Contacts of the helix formed by residues 200 - 216 (chain B) in PDB entry 3VPM
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 MET 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 3.4 50.5 - - + +
132B ALA* 3.8 12.8 - - + -
192B PHE* 3.9 27.8 - - + -
193B LEU* 4.5 2.7 - - - -
196B ALA* 3.0 30.3 + - - +
197B ILE 4.8 2.6 - - - +
198B GLU 3.7 1.0 - - - -
199B THR* 1.3 76.8 + - - +
201B PRO* 1.3 68.3 - - + +
202B CYS* 3.2 25.4 + - - -
203B VAL* 3.2 34.6 + - + +
204B LYS* 3.6 3.5 + - - +
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 6.1 0.2 - - + -
199B THR 3.4 11.7 - - - +
200B MET* 1.3 83.8 - - + +
202B CYS* 1.3 62.7 + - - +
204B LYS* 3.1 24.9 + - + +
205B LYS* 4.4 1.4 + - - +
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Residues in contact with CYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS* 4.1 14.8 - - - -
200B MET* 3.2 36.2 - - - -
201B PRO* 1.3 81.2 - - - +
203B VAL* 1.3 60.9 + - - +
205B LYS* 4.6 6.1 + - - +
206B LYS* 5.0 1.9 + - - +
302B GLU* 5.7 0.7 - - - +
303B PHE* 3.2 31.9 - - + +
307B ALA* 3.6 40.9 - - + +
308B LEU* 4.5 10.1 - - + -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.8 35.9 - - + -
136B ALA* 5.4 2.9 - - + -
196B ALA* 3.2 32.1 - - + +
197B ILE* 4.0 11.7 - - + -
200B MET* 3.2 35.9 + - + +
202B CYS* 1.3 79.2 - - - +
204B LYS* 1.3 70.2 + - - +
205B LYS 3.4 0.2 - - - -
206B LYS* 3.0 7.3 + - - +
207B ALA* 2.8 29.3 + - + +
303B PHE* 4.6 4.3 - - + -
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 4.5 17.0 - - + +
200B MET 3.6 1.7 + - - +
201B PRO* 3.1 22.4 + - + +
203B VAL* 1.3 81.2 - - - +
205B LYS* 1.3 56.7 - - - +
207B ALA* 4.7 2.5 - - + -
208B ASP* 2.7 70.6 + - - +
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO 4.4 1.8 + - - -
202B CYS 4.6 5.5 + - - +
203B VAL 3.4 0.4 - - - -
204B LYS* 1.3 79.3 - - + +
206B LYS* 1.3 62.3 + - + +
208B ASP* 4.0 3.9 - - - +
209B TRP* 3.1 24.9 + - - +
299B ILE* 4.1 30.6 - - + +
302B GLU* 3.7 35.4 - - - +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.3 29.5 - - + -
202B CYS 5.0 0.9 + - - +
203B VAL 3.0 8.9 + - - +
205B LYS* 1.3 75.6 - - + +
207B ALA* 1.3 64.5 + - - +
209B TRP 3.4 0.9 + - - -
210B ALA* 3.2 21.1 + - - +
235B PHE* 2.9 62.1 + - + -
239B SER* 4.7 0.2 + - - -
299B ILE* 3.7 20.4 - - + -
300B GLU* 2.5 26.9 + - - +
303B PHE* 3.3 46.4 - - + -
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Residues in contact with ALA 207 (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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133B PHE* 6.0 0.2 - - - -
136B ALA* 6.2 0.4 - - + -
140B ILE* 3.7 25.5 - - + +
197B ILE* 4.2 22.4 - - + -
203B VAL* 2.8 26.7 + - + +
204B LYS* 3.9 3.8 - - + +
206B LYS* 1.3 72.5 - - - +
208B ASP* 1.3 63.6 + - - +
210B ALA* 3.4 2.3 + - - +
211B LEU* 3.0 35.2 + - + +
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Residues in contact with ASP 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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204B LYS* 2.7 60.6 + - - +
205B LYS* 4.0 4.0 - - - +
207B ALA* 1.3 74.5 - - - +
209B TRP* 1.3 56.4 + - - +
211B LEU* 3.5 11.0 + - - +
212B ARG* 3.0 28.9 + - - +
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Residues in contact with TRP 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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205B LYS 3.1 19.2 + - - +
