Contacts of the helix formed by residues 189 - 210 (chain B) in PDB entry 4WFH
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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187B HIS 3.6 5.8 - - - +
188B VAL* 1.4 93.2 - - + +
190B PRO* 1.3 75.4 - - + +
191B GLU* 4.0 11.7 - - + +
192B LEU* 3.1 26.5 + - + +
193B VAL* 3.0 19.4 + - - +
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Residues in contact with PRO 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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184B LEU* 4.0 24.9 - - + -
188B VAL 3.5 2.6 - - - +
189B PRO* 1.3 82.0 - - + +
191B GLU* 1.3 76.4 + - - +
193B VAL* 3.9 2.0 - - + -
194B ARG* 2.9 43.4 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PRO* 3.1 9.8 + - + +
190B PRO* 1.3 96.8 - - - +
192B LEU* 1.3 65.6 + - + +
194B ARG* 3.5 9.7 + - - +
195B VAL* 3.4 23.9 + - - +
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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
----------------------------------------------------------
188B VAL* 4.0 12.1 - - + -
189B PRO* 3.1 34.1 + - + +
191B GLU* 1.3 76.3 - - + +
193B VAL* 1.3 55.8 - - - +
194B ARG 3.1 2.0 - - - -
195B VAL* 2.8 16.4 + - + +
196B LEU* 2.7 42.3 + - + +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLU* 3.7 29.8 - - + +
183B PHE* 3.7 38.3 - - + -
184B LEU* 4.1 9.6 - - + -
188B VAL* 3.4 24.7 - - + +
189B PRO 3.0 17.8 + - - +
190B PRO* 3.9 6.3 - - + +
192B LEU* 1.3 75.5 - - - +
194B ARG* 1.3 64.0 + - - +
196B LEU* 3.9 8.9 - - + +
197B SER* 3.0 28.4 + - - -
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Residues in contact with ARG 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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180B GLU* 2.8 49.6 + - - +
184B LEU* 4.6 12.9 - - - +
190B PRO* 2.9 38.6 + - - +
191B GLU* 3.5 10.8 - - - +
192B LEU 3.1 0.2 - - - -
193B VAL* 1.3 86.8 - - - +
195B VAL* 1.3 60.7 + - + +
197B SER* 2.5 20.5 + - - -
198B ALA* 3.1 11.1 + - - +
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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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191B GLU 3.4 14.6 + - - +
192B LEU* 2.8 20.8 + - + +
194B ARG* 1.3 74.7 - - + +
196B LEU* 1.3 70.6 + - + +
198B ALA* 3.0 9.8 + - + +
199B MET* 3.0 33.7 + - + +
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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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183B PHE* 4.7 28.5 - - + -
188B VAL* 4.7 20.0 - - + -
192B LEU* 2.7 26.3 + - + +
193B VAL* 3.9 7.9 - - - +
195B VAL* 1.3 77.3 - - + +
197B SER* 1.3 58.2 + - - +
199B MET* 3.2 14.9 - - + +
200B LEU* 2.9 33.1 + - + +
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Residues in contact with SER 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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176B ILE* 3.9 28.4 - - - +
180B GLU* 4.3 9.1 + - - -
183B PHE* 5.4 5.2 - - - -
193B VAL* 3.0 16.6 + - - -
194B ARG* 2.5 27.7 + - - -
196B LEU* 1.3 73.5 - - - +
198B ALA* 1.3 54.6 + - - +
200B LEU* 3.4 11.7 - - - +
201B PHE* 2.5 37.3 + - - +
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Residues in contact with ALA 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 ARG 3.7 7.9 - - - +
195B VAL* 3.0 12.4 + - + +
197B SER* 1.3 77.4 + - - +
199B MET* 1.3 63.1 + - + +
201B PHE* 3.2 10.9 - - + +
202B LEU* 2.8 42.0 + - + +
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Residues in contact with MET 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* 3.0 30.0 + - + +
196B LEU* 3.2 18.4 - - + +
198B ALA* 1.3 80.1 - - + +
200B LEU* 1.3 52.8 - - + +
202B LEU* 3.4 23.4 - - + +
203B LEU* 2.8 52.0 + - + +
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Residues in contact with LEU 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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176B ILE* 5.5 5.6 - - + -
179B ILE* 5.1 9.6 - - + -
183B PHE* 3.9 33.2 - - + -
196B LEU* 2.9 20.0 + - + +
197B SER* 3.5 9.4 - - - +
199B MET* 1.3 73.6 - - + +
201B PHE* 1.3 61.1 + - - +
203B LEU* 3.8 11.8 - - + +
204B ILE* 2.8 37.7 + - - +
