Contacts of the helix formed by residues 190 - 212 (chain B) in PDB entry 4GWR
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 CYS 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B ALA* 3.3 12.6 + - + +
188B PRO 3.4 0.8 - - - -
189B TRP* 1.3 88.5 - - + +
191B GLY* 1.3 62.9 + - - +
192B HIS* 3.8 13.7 - - - -
193B CYS* 3.1 45.2 + - - +
194B LYS* 2.9 31.9 + - - +
237B PHE* 4.0 22.9 - - + -
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Residues in contact with GLY 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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189B TRP 3.4 5.7 + - - -
190B CYS* 1.3 68.1 - - - +
192B HIS* 1.3 61.7 + - - +
194B LYS* 3.3 17.8 + - - +
195B ASN* 2.7 39.3 + - - +
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B CYS* 3.4 7.0 - - - -
191B GLY* 1.3 75.6 - - - +
193B CYS* 1.3 63.0 + - - +
195B ASN* 3.5 11.1 + - - +
196B LEU* 3.1 24.0 + - - +
237B PHE 5.0 1.6 - - - +
238B PRO* 3.8 23.2 - - + +
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Residues in contact with CYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 4.3 8.9 - - - +
186B TYR* 3.5 35.0 - - + -
187B ALA 4.0 5.6 - - - +
190B CYS* 3.1 41.7 + - + +
192B HIS* 1.3 79.4 - - - +
194B LYS* 1.3 62.5 + - + +
196B LEU* 3.2 5.6 + - - +
197B GLU* 3.1 23.6 + - - +
237B PHE* 3.8 6.3 - - - -
238B PRO* 3.7 24.5 - - - -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO 4.3 14.1 - - - +
189B TRP* 3.7 14.5 + - - +
190B CYS 2.9 34.5 + - - +
191B GLY* 3.3 13.0 + - - +
193B CYS* 1.3 73.4 - - + +
195B ASN* 1.3 64.2 + - - +
197B GLU* 3.4 15.7 + - - +
198B PRO* 3.4 11.1 - - - +
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Residues in contact with ASN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY* 2.7 26.0 + - - +
192B HIS* 3.8 10.3 - - - +
194B LYS* 1.3 78.8 - - - +
196B LEU* 1.3 60.6 + - - +
198B PRO* 3.4 11.5 - - - +
199B GLU* 4.5 9.0 + - - +
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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
----------------------------------------------------------
184B GLU* 3.5 28.5 - - + +
192B HIS 3.1 16.7 + - - +
193B CYS 3.2 4.9 + - - +
195B ASN* 1.3 76.9 - - - +
197B GLU* 1.3 56.3 + - - +
198B PRO 3.4 0.4 - - - -
199B GLU* 3.0 6.1 + - + -
200B TRP* 2.7 51.2 + - + +
238B PRO* 4.2 15.9 - - + -
240B ILE* 4.1 20.9 - - + -
256B ARG* 4.0 38.6 - - + +
261B ILE* 4.4 8.7 - - + -
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Residues in contact with GLU 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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162B VAL* 5.6 2.1 - - - +
184B GLU* 5.5 4.0 - - - +
193B CYS 3.1 12.7 + - - +
194B LYS* 3.6 11.0 - - - +
196B LEU* 1.3 74.8 - - - +
198B PRO* 1.4 75.6 - - + +
200B TRP* 3.4 6.8 + - - +
201B ALA* 3.0 32.7 + - - +
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Residues in contact with PRO 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 LYS 3.4 11.0 - - - +
195B ASN* 3.4 17.5 - - - +
197B GLU* 1.4 100.8 - - + +
199B GLU* 1.3 56.7 + - + +
201B ALA* 3.4 5.4 + - + +
202B ALA* 2.9 28.3 + - - +
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Residues in contact with GLU 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 ASN 4.8 7.0 - - - +
196B LEU* 3.0 11.9 + - + +
198B PRO* 1.3 77.3 - - + +
200B TRP* 1.3 61.8 + - - +
202B ALA* 3.7 8.7 - - - +
203B ALA* 2.9 30.8 + - - +
256B ARG 4.0 18.4 - - - +
257B THR* 3.6 9.4 - - - +
258B ARG* 2.9 38.6 + - - +
261B ILE* 4.7 1.5 - - - +
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Residues in contact with TRP 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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162B VAL* 3.8 24.0 - - + +
182B MET* 3.4 33.0 - - + -
184B GLU* 3.6 30.6 - - + +
196B LEU* 2.7 34.9 + - + +
197B GLU* 3.7 6.5 - - - +
199B GLU* 1.3 72.2 - - - +
201B ALA* 1.3 58.4 + - - +
203B ALA* 3.4 3.7 + - - +
204B ALA* 2.8 28.9 + - - +
217B LEU* 3.8 21.9 - - + +
218B ALA 3.1 25.2 + - - +
219B ALA* 4.9 0.9 - - + -
240B ILE* 3.6 40.2 - - + -
252B TYR* 5.5 0.4 - + - -
261B ILE* 3.8 35.7 - - + -
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Residues in contact with ALA 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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160B LYS* 5.4 13.6 - - + +
161B ASP* 5.0 1.8 + - - +
162B VAL* 3.7 20.2 - - + +
197B GLU* 3.0 27.0 + - - +
198B PRO* 3.7 7.2 - - + +
200B TRP* 1.3 73.7 - - - +
202B ALA* 1.3 64.6 + - - +
204B ALA* 3.2 2.6 + - - +