206B LYS 3.6 4.9 - - - +
207B ALA 3.3 0.2 - - - -
208B ASP* 1.3 76.4 - - - +
210B ALA* 1.3 64.3 + - - +
212B ARG* 3.5 19.8 - - - +
213B TRP* 2.9 53.7 + + - +
227B ALA* 3.5 26.0 - - + -
230B ALA* 4.0 11.0 - - + -
231B VAL* 3.9 8.3 - - + -
235B PHE* 3.6 26.5 - + + -
292B ILE* 3.6 37.7 - - + -
295B ASN* 3.1 27.1 - - - +
296B ALA* 4.2 6.3 - - + -
299B ILE* 3.4 21.7 - - + +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 3.6 24.9 - - + -
206B LYS 3.2 13.6 + - - +
207B ALA* 3.9 2.7 - - - +
208B ASP 3.3 0.2 - - - -
209B TRP* 1.3 84.4 - - - +
211B LEU* 1.3 65.6 + - - +
213B TRP* 3.1 18.1 + - - +
214B ILE* 3.4 7.3 + - - +
228B PHE* 3.7 12.1 - - + -
231B VAL* 3.9 26.5 - - + -
235B PHE* 5.4 0.2 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 4.2 26.9 - - + +
143B GLU* 3.7 26.9 - - - +
197B ILE* 5.2 11.4 - - + -
207B ALA* 3.0 30.6 + - + +
208B ASP* 4.0 11.9 - - - +
210B ALA* 1.3 74.0 - - - +
212B ARG* 1.3 65.5 + - - +
214B ILE* 3.1 10.8 + - + +
215B GLY* 3.1 18.9 + - - -
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Residues in contact with ARG 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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208B ASP 3.0 14.0 + - - +
209B TRP* 3.5 19.7 + - - +
210B ALA 3.2 0.2 - - - -
211B LEU* 1.3 74.8 - - - +
213B TRP* 1.3 95.6 + - - +
215B GLY* 3.0 5.3 + - - -
216B ASP* 2.8 56.9 + - - +
288B ARG* 4.7 4.9 - - - +
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Residues in contact with TRP 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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144B ASN* 4.7 2.4 - - - +
148B ARG* 3.5 13.2 + - - -
209B TRP* 2.9 56.8 + + - -
210B ALA* 3.1 10.1 + - - +
212B ARG* 1.3 103.3 - - - +
214B ILE* 1.3 63.3 + - - +
216B ASP* 4.0 6.9 + - - +
219B ALA* 4.1 20.2 - - + -
223B GLU* 4.3 11.7 - - + -
224B ARG* 3.8 31.1 + - + +
227B ALA* 3.5 21.1 - - + -
228B PHE* 3.9 16.9 - + + -
231B VAL* 6.0 0.2 - - + -
288B ARG* 3.4 29.4 - - - -
292B ILE* 3.8 31.9 - - + -
295B ASN* 6.2 0.4 - - - -
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Residues in contact with ILE 214 (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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140B ILE* 3.6 38.4 - - + +
143B GLU* 3.6 32.5 - - + +
144B ASN* 3.6 29.4 - - + +
147B GLU* 4.1 10.1 - - - +
148B ARG* 3.0 38.7 + - + +
210B ALA 3.4 3.1 + - - +
211B LEU* 3.1 13.3 + - + +
213B TRP* 1.3 78.7 - - - +
215B GLY* 1.3 60.0 + - - +
217B LYS* 5.9 0.2 - - - +
228B PHE* 3.8 9.2 - - + -
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Residues in contact with GLY 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 LEU 3.1 8.8 + - - -
212B ARG* 3.0 8.2 + - - -
214B ILE* 1.3 76.6 - - - +
216B ASP* 1.3 64.4 + - - +
217B LYS* 3.2 23.6 + - - +
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.0 26.6 + - - -
212B ARG* 2.8 50.3 + - - +
213B TRP* 4.3 12.5 - - + +
214B ILE 3.3 1.2 - - - -
215B GLY* 1.3 70.3 - - - +
217B LYS* 1.3 64.4 + - - +
218B GLU* 3.0 19.1 + - - +
219B ALA* 3.2 30.7 + - + +
224B ARG* 4.2 2.4 - - - -
288B ARG* 5.6 0.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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