Contacts of the helix formed by residues 194 - 209 (chain B) in PDB entry 3P3W
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 GLU 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ASP* 3.4 13.0 + - - +
140B GLU* 5.3 9.2 - - + +
193B CYS* 1.3 76.0 - - - +
195B VAL* 1.3 67.6 + - - +
196B GLU* 3.2 6.3 - - + +
197B ARG* 2.9 18.6 + - + +
198B ILE* 2.9 11.4 + - - +
221B ASN* 3.6 6.3 - - - +
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Residues in contact with VAL 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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194B GLU* 1.3 72.5 - - - +
196B GLU* 1.3 62.0 + - - +
197B ARG 3.3 0.2 + - - -
198B ILE* 3.4 2.8 + - - +
199B ASN* 3.1 30.1 + - - +
221B ASN* 3.2 29.5 - - - +
223B GLY* 3.9 4.7 - - - +
226B ASP* 3.5 42.0 - - + +
227B ILE* 3.8 16.8 - - + -
277B TYR* 4.2 17.9 - - + +
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Residues in contact with GLU 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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15B ASN* 5.6 7.6 - - - +
194B GLU* 3.2 4.5 - - + +
195B VAL* 1.3 79.8 - - - +
197B ARG* 1.3 59.9 + - - +
199B ASN* 4.1 8.9 + - - +
200B THR* 3.7 21.3 + - - +
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Residues in contact with ARG 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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138B ASP* 3.5 25.3 + - - +
165B VAL* 2.9 37.5 + - - +
166B GLY* 3.3 25.3 + - - -
168B ILE 3.5 14.8 + - - -
174B PHE* 4.7 7.6 - - + -
193B CYS* 3.9 10.5 - - + -
194B GLU* 2.9 14.0 + - + +
196B GLU* 1.3 76.3 - - - +
198B ILE* 1.3 60.0 + - - +
199B ASN 3.2 2.0 - - - -
200B THR* 2.4 29.0 + - - +
201B ILE* 2.7 24.8 - - + +
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Residues in contact with ILE 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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191B ILE* 3.8 15.7 - - + +
193B CYS* 3.3 36.6 - - + +
194B GLU 2.9 13.4 + - - +
195B VAL 3.4 7.6 + - - +
197B ARG* 1.3 75.9 - - - +
199B ASN* 1.3 63.3 + - - +
201B ILE* 3.0 20.7 + - - +
202B LEU* 3.1 23.4 + - + +
219B LEU* 3.7 35.7 - - + -
221B ASN* 3.7 22.4 - - + -
227B ILE* 4.0 20.2 - - + -
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Residues in contact with ASN 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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195B VAL* 3.1 23.0 + - - +
196B GLU* 4.1 8.9 - - - +
197B ARG 3.2 0.6 - - - -
198B ILE* 1.3 76.0 - - - +
200B THR* 1.3 62.0 + - + +
202B LEU* 3.5 8.2 + - - +
203B GLU* 3.2 32.0 + - - +
226B ASP 3.4 19.2 + - - -
227B ILE* 3.3 13.6 - - - +
228B LEU* 2.9 48.0 + - + +
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Residues in contact with THR 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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171B VAL* 5.2 6.5 - - - +
174B PHE* 5.1 12.2 - - - -
196B GLU 3.7 13.5 - - - +
197B ARG* 2.4 29.0 + - - +
199B ASN* 1.3 78.4 - - + +
201B ILE* 1.3 64.9 + - - +
203B GLU* 3.7 20.0 + - - +
204B GLN* 3.4 27.2 + - - +
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Residues in contact with ILE 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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136B LEU* 4.7 20.6 - - + -
165B VAL* 5.3 1.8 - - + -
174B PHE* 4.3 27.8 - - + -
178B ILE* 5.1 9.3 - - + +
191B ILE* 4.7 15.5 - - + -
193B CYS* 4.1 16.4 - - - -
197B ARG* 2.7 50.1 + - + +
198B ILE* 3.0 13.5 + - - +
200B THR* 1.3 78.1 - - - +
202B LEU* 1.3 64.5 + - + +
204B GLN* 3.3 22.3 + - - +
205B VAL* 3.5 12.7 + - + +