205B SER* 3.1 26.6 + - - -
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Residues in contact with ALA 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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198B PRO 2.9 17.9 + - - +
199B GLU* 3.7 14.4 - - - +
200B TRP 3.4 0.2 - - - -
201B ALA* 1.3 72.4 - - - +
203B ALA* 1.3 64.4 + - - +
205B SER* 3.4 4.5 + - - -
206B GLU 3.2 9.0 + - - -
258B ARG* 2.9 47.6 + - + +
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Residues in contact with ALA 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 GLU 2.9 18.4 + - - +
200B TRP 3.7 3.8 - - - +
202B ALA* 1.3 76.9 - - - +
204B ALA* 1.3 58.5 + - - +
206B GLU* 3.2 1.9 + - - +
207B VAL* 2.9 33.3 + - - +
217B LEU* 3.9 3.8 - - + -
258B ARG* 3.8 14.5 - - + +
261B ILE* 3.6 37.9 - - + -
262B VAL* 4.0 9.6 - - + -
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Residues in contact with ALA 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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161B ASP* 3.8 20.6 - - - +
162B VAL* 3.7 20.6 - - + -
200B TRP 2.8 18.4 + - - +
201B ALA 3.5 5.8 - - - +
202B ALA 3.2 0.2 - - - -
203B ALA* 1.3 76.6 - - - +
205B SER* 1.3 56.5 + - - +
207B VAL* 3.5 3.0 + - - +
208B LYS* 3.0 30.0 + - - +
217B LEU* 3.7 22.8 - - + +
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Residues in contact with SER 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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160B LYS* 5.8 1.9 - - - +
161B ASP* 2.9 28.5 + - - +
201B ALA 3.1 15.2 + - - -
202B ALA* 3.6 8.8 - - - -
204B ALA* 1.3 75.8 - - - +
206B GLU* 1.3 64.3 + - - +
208B LYS* 3.4 3.0 + - - +
209B GLU* 3.0 22.3 + - - +
258B ARG* 4.3 7.9 - - - -
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Residues in contact with GLU 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 ALA 3.2 11.2 + - - +
203B ALA 3.7 6.3 - - - +
205B SER* 1.3 79.3 - - - +
207B VAL* 1.3 57.5 + - - +
209B GLU* 3.3 15.7 + - - +
210B GLN* 2.9 55.9 + - + +
258B ARG* 3.7 32.0 + - - +
259B SER* 5.7 1.4 - - - -
262B VAL* 3.7 35.4 - - + +
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Residues in contact with VAL 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 ALA* 2.9 21.7 + - + +
204B ALA 4.0 3.1 - - - +
206B GLU* 1.3 75.2 - - - +
208B LYS* 1.3 53.1 + - - +
210B GLN* 4.7 3.8 - - - -
211B THR* 2.7 47.2 + - + +
215B VAL* 3.4 40.6 - - + +
216B LYS* 5.0 0.4 - - - -
217B LEU* 3.9 23.8 - - + +
261B ILE* 5.1 0.4 - - + +
262B VAL* 4.2 18.8 - - + +
265B ALA* 3.5 23.6 - - + -
266B LEU* 5.9 0.9 - - + -
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Residues in contact with LYS 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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161B ASP* 3.3 36.5 + - + +
163B ILE* 6.0 4.0 - - - +
204B ALA 3.0 18.4 + - - +
205B SER 3.6 5.2 - - - +
207B VAL* 1.3 77.9 - - - +
209B GLU* 1.3 56.4 + - - +
211B THR* 4.5 0.2 - - - -
212B LYS* 2.9 31.7 + - - -
213B GLY* 4.4 15.7 - - - +
215B VAL 5.1 1.8 - - - -
216B LYS* 5.9 5.5 - - - +
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Residues in contact with GLU 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 SER 3.0 14.4 + - - +
206B GLU* 3.5 21.0 - - - +
208B LYS* 1.3 78.8 - - - +
210B GLN* 1.3 73.3 + - - +
211B THR 3.6 0.2 + - - -
212B LYS* 3.8 7.4 + - - +
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Residues in contact with GLN 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 GLU* 2.9 52.7 + - + +
207B VAL* 4.1 2.2 - - - +
209B GLU* 1.3 84.5 - - + +
211B THR* 1.3 60.6 + - - +
262B VAL* 4.8 1.8 - - + +
266B LEU* 3.9 38.6 - - + +
269B PHE* 5.1 5.5 - - - -
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Residues in contact with THR 211 (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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207B VAL* 2.7 32.6 + - + +
210B GLN* 1.3 75.5 - - - +
212B LYS* 1.3 69.3 + - - +
213B GLY 3.1 6.8 + - - -
214B LYS* 3.1 19.2 + - - +
215B VAL* 3.2 36.4 + - + -
265B ALA 4.9 1.8 - - - +
266B LEU* 3.9 21.5 - - + -
269B PHE* 3.7 33.2 - - + -
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Residues in contact with LYS 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 LYS* 2.9 17.7 + - - -
209B GLU 3.8 6.4 + - - +
210B GLN 3.5 1.8 - - - -
211B THR* 1.3 80.0 - - - +
213B GLY* 1.3 57.9 + - - +
214B LYS* 3.7 2.7 + - + +
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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