Contacts of the helix formed by residues 186 - 202 (chain B) in PDB entry 4BL8
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 ASN 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 4.0 3.6 + - - -
167B GLY* 3.7 9.0 - - - -
168B TYR* 3.4 30.1 - - - -
183B GLY* 3.3 21.3 + - - +
184B VAL 3.7 0.4 - - - -
185B ASP* 1.3 83.9 - - - +
187B ALA* 1.3 65.7 + - - +
188B GLY* 3.6 4.7 + - - +
189B ALA* 3.1 19.1 + - - +
190B LYS* 3.2 21.4 + - - +
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Residues in contact with ALA 187 (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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165B ASP* 4.5 2.7 - - - +
186B ASN* 1.3 74.3 - - - +
188B GLY* 1.3 64.5 + - - +
190B LYS* 3.1 12.1 + - - +
191B ALA* 2.9 22.9 + - - +
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Residues in contact with GLY 188 (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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162B ILE 3.6 6.6 - - - +
165B ASP* 3.2 49.7 - - - +
167B GLY 4.4 2.2 - - - -
186B ASN* 3.3 6.6 + - - -
187B ALA* 1.3 79.1 - - - +
189B ALA* 1.3 60.9 + - - +
191B ALA 3.3 1.0 + - - -
192B GLY* 3.2 17.2 + - - -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 5.9 0.2 - - + -
162B ILE* 3.4 31.7 + - + +
167B GLY* 4.1 7.0 - - - -
168B TYR 5.4 0.2 - - - +
183B GLY 4.2 7.2 - - - +
184B VAL* 4.3 17.0 - - - +
186B ASN* 3.1 22.0 + - - +
188B GLY* 1.3 75.9 - - - +
190B LYS* 1.3 59.5 + - - +
192B GLY 3.3 1.0 + - - -
193B LEU* 3.0 30.7 + - - +
362B LEU* 4.0 6.5 - - + -
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Residues in contact with LYS 190 (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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185B ASP* 3.6 36.1 + - - -
186B ASN 3.2 12.1 + - - +
187B ALA* 3.1 11.1 + - - +
189B ALA* 1.3 74.8 - - - +
191B ALA* 1.3 60.1 + - - +
194B THR* 2.7 39.0 + - - +
358B VAL* 4.2 9.8 - - + +
359B ASP* 3.4 38.6 + - - +
362B LEU* 3.8 22.4 - - + -
363B ALA* 6.1 0.2 - - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASP* 3.5 19.3 - - - +
187B ALA 2.9 9.6 + - - +
188B GLY 3.5 9.4 - - - +
190B LYS* 1.3 75.8 - - - +
192B GLY* 1.3 62.5 + - - +
194B THR* 4.0 4.7 - - - +
195B PHE* 3.3 14.6 + - - +
251B PHE* 3.1 24.1 - - + -
252B LYS* 3.9 15.5 - - + +
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Residues in contact with GLY 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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161B LEU* 3.5 41.6 - - - +
162B ILE* 4.1 5.2 - - - -
188B GLY 3.2 9.3 + - - -
189B ALA 3.8 2.7 - - - -
191B ALA* 1.3 79.1 - - - +
193B LEU* 1.3 62.7 + - - +
195B PHE* 3.5 2.3 + - - +
196B LEU* 3.2 15.8 + - - +
251B PHE* 3.8 10.5 - - - -
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Residues in contact with LEU 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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162B ILE* 4.2 13.5 - - + +
189B ALA 3.0 16.6 + - - +
192B GLY* 1.3 73.3 - - - +
194B THR* 1.3 67.2 + - - +
196B LEU* 3.1 26.4 + - + -
197B VAL* 2.9 28.4 + - + +
347B ALA 4.5 5.6 - - - +
348B VAL* 4.3 25.6 - - + +
351B ALA* 3.9 19.1 - - + -
352B ALA* 6.1 0.4 - - + -
358B VAL* 4.0 14.6 - - + +
361B ALA* 5.3 0.4 - - + -
362B LEU* 3.7 37.5 - - + -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 2.7 26.9 + - - +
191B ALA* 4.0 5.6 - - - +
193B LEU* 1.3 78.4 - - - +
195B PHE* 1.3 58.3 + - - +
197B VAL* 3.3 2.9 + - - +