217B TYR* 6.0 2.9 - - + -
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Residues in contact with LEU 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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191B ILE* 5.9 1.6 - - + -
198B ILE* 3.1 19.9 + - + +
199B ASN* 3.5 9.8 + - - +
201B ILE* 1.3 76.2 - - + +
203B GLU* 1.3 64.5 + - - +
204B GLN 3.2 2.2 - - - -
205B VAL* 3.2 28.5 + - + +
206B VAL* 3.4 12.9 - - - +
217B TYR* 4.7 20.0 - - + -
219B LEU* 4.7 11.7 - - + -
227B ILE* 3.8 22.2 - - + -
228B LEU 3.6 24.5 - - - +
229B LEU* 4.5 7.2 - - + -
232B VAL* 4.2 27.6 - - + +
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Residues in contact with GLU 203 (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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199B ASN* 3.2 22.2 + - - +
200B THR* 3.8 19.8 - - - +
201B ILE 3.4 0.6 - - - -
202B LEU* 1.3 76.1 - - - +
204B GLN* 1.3 71.3 + - - +
206B VAL* 3.4 10.8 + - - +
207B ILE* 3.4 23.9 + - - +
228B LEU* 4.7 16.4 - - + +
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Residues in contact with GLN 204 (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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171B VAL* 3.4 32.0 - - + +
174B PHE* 4.1 21.8 - - + +
175B ARG* 3.7 37.9 + - + +
178B ILE* 4.7 14.4 - - + +
200B THR* 3.4 20.2 + - - +
201B ILE* 3.3 8.9 + - - +
202B LEU 3.2 0.4 - - - -
203B GLU* 1.3 88.0 + - - +
205B VAL* 1.3 60.1 + - - +
206B VAL 3.1 2.0 - - - -
207B ILE* 4.3 5.4 - - - +
208B LEU* 3.1 32.6 + - - +
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Residues in contact with VAL 205 (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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178B ILE* 5.0 11.7 - - + -
201B ILE* 3.6 18.4 - - + +
202B LEU* 3.2 23.7 + - + +
204B GLN* 1.3 76.4 - - - +
206B VAL* 1.3 58.0 - - + +
208B LEU* 5.0 2.0 - - - -
209B GLY* 3.1 25.3 + - - +
211B HIS* 3.8 31.7 + - + +
212B SER* 5.1 2.7 - - - +
217B TYR* 3.9 29.8 - - + +
232B VAL* 5.0 14.4 - - + -
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Residues in contact with VAL 206 (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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202B LEU 3.4 15.9 - - - +
203B GLU* 3.6 10.1 - - - +
204B GLN 3.1 0.6 - - - -
205B VAL* 1.3 78.6 - - + +
207B ILE* 1.3 68.2 - - + +
208B LEU 3.3 0.2 - - - -
209B GLY* 3.1 14.2 + - - -
231B ARG* 3.8 39.0 - - + -
232B VAL* 5.0 5.2 - - + -
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Residues in contact with ILE 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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175B ARG* 3.2 35.7 - - - +
203B GLU 3.4 13.3 + - - +
204B GLN* 3.6 6.0 + - - +
206B VAL* 1.3 82.0 - - + +
208B LEU* 1.3 66.8 + - - +
209B GLY* 4.4 0.2 - - - -
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Residues in contact with LEU 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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175B ARG* 4.5 14.8 - - + +
178B ILE* 6.2 3.1 - - + -
204B GLN 3.1 19.3 + - - +
205B VAL* 4.6 1.8 - - - +
207B ILE* 1.3 82.6 - - - +
209B GLY* 1.3 69.0 + - - +
210B LYS* 5.0 1.0 - - - +
211B HIS* 4.4 14.0 - - + +
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Residues in contact with GLY 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 VAL 3.1 18.6 + - - -
206B VAL* 3.1 11.9 + - - -
207B ILE 4.4 0.2 - - - -
208B LEU* 1.3 78.4 - - - +
210B LYS* 1.3 58.7 - - - +
211B HIS* 2.2 39.1 + - - -
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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