Contacts of the strand formed by residues 191 - 198 (chain B) in PDB entry 4BLV
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 ILE 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ILE* 4.1 20.6 - - + -
29B LEU* 4.0 26.7 - - + -
159B GLY 3.0 14.6 + - - +
160B LEU* 3.4 9.9 - - + +
161B ILE* 2.7 33.1 + - - +
189B THR 4.5 4.0 - - - +
190B GLY* 1.3 74.6 - - - -
192B TYR* 1.3 57.0 + - - +
242B VAL* 3.8 17.7 - - + -
243B ILE 3.4 7.2 - - - +
244B ASN* 3.3 26.9 - - + +
245B PRO* 4.4 2.0 - - + -
246B PRO* 4.0 22.0 - - + -
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Residues in contact with TYR 192 (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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148B LEU* 5.0 1.8 - - + -
152B LEU* 3.5 10.6 - - + +
161B ILE* 3.5 39.9 - - + +
163B ILE* 4.5 14.1 - - + -
180B ILE* 4.8 13.0 - - + -
183B GLY* 3.1 25.0 + - - -
184B TYR* 4.0 18.4 - + + -
187B PHE* 2.7 38.9 + - - +
190B GLY* 3.4 21.3 - - - -
191B ILE* 1.3 72.7 - - - +
193B ALA* 1.3 58.4 - - - +
194B LEU* 4.0 0.9 - - + -
241B ILE 3.3 2.0 - - - +
242B VAL* 3.1 9.1 - - - +
243B ILE* 2.9 59.9 + - + +
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Residues in contact with ALA 193 (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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22B GLN* 6.0 1.3 - - - -
25B ILE* 4.1 15.3 - - + -
160B LEU* 3.9 21.3 - - + -
161B ILE 2.8 10.6 + - - +
162B LEU* 3.5 13.3 - - + +
163B ILE* 2.9 27.7 + - - -
191B ILE 4.0 0.6 + - - -
192B TYR* 1.3 73.2 - - - +
194B LEU* 1.3 58.4 + - - +
195B TRP 4.0 0.2 - - - -
240B MET* 3.8 22.0 - - + -
241B ILE 3.6 3.6 - - - -
242B VAL* 4.4 3.8 - - + -
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Residues in contact with LEU 194 (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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163B ILE* 3.5 28.7 - - + +
165B PRO* 4.2 2.0 - - + -
167B TYR* 3.3 19.7 - - - +
176B VAL* 3.5 32.1 - - + -
180B ILE* 4.1 19.7 - - + -
192B TYR 4.0 1.3 - - - -
193B ALA* 1.3 71.8 - - - +
195B TRP* 1.3 68.3 + - - +
196B TYR* 3.9 2.1 + - + -
207B MET* 4.1 23.1 - - + -
211B LEU* 5.4 2.7 - - + -
239B GLY 3.9 0.2 - - - +
240B MET* 3.3 6.5 - - - +
241B ILE* 2.9 57.4 + - + +
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Residues in contact with TRP 195 (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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14B ALA* 3.6 23.2 + - + +
15B ASP* 6.1 0.2 - - - -
17B LEU* 5.7 0.2 - - + -
18B LYS* 3.9 28.9 - - + -
162B LEU* 5.5 0.7 - - + -
163B ILE 3.0 11.1 + - - +
164B ASP* 3.4 25.8 - - - +
165B PRO* 4.0 5.7 - - - +
167B TYR* 2.7 42.7 + + - -
193B ALA 3.9 1.2 + - - -
194B LEU* 1.3 75.6 - - - +
196B TYR* 1.3 60.2 + - - +
197B PRO* 3.6 31.0 - - + -
235B MET* 4.0 9.9 - - + -
238B SER* 3.1 38.4 + - - -
239B GLY 3.3 19.3 - - - -
240B MET* 3.6 20.0 - - + +
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Residues in contact with TYR 196 (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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167B TYR* 3.8 10.1 - - + +
194B LEU* 4.2 4.9 - - + -
195B TRP* 1.3 80.8 - - - +
197B PRO* 1.3 78.5 - - + +
198B VAL* 3.7 12.6 - - + -
204B ILE* 3.8 22.0 - - + -
207B MET* 4.2 13.5 - - + -
221B GLN* 2.7 31.8 + - + +
223B GLU* 2.8 28.5 + - - +
238B SER* 3.2 4.9 - - - -
239B GLY* 2.9 62.8 + - - -
240B MET 3.7 2.2 - - - -
241B ILE* 3.7 34.8 - - + -
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Residues in contact with PRO 197 (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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167B TYR* 3.3 45.1 - - + -
173B TYR* 4.4 7.3 + - - +
195B TRP* 3.6 23.8 - - + -
196B TYR* 1.3 87.8 - - + +
198B VAL* 1.3 61.2 + - - +
199B VAL* 3.8 12.6 + - + -
204B ILE* 3.3 21.6 - - + +
235B MET* 3.7 15.0 - - + -
237B ALA 3.8 4.7 - - - +
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Residues in contact with VAL 198 (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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196B TYR* 3.7 16.8 - - + -
197B PRO* 1.3 72.3 - - - +
199B VAL* 1.3 61.6 + - - +
201B ARG* 3.8 44.4 - - - +
204B ILE* 4.4 6.3 - - + -
223B GLU* 3.6 24.5 - - - +
229B ASP* 4.0 4.9 - - + +
235B MET* 3.5 2.2 - - - -
236B THR* 3.0 39.0 + - - +
237B ALA* 2.7 32.6 + - + +
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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