198B ASP* 3.0 42.3 + - - +
358B VAL* 3.6 24.8 - - - +
359B ASP* 5.6 0.9 + - - -
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Residues in contact with PHE 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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130B TRP* 3.5 40.8 - + + -
131B GLU* 3.9 23.3 - - + -
134B PRO* 4.4 16.2 - - + -
161B LEU* 4.2 12.3 - - + -
191B ALA 3.3 15.8 + - - +
192B GLY 3.7 4.9 - - - +
193B LEU 3.2 0.4 - - - -
194B THR* 1.3 80.5 - - - +
196B LEU* 1.3 60.4 + - - +
198B ASP* 3.4 15.0 - - + +
199B LEU* 3.2 44.9 + - + +
251B PHE* 3.7 22.7 - + + -
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Residues in contact with LEU 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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130B TRP* 5.4 0.2 - - + -
150B PHE* 4.3 9.9 - - + -
152B LEU* 4.2 10.3 - - + -
158B THR* 3.7 31.0 - - + +
161B LEU* 4.1 16.4 - - + -
162B ILE* 5.6 1.3 - - + -
192B GLY 3.2 10.7 + - - +
193B LEU* 3.1 29.0 + - + +
195B PHE* 1.3 78.0 - - - +
197B VAL* 1.3 64.6 + - + +
199B LEU* 3.4 19.2 + - + +
200B ILE* 3.5 20.5 + - + +
205B MET* 3.5 32.1 - - + -
348B VAL* 4.2 10.5 - - + -
352B ALA* 5.6 3.4 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 2.9 25.1 + - + +
194B THR 3.8 4.0 - - - +
196B LEU* 1.3 74.0 - - + +
198B ASP* 1.3 67.2 + - - +
200B ILE* 3.2 11.5 + - - +
201B LYS* 3.1 48.3 + - + +
351B ALA* 3.2 36.1 - - + +
352B ALA* 4.2 8.5 - - + +
358B VAL* 3.4 22.9 - - + -
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B THR* 3.0 33.9 + - - +
195B PHE* 3.4 18.8 - - + +
197B VAL* 1.3 79.2 - - - +
199B LEU* 1.3 63.6 + - - +
201B LYS* 2.9 27.5 + - - +
202B ASN* 3.0 25.7 + - - +
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Residues in contact with LEU 199 (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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130B TRP* 4.0 21.5 - - + -
133B ILE* 4.7 9.0 - - + -
134B PRO* 4.1 23.3 - - + -
148B LEU* 5.3 2.0 - - + -
195B PHE* 3.2 37.4 + - + +
196B LEU* 3.4 12.5 + - + +
198B ASP* 1.3 78.7 - - - +
200B ILE* 1.3 59.2 + - - +
202B ASN* 3.8 1.3 + - - -
203B LYS 3.4 2.4 + - - -
204B HIS* 2.9 58.0 + - + +
205B MET* 3.3 32.1 + - + -
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Residues in contact with ILE 200 (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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152B LEU* 4.0 20.2 - - + -
196B LEU* 3.5 19.1 - - + +
197B VAL* 3.2 7.4 + - - +
198B ASP 3.0 0.8 - - - -
199B LEU* 1.3 76.7 - - - +
201B LYS* 1.3 66.2 + - - +
203B LYS* 3.1 14.7 + - - +
205B MET* 3.3 30.3 - - + +
206B ASN* 4.4 2.2 - - - +
207B ALA* 3.7 25.1 - - + +
352B ALA* 3.5 41.7 - - + +
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Residues in contact with LYS 201 (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 VAL* 3.1 38.5 + - + +
198B ASP* 2.9 20.0 + - - +
200B ILE* 1.3 78.3 - - - +
202B ASN* 1.3 63.7 + - - +
203B LYS* 3.1 16.5 + - - +
351B ALA 5.4 0.2 + - - -
354B GLY* 6.1 2.8 - - - -
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Residues in contact with ASN 202 (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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134B PRO* 6.0 0.7 - - - +
198B ASP* 3.0 24.7 + - - +
201B LYS* 1.3 77.4 - - - +
203B LYS* 1.3 70.8 + - - +
204B HIS* 3.3 37.2 + - + +
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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