Contacts of the helix formed by residues 189 - 200 (chain B) in PDB entry 4BVH
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 PRO 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B PHE* 3.2 44.6 - - + +
186B PHE 4.7 3.1 - - - +
188B ASN* 1.3 86.8 - - - +
190B LYS* 1.3 60.4 + - + +
191B PRO* 3.5 1.1 - - - -
192B PHE* 3.5 4.7 + - + +
193B PHE* 3.0 37.5 + - + -
277B VAL* 4.4 22.9 - - + -
279B ARG* 6.2 1.6 - - - +
286B VAL* 4.9 9.0 - - + -
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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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188B ASN* 3.2 8.8 + - - +
189B PRO* 1.3 79.3 - - + +
191B PRO* 1.4 76.4 - - + +
193B PHE* 3.0 12.0 + - - +
194B THR* 2.8 43.0 + - - +
272B VAL 5.8 0.2 + - - -
275B ASP* 3.2 39.2 + - - +
276B ARG 4.5 1.0 - - - -
277B VAL* 4.2 25.8 - - + +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.5 29.0 - - + +
172B ASP 5.7 0.9 - - - +
173B LEU* 3.7 26.0 - - + -
179B ILE* 3.5 10.4 - - + +
184B PHE* 4.0 13.7 - - + -
188B ASN* 3.3 35.0 - - - +
189B PRO 3.7 0.4 - - - -
190B LYS* 1.4 91.8 - - + +
192B PHE* 1.3 64.0 + - - +
194B THR* 3.1 5.5 + - - +
195B LEU 3.1 16.8 + - - -
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Residues in contact with PHE 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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179B ILE* 3.6 34.5 - - + +
180B PHE* 4.2 19.3 - + - -
184B PHE* 5.8 0.6 - - - -
185B PHE* 4.0 26.2 - + + -
188B ASN 5.2 0.8 + - - +
189B PRO* 3.5 7.7 + - + +
190B LYS 3.2 0.8 - - - -
191B PRO* 1.3 80.1 - - - +
193B PHE* 1.3 74.4 + + - +
195B LEU* 3.4 2.4 + - + +
196B ALA* 2.8 41.4 + - + -
199B LEU* 4.3 8.7 - - + -
251B PHE* 4.4 6.7 - + - -
289B PRO* 4.2 21.1 - - + -
291B ILE* 3.5 33.4 - - + -
293B PHE* 3.8 15.5 - + - -
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Residues in contact with PHE 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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185B PHE* 3.6 28.7 - + - -
189B PRO* 3.0 32.4 + - + +
190B LYS* 3.0 17.0 + - - +
192B PHE* 1.3 85.7 - + - +
194B THR* 1.3 64.1 + - - +
196B ALA* 3.4 14.9 + - + +
197B LYS* 3.8 6.8 + - - +
268B ILE* 4.1 7.6 - - + -
272B VAL* 3.6 38.6 - - + +
276B ARG 5.3 2.0 - - - +
277B VAL* 4.3 12.1 - - + -
278B PRO* 3.6 26.9 - - + -
286B VAL* 4.2 8.1 - - + -
287B VAL 3.3 24.7 - - - -
289B PRO* 4.0 17.7 - - + -
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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
----------------------------------------------------------
171B TYR* 3.8 13.5 - - + -
190B LYS* 2.8 35.7 + - - +
191B PRO* 3.1 10.1 + - - +
193B PHE* 1.3 75.6 - - - +
195B LEU* 1.3 61.6 + - - +
197B LYS* 2.8 47.3 + - - +
139C ARG* 3.9 28.0 - - - +
311C MET* 3.3 7.4 - - + +
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Residues in contact with LEU 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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164B LEU* 4.3 15.5 - - + -
168B LEU* 4.4 7.6 - - + -
171B TYR* 3.4 28.6 - - + +
179B ILE* 3.8 21.1 - - + -
180B PHE* 3.6 32.3 - - + -
