B VAL* 3.5 23.6 - - + +
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Residues in contact with TRP 216 (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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154B LEU* 5.5 4.7 - - + -
157B VAL* 4.3 20.4 - - + -
158B LEU* 3.6 34.5 - - + -
161B LEU* 3.5 33.4 - - + -
170B LEU 5.9 0.9 - - - -
171B LEU* 4.0 5.1 - - + +
175B GLN* 3.8 24.4 + - - -
212B PHE* 2.7 42.2 + + + +
213B PRO 3.6 5.6 - - - +
215B HIS* 1.3 72.4 - - - +
217B GLN* 1.3 83.1 + - + +
219B GLY* 2.8 20.7 + - - -
220B GLN* 2.9 52.9 + - + +
284B LEU 4.3 6.9 + - - -
285B VAL 5.0 4.3 - - - +
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TRP* 3.2 37.4 - - - -
154B LEU* 3.3 23.5 - - + +
157B VAL* 6.3 0.4 - - - +
213B PRO 3.1 10.1 + - - +
214B VAL 4.1 0.2 - - - +
215B HIS 3.4 0.2 - - - -
216B TRP* 1.3 92.2 - - + +
218B PHE* 1.3 62.1 + - - +
220B GLN* 3.2 15.4 + - - +
221B LEU* 3.1 33.6 + - + +
238B LEU* 3.4 10.5 - - + +
269B TRP* 3.5 29.6 - - + -
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL 3.7 2.6 + - - +
215B HIS 3.4 9.6 + - - +
216B TRP 3.1 0.6 + - - -
217B GLN* 1.3 78.1 - - - +
219B GLY* 1.3 60.3 + - - +
221B LEU* 3.1 5.6 + - - +
222B ASP* 2.8 43.5 + - + +
228B GLY* 3.2 37.9 - - - -
229B TYR 4.0 0.2 - - - -
230B LEU* 3.6 26.2 - - + +
264B ILE 3.7 1.8 - - - -
265B ALA 3.6 8.3 - - - -
266B LEU* 3.6 39.0 - - + -
269B TRP* 3.5 43.4 - + + +
285B VAL* 4.2 13.9 - - + -
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Residues in contact with GLY 219 (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 HIS 3.3 4.0 + - - -
216B TRP 2.8 8.1 + - - -
218B PHE* 1.3 80.1 - - - +
220B GLN* 1.3 63.9 + - - +
221B LEU 3.1 1.0 + - - -
222B ASP* 3.4 19.5 + - - +
223B GLN* 3.9 7.0 - - - +
285B VAL* 3.6 33.2 - - - +
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Residues in contact with GLN 220 (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 GLN* 5.6 1.8 + - - +
216B TRP* 2.9 67.1 + - + +
217B GLN* 3.4 17.0 - - - +
219B GLY* 1.3 76.0 - - - +
221B LEU* 1.3 63.2 + - + +
223B GLN* 2.8 30.8 + - - -
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Residues in contact with LEU 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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217B GLN* 3.1 34.6 + - + +
218B PHE 3.7 2.5 - - - +
219B GLY 3.0 0.4 - - - -
220B GLN* 1.3 84.4 - - + +
222B ASP* 1.3 55.1 + - - +
223B GLN* 2.7 20.7 + - - +
224B HIS* 5.1 1.4 - - - -
230B LEU* 3.9 26.9 - - + -
234B GLU* 3.3 41.1 - - - +
235B LEU* 4.9 0.7 - - + -
237B PRO* 3.8 25.8 - - + -
238B LEU* 3.8 32.5 - - + -
269B TRP* 4.3 1.6 - - + -
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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