Contacts of the helix formed by residues 184 - 202 (chain B) in PDB entry 4ZDR
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 SER 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 2.8 34.5 + - - +
179B TYR* 4.5 0.2 - - - -
182B LEU* 4.1 12.5 + - - +
183B ASN* 1.3 75.5 + - - +
185B PRO* 1.3 61.1 - - - +
186B GLU 3.3 2.7 - - - -
187B LYS* 3.3 10.7 + - - +
188B ALA* 3.0 26.9 + - - +
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Residues in contact with PRO 185 (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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179B TYR* 3.8 32.5 - - + -
183B ASN* 3.2 15.9 - - + +
184B SER* 1.3 85.3 - - - +
186B GLU* 1.3 77.1 + - - +
188B ALA* 3.6 0.7 - - + +
189B CYS* 2.9 36.4 + - - -
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Residues in contact with GLU 186 (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 SER 3.3 0.8 - - - -
185B PRO* 1.3 92.6 - - - +
187B LYS* 1.3 61.7 + - - +
189B CYS* 4.0 7.0 - - - +
190B SER* 2.9 31.7 + - - -
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Residues in contact with LYS 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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178B TYR* 4.2 25.8 - - + -
184B SER* 3.3 16.5 + - - +
186B GLU* 1.3 75.2 - - - +
188B ALA* 1.3 61.2 + - - +
190B SER* 3.8 5.0 - - - -
191B LEU* 2.8 34.0 + - - +
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Residues in contact with ALA 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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175B SER* 3.3 36.3 - - - +
178B TYR* 3.9 7.5 - - - +
179B TYR* 3.5 22.9 - - + +
184B SER 3.0 17.5 + - - +
185B PRO 3.6 5.2 - - - +
187B LYS* 1.3 77.7 - - - +
189B CYS* 1.3 58.5 + - - +
192B ALA* 2.9 26.5 + - - +
228B TRP* 3.9 8.7 - - + -
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Residues in contact with CYS 189 (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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179B TYR* 5.1 0.9 - - - -
185B PRO* 2.9 26.0 + - - +
186B GLU* 4.0 7.4 - - - +
188B ALA* 1.3 73.4 - - - +
190B SER* 1.3 61.6 + - - +
192B ALA* 4.5 0.2 - - - -
193B LYS* 2.9 32.1 + - - +
225B LEU* 3.5 18.2 - - + +
228B TRP* 3.5 39.3 - - - -
229B THR* 4.0 19.3 - - + -
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU 2.9 20.5 + - - -
187B LYS* 3.8 5.3 + - - -
189B CYS* 1.3 77.8 - - - +
191B LEU* 1.3 56.9 + - - +
193B LYS* 4.1 4.1 - - - +
194B THR* 2.8 38.5 + - - -
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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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153B PHE* 4.6 22.7 - - + -
171B ALA* 3.5 40.4 - - + +
174B PHE* 4.1 18.6 - - + -
175B SER* 4.2 6.7 - - - +
178B TYR* 3.9 30.1 - - + -
187B LYS 2.8 21.0 + - - +
188B ALA* 3.8 3.1 - - - +
190B SER* 1.3 71.1 + - - +
192B ALA* 1.3 70.6 + - - +
194B THR* 3.9 3.5 - - - -
195B ALA* 3.1 20.1 + - + +
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Residues in contact with ALA 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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175B SER* 4.1 14.1 - - - +
188B ALA 2.9 18.0 + - - +
189B CYS 3.8 4.3 - - - +
191B LEU* 1.3 78.1 - - - +
193B LYS* 1.3 63.2 + - - +
195B ALA* 3.4 3.1 + - - +
196B PHE* 3.1 22.7 + - - +
221B LEU* 4.1 35.8 - - + +
224B ASN* 5.5 0.7 - - + -
225B LEU* 4.4 8.5 - - + -
228B TRP* 4.3 10.1 - - + -
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Residues in contact with LYS 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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189B CYS 2.9 19.2 + - - +
190B SER* 4.1 5.4 - - - +
192B ALA* 1.3 73.8 - - - +
194B THR* 1.3 62.0 + - - +
196B PHE* 3.0 8.4 + - + +
197B ASP* 2.8 53.3 + - - +