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Residues in contact with PHE 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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169B GLY* 4.6 15.9 - - - -
172B LEU* 3.6 25.0 - - + +
173B ARG* 4.9 4.7 - - + -
176B ILE* 3.9 25.0 - - + +
197B SER 2.5 23.0 + - - +
198B ALA* 3.2 13.0 - - + +
200B LEU* 1.3 72.6 - - - +
202B LEU* 1.3 59.8 + - + +
204B ILE* 3.1 22.3 - - - +
205B GLY* 3.3 1.2 + - - -
271B TYR* 2.7 52.1 + + - -
274B SER* 5.3 12.6 - - - -
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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
----------------------------------------------------------
198B ALA* 2.8 18.9 + - + +
199B MET* 3.4 34.3 - - + +
201B PHE* 1.3 77.6 - - + +
203B LEU* 1.3 87.4 + - + +
205B GLY 3.2 0.2 + - - -
206B CYS* 2.6 44.1 + - + +
271B TYR* 2.9 13.8 - - + +
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Residues in contact with LEU 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 MET* 2.8 39.3 + - + +
200B LEU* 3.8 13.9 - - + +
202B LEU* 1.3 88.0 - - + +
204B ILE* 1.3 51.8 + - - +
206B CYS* 3.5 10.3 - - + +
207B LEU* 2.7 33.0 + - - +
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Residues in contact with ILE 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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172B LEU* 4.8 18.4 - - + -
176B ILE* 5.5 3.4 - - + -
200B LEU* 2.8 23.2 + - + +
201B PHE* 3.1 12.3 - - - +
203B LEU* 1.3 75.0 - - - +
205B GLY* 1.3 58.2 + - - +
207B LEU* 3.1 17.7 + - + +
208B LEU* 2.7 51.7 + - + +
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Residues in contact with GLY 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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172B LEU* 5.3 2.7 - - - -
201B PHE 3.3 1.6 + - - -
202B LEU 3.2 2.4 + - - -
204B ILE* 1.3 81.7 - - - +
206B CYS* 1.3 55.9 + - - +
208B LEU* 2.8 6.8 + - - -
209B PHE* 2.6 45.7 + - - +
271B TYR* 3.5 31.6 - - - -
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Residues in contact with CYS 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* 2.6 28.3 + - + +
203B LEU* 3.5 13.5 - - - +
205B GLY* 1.3 69.0 - - - -
207B LEU* 1.3 58.9 - - - +
210B VAL* 2.7 49.7 + - + +
211B LEU* 2.8 30.2 + - - -
271B TYR* 4.0 5.4 - - - -
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Residues in contact with LEU 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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203B LEU 2.7 19.8 + - - +
204B ILE* 3.1 22.2 + - + +
206B CYS* 1.3 71.7 - - - +
208B LEU* 1.3 58.2 + - + +
211B LEU* 3.6 28.4 - - + +
212B THR* 2.3 47.0 + - - +
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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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172B LEU* 5.6 8.5 - - + -
204B ILE* 2.7 40.3 + - + +
205B GLY* 3.7 4.7 - - - +
207B LEU* 1.3 81.4 - - + +
209B PHE* 1.3 85.6 - - + +
212B THR* 3.5 15.4 - - + +
213B PRO* 3.3 14.7 - - - +
264B TRP* 4.8 1.4 - - - -
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Residues in contact with PHE 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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168B LEU* 3.9 22.2 - - + -
172B LEU* 5.6 2.5 - - + -
205B GLY* 2.6 28.6 + - - +
208B LEU* 1.3 95.7 - - + +
210B VAL* 1.3 63.0 + - + +
213B PRO* 3.2 9.8 - - - +
232B VAL* 4.3 0.2 - - - +
236B LEU* 3.8 12.5 - - + +
264B TRP* 3.0 34.6 + + - +
267B LEU* 4.0 32.1 - - + -
268B GLY* 4.2 17.7 - - - -
271B TYR* 3.7 45.1 - + + -
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Residues in contact with VAL 210 (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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206B CYS* 2.7 36.7 + - - +
209B PHE* 1.3 79.9 - - + +
211B LEU* 1.3 77.9 + - + +
213B PRO* 3.3 3.9 - - - +
214B THR* 3.0 32.5 + - + +
229B ILE* 5.2 10.3 - - + -
232B VAL* 4.2 18.8 - - + +
233B ILE* 5.2 8.5 - - + -
236B LEU* 4.7 8.3 - - + -
272B PHE* 4.7 13.9 - - + -
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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
------------------------------------------------------------
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