Contacts of the helix formed by residues 186 - 199 (chain B) in PDB entry 3F7P
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 THR 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B ASP 4.9 4.0 - - - +
185B MET* 1.3 76.2 - - - +
187B ALA* 1.3 64.1 + - - +
188B LYS* 3.6 10.6 + - - +
189B GLU* 2.9 40.1 + - - +
190B LYS* 3.0 22.0 + - - +
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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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169B LEU* 4.6 9.6 - - + -
173B ILE* 3.3 32.8 - - + +
174B SER* 3.8 19.1 - - - +
176B ILE* 4.4 5.9 - - - +
185B MET 3.9 0.2 + - - -
186B THR* 1.3 72.3 - - - +
188B LYS* 1.3 62.6 + - - +
190B LYS* 3.3 16.4 + - - +
191B LEU* 3.0 22.5 + - - +
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Residues in contact with LYS 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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165B TRP* 6.5 0.4 - - + -
169B LEU* 5.7 2.8 - - + +
173B ILE* 4.8 5.9 - - + +
186B THR* 3.7 10.2 - - - +
187B ALA* 1.3 79.0 - - - +
189B GLU* 1.3 65.2 + - + +
191B LEU* 3.1 8.5 + - - +
192B LEU* 3.0 19.9 + - + +
210B PHE* 3.6 20.8 - - + -
275B GLU* 3.2 36.1 + - - -
279B ILE* 4.0 20.0 - - + -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP 3.9 4.3 - - - +
185B MET* 3.2 29.9 - - + +
186B THR* 2.9 44.3 + - - +
188B LYS* 1.3 77.3 - - + +
190B LYS* 1.3 56.7 + - - +
192B LEU* 3.5 8.4 + - - +
193B LEU* 3.0 27.7 + - - +
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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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174B SER 4.7 9.5 + - - -
176B ILE* 4.0 24.8 + - + +
177B GLN* 5.9 0.4 - - - +
178B VAL* 3.4 20.2 - - + +
181B GLN* 3.4 41.6 - - + +
182B SER 4.2 6.3 - - - -
183B GLU* 5.4 2.9 - - - +
185B MET* 3.5 35.7 - - + -
186B THR 3.0 15.3 + - - +
187B ALA* 3.5 12.2 - - - +
189B GLU* 1.3 75.2 - - - +
191B LEU* 1.3 60.2 + - - +
193B LEU* 3.4 4.6 + - - +
194B TRP* 2.9 28.4 + - - +
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Residues in contact with LEU 191 (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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173B ILE* 4.7 5.4 - - + -
176B ILE* 4.5 19.4 - - + +
187B ALA 3.0 13.8 + - - +
188B LYS* 3.5 8.3 - - - +
190B LYS* 1.3 76.5 - - - +
192B LEU* 1.3 58.1 + - - +
194B TRP* 3.3 23.8 + - + +
195B SER* 2.9 31.9 + - - -
210B PHE* 3.6 17.7 - - + -
279B ILE* 3.7 41.1 - - + +
282B VAL* 4.1 5.8 - - + -
283B SER* 3.9 26.2 - - - +
286B TYR* 4.4 8.1 - - + -
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Residues in contact with LEU 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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188B LYS* 3.0 11.8 + - + +
189B GLU* 3.8 8.7 - - - +
191B LEU* 1.3 74.3 - - - +
193B LEU* 1.3 60.1 + - - +
195B SER* 3.3 3.0 + - - -
196B GLN* 2.9 52.3 + - - +
207B CYS* 3.8 15.3 - - - -
208B ASP 4.1 13.0 - - - +
209B ASN* 3.7 32.8 - - - +
210B PHE* 3.3 25.4 - - + -
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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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178B VAL* 4.3 14.6 - - + -
179B SER 4.6 0.2 - - - +
180B GLY 4.0 14.4 - - - +
181B GLN* 4.9 1.3 - - + -
185B MET* 4.0 22.2 - - + -
189B GLU 3.0 18.1 + - - +
190B LYS* 3.6 6.1 - - - +
192B LEU* 1.3 72.7 - - - +
194B TRP* 1.3 66.5 + - - +
196B GLN* 3.3 19.8 + - + +
197B ARG* 2.9 64.4 + - + +
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Residues in contact with TRP 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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176B ILE* 5.1 0.9 - - + -
177B GLN 5.2 1.3 - - - -
178B VAL* 4.2 22.6 - - + +
190B LYS 2.9 14.3 + - - +
191B LEU* 3.4 21.1 - - + +
193B LEU* 1.3 76.6 - - - +
195B SER* 1.3 80.2 + - - +
197B ARG* 2.9 17.0 + - + +
198B MET* 2.9 50.4 + - + +
223B ILE* 3.7 31.4 - - + -
282B VAL* 3.9 25.4 - - + -
285B LEU* 4.3 3.1 - - + -
286B TYR* 3.4 57.2 - + + -
289B MET* 4.3 9.8 - - + +
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Residues in contact with SER 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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191B LEU 2.9 18.3 + - - -
192B LEU* 3.5 8.7 - - - -
194B TRP* 1.3 79.4 - - - +
196B GLN* 1.3 63.1 + - - +
198B MET* 3.2 6.7 + - - +
199B VAL* 3.1 29.8 + - - +
207B CYS* 3.8 20.6 - - - -
210B PHE* 3.9 3.1 - - - -
214B TRP* 3.7 14.7 - - - -
223B ILE* 4.6 2.2 - - - -
282B VAL* 3.6 24.4 - - - +
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Residues in contact with GLN 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 LEU* 2.9 41.1 + - - +
193B LEU* 3.5 23.9 - - + +
195B SER* 1.3 77.6 - - - +
197B ARG* 1.3 61.6 + - + +
199B VAL* 3.5 9.7 + - - +
200B GLU* 3.1 23.0 + - - +
207B CYS* 2.8 35.8 + - + +
208B ASP* 4.6 3.0 + - - +
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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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178B VAL* 3.9 17.4 - - - +
179B SER* 3.3 38.5 + - - -
180B GLY* 3.7 14.1 + - - -
193B LEU* 2.9 36.2 + - + +
194B TRP* 2.9 11.9 + - + +
196B GLN* 1.3 76.1 - - + +
198B MET* 1.3 65.1 + - + +
200B GLU* 3.4 30.0 + - - +
226B ARG* 3.4 8.8 + - - -
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Residues in contact with MET 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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194B TRP* 2.9 64.2 + - + +
195B SER 3.2 7.2 + - - +
197B ARG* 1.3 80.3 - - - +
199B VAL* 1.3 56.3 + - - +
200B GLU 3.2 0.2 - - - -
202B TYR* 3.5 7.4 - - - -
222B ALA 5.5 0.4 - - - -
223B ILE* 3.9 31.4 - - + +
226B ARG* 2.8 58.0 + - + +
227B HIS* 4.9 4.0 - - + +
289B MET* 4.2 12.3 - - + -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER* 3.1 18.6 + - - +
196B GLN* 3.7 11.2 - - - +
198B MET* 1.3 74.1 - - - +
200B GLU* 1.3 68.1 + - - +
201B GLY 3.4 0.3 + - - -
202B TYR* 3.3 28.0 + - + +
205B LEU* 4.3 12.8 - - + +
206B ARG* 4.9 2.5 - - - +
207B CYS* 4.4 10.1 - - + +
214B TRP* 6.1 0.2 - - + -
219B LEU* 3.8 34.5 - - + +
222B ALA* 3.9 15.3 - - + -
223B ILE* 3.8 24.9 - - + +
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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
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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