225B LEU* 3.7 25.1 - - + +
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Residues in contact with THR 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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190B SER* 2.8 27.5 + - - -
191B LEU* 3.9 4.2 - - - -
193B LYS* 1.3 77.7 - - - +
195B ALA* 1.3 65.8 + - - +
197B ASP* 2.9 19.3 + - + +
198B GLU* 2.9 40.6 + - + +
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Residues in contact with ALA 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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153B PHE* 6.3 1.3 - - + -
162B PRO* 4.7 1.9 - - - +
168B LEU* 4.1 9.8 - - + +
171B ALA* 3.4 33.2 - - + -
191B LEU* 3.1 13.9 + - + +
192B ALA 3.6 4.5 - - - +
194B THR* 1.3 79.4 - - - +
196B PHE* 1.3 61.8 + - - +
198B GLU* 3.7 7.2 + - - +
199B ALA* 3.3 23.2 + - - +
221B LEU* 4.3 7.4 - - + -
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Residues in contact with PHE 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 ALA 3.1 13.0 + - - +
193B LYS* 3.0 12.5 + - + +
195B ALA* 1.3 75.8 - - - +
197B ASP* 1.3 70.6 + - - +
199B ALA* 3.3 5.0 + - - +
200B ILE* 2.9 53.7 + - + +
218B MET* 3.3 52.2 - - + +
219B GLN* 5.2 0.2 - - - -
221B LEU* 4.4 14.1 - - + +
222B ARG* 4.1 25.8 - - + -
225B LEU* 6.0 5.4 - - + -
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Residues in contact with ASP 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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193B LYS* 2.8 53.0 + - - +
194B THR* 3.5 9.2 - - + +
196B PHE* 1.3 85.9 - - - +
198B GLU* 1.3 59.4 + - + +
200B ILE* 3.1 12.3 + - - +
201B ALA* 2.9 26.3 + - - +
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Residues in contact with GLU 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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162B PRO* 3.4 27.4 - - + +
167B ARG* 3.6 21.4 + - - -
194B THR* 2.9 38.6 + - + +
195B ALA* 4.3 5.9 - - - +
197B ASP* 1.3 79.5 - - + +
199B ALA* 1.3 61.7 + - - +
201B ALA* 3.6 18.9 - - - +
202B GLU* 3.6 7.3 + - - +
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Residues in contact with ALA 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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162B PRO* 3.6 19.9 - - - +
163B THR* 3.6 21.7 - - + +
168B LEU* 4.1 7.0 - - + -
195B ALA 3.3 17.9 + - - +
196B PHE 3.7 4.0 - - - +
197B ASP 3.1 0.4 - - - -
198B GLU* 1.3 78.2 - - - +
200B ILE* 1.3 66.4 + - - +
202B GLU 3.6 6.6 + - - -
203B LEU* 3.7 10.7 + - - +
218B MET* 3.8 24.7 - - + +
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Residues in contact with ILE 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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196B PHE* 2.9 41.7 + - + +
197B ASP* 3.1 13.6 + - - +
199B ALA* 1.3 73.4 - - - +
201B ALA* 1.3 70.4 + - - +
203B LEU* 3.1 37.6 - - + +
218B MET* 3.6 25.1 - - + -
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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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197B ASP 2.9 12.0 + - - +
198B GLU* 3.6 14.6 - - - +
200B ILE* 1.3 80.8 - - - +
202B GLU* 1.3 64.3 + - + +
203B LEU* 3.2 4.5 + - - +
204B ASP* 4.3 6.4 - - - +
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Residues in contact with GLU 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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161B GLN* 3.1 26.0 - - - +
162B PRO* 3.4 22.8 - - - +
163B THR* 3.8 7.0 - - + +
198B GLU 3.6 14.3 + - - +
199B ALA 3.6 4.7 + - - -
200B ILE 3.3 1.2 + - - -
201B ALA* 1.3 83.6 - - + +
203B LEU* 1.3 50.5 + - - +
204B ASP* 2.6 28.4 + - - +
205B THR* 2.9 31.4 + - + +
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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