191B PRO 3.1 8.8 + - - +
192B PHE* 3.7 7.9 - - + +
194B THR* 1.3 73.2 - - - +
196B ALA* 1.3 57.4 + - - +
197B LYS 2.9 11.5 + - - -
198B GLU* 3.0 47.2 + - - +
199B LEU* 3.3 18.0 + - + -
311C MET* 4.2 1.3 - - - -
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Residues in contact with ALA 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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192B PHE* 2.8 39.9 + - + +
193B PHE* 3.5 17.7 - - + +
194B THR 3.2 0.8 - - - -
195B LEU* 1.3 71.9 - - - +
197B LYS* 1.3 56.4 + - - +
199B LEU* 3.6 12.3 - - - +
200B TYR* 2.9 34.4 + - + +
251B PHE* 4.9 9.0 - - + -
272B VAL* 4.0 13.0 - - + +
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Residues in contact with LYS 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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193B PHE 3.9 4.9 - - - +
194B THR* 2.8 49.8 + - - +
195B LEU 2.9 1.4 + - - -
196B ALA* 1.3 77.1 - - - +
198B GLU* 1.3 60.0 + - - +
200B TYR* 4.3 3.5 - - - +
203B ASN* 5.0 0.5 - - - +
269B ARG* 5.0 0.7 + - - -
272B VAL* 3.6 28.0 - - + +
273B MET* 3.4 25.8 - - - +
275B ASP* 3.7 11.2 + - - +
139C ARG* 5.6 0.6 - - - +
310C PRO* 3.4 32.3 - - - +
311C MET* 3.9 17.7 + - - +
335C ARG* 3.6 46.4 - - - +
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Residues in contact with GLU 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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154B ILE* 6.1 0.2 - - - +
155B PRO* 4.2 16.6 - - - +
164B LEU* 4.3 4.2 - - - +
171B TYR* 5.1 0.2 + - - -
195B LEU* 3.0 34.4 + - + +
197B LYS* 1.3 80.3 - - - +
199B LEU* 1.3 71.2 - - + +
200B TYR 3.3 3.3 - - - +
204B TYR* 3.8 16.1 - - - -
223C LEU* 6.1 0.2 - - - +
306C VAL 4.8 2.1 - - - +
307C VAL* 3.4 55.3 - - + +
308C ASP* 5.5 0.9 - - - +
310C PRO* 4.3 7.4 - - - +
311C MET* 3.2 25.1 - - + +
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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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154B ILE* 5.5 4.9 - - + -
155B PRO* 6.0 0.2 - - + -
164B LEU* 4.8 5.4 - - + -
180B PHE* 3.8 24.7 - - + -
192B PHE* 4.3 13.9 - - + -
195B LEU* 3.3 37.4 + - + +
196B ALA* 3.3 6.9 + - - -
198B GLU* 1.3 93.8 - - + +
200B TYR* 1.3 56.7 + - - +
201B PRO 3.5 0.3 - - - -
204B TYR* 2.7 27.7 + - - -
230B ILE* 4.6 7.2 - - + +
231B ASP* 5.1 0.5 - - - -
251B PHE* 3.7 22.8 - - + -
1392B OCZ 3.8 32.1 - - + -
307C VAL* 6.2 0.4 - - + -
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Residues in contact with TYR 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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196B ALA* 2.9 19.4 + - + +
197B LYS 4.3 1.7 - - - +
198B GLU 3.3 4.0 - - - +
199B LEU* 1.3 78.1 - - - +
201B PRO* 1.3 82.7 - - + +
202B GLY 3.8 0.3 + - - -
203B ASN* 4.8 3.8 + - - +
204B TYR* 3.9 8.0 - - - -
251B PHE* 3.4 40.9 + + + -
265B GLY* 2.9 31.7 + - - -
266B GLU* 5.2 1.6 - - - -
268B ILE* 3.4 23.3 - - + +
269B ARG* 3.4 47.2 + - + -
272B VAL* 4.6 14.4 - - + -
273B MET* 3.7 18.6 - - + -
289B PRO* 5.4 0.5 - - - +
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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