Contacts of the helix formed by residues 187 - 209 (chain B) in PDB entry 4AUP
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.4 20.1 - - + +
184B SER 3.1 17.1 + - - +
186B LEU* 1.3 81.8 + - + +
188B SER* 1.3 58.5 + - - +
189B TRP* 3.1 10.1 - - - +
190B LYS* 2.8 58.8 + - + +
191B GLY 3.4 3.6 + - - -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR 4.0 9.4 + - - -
184B SER* 3.7 4.6 + - - -
185B GLY* 2.9 33.2 + - - -
186B LEU 3.4 0.6 - - - -
187B GLU* 1.3 76.9 - - - +
189B TRP* 1.3 56.0 + - - +
191B GLY* 3.0 17.3 + - - -
192B VAL* 3.0 19.6 + - - +
195B ARG* 4.6 1.7 + - - -
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Residues in contact with TRP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 3.3 27.1 + - - -
187B GLU* 3.1 6.3 - - - +
188B SER* 1.3 76.9 - - - +
190B LYS* 1.3 98.6 + - + +
191B GLY 3.3 0.2 - - - -
192B VAL* 3.6 9.7 + - - +
193B ALA* 3.2 27.0 + - + +
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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
----------------------------------------------------------
138B PHE* 3.2 25.5 - - + -
183B TYR* 3.7 33.0 - - + -
187B GLU* 2.8 38.8 + - + +
189B TRP* 1.3 120.6 - - + +
191B GLY* 1.3 57.7 + - - +
193B ALA* 3.4 2.3 + - - -
194B CYS* 2.9 23.6 + - - +
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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
----------------------------------------------------------
180B CYS 3.9 20.9 - - - -
183B TYR* 3.6 9.1 - - - +
187B GLU 3.4 3.8 + - - -
188B SER 3.0 7.6 + - - -
190B LYS* 1.3 77.1 - - - +
192B VAL* 1.3 64.5 + - - +
194B CYS* 3.7 4.8 - - - +
195B ARG* 3.1 42.3 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 3.0 17.5 + - - +
189B TRP* 3.9 10.1 - - - +
190B LYS 3.3 0.2 - - - -
191B GLY* 1.3 76.3 - - - +
193B ALA* 1.3 66.5 + - - +
195B ARG* 3.5 20.4 + - - +
196B LYS* 3.1 22.0 + - + +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 4.3 12.3 - - + -
189B TRP* 3.2 18.0 + - + +
190B LYS* 3.6 9.4 - - - +
192B VAL* 1.3 78.9 - - - +
194B CYS* 1.3 63.4 + - - +
196B LYS* 3.2 11.8 + - - +
197B ILE* 3.0 29.2 + - + +
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Residues in contact with CYS 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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138B PHE* 3.7 35.0 - - + -
140B PHE* 3.6 17.4 - - - -
179B GLU* 4.7 2.2 - - - -
180B CYS* 2.1 54.5 - - + -
183B TYR* 4.7 2.5 - - + -
190B LYS 2.9 18.2 + - - +
191B GLY* 3.7 4.3 - - - +
193B ALA* 1.3 76.3 - - - +
195B ARG* 1.4 49.9 + - - +
197B ILE* 3.2 4.2 + - - -
198B ALA* 2.7 32.4 + - - +
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Residues in contact with ARG 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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177B TYR* 3.6 40.8 + - + +
180B CYS* 3.8 25.8 + - + +
181B ALA* 4.6 5.9 - - - +
183B TYR 5.4 1.4 + - - -
188B SER 4.6 1.6 + - - -
191B GLY* 3.1 42.0 + - - +
192B VAL* 3.6 22.5 - - - +
193B ALA 3.4 0.2 - - - -
194B CYS* 1.4 75.3 - - - +
196B LYS* 1.3 60.0 + - - +
198B ALA* 3.6 8.7 - - - +
199B ASN* 3.0 36.7 + - - +
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Residues in contact with LYS 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 VAL* 3.1 15.8 + - + +
193B ALA* 3.2 13.9 + - - +
195B ARG* 1.3 77.0 - - - +
197B ILE* 1.3 64.5 + - + +
199B ASN* 3.5 8.3 + - - +
200B THR* 3.3 31.3 + - + +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PRO* 3.8 15.5 - - + +
136B ALA* 4.1 14.8 - - + -
138B PHE* 3.8 28.0 - - + -
140B PHE* 3.7 11.9 - - + -
193B ALA* 3.0 18.3 + - + +
194B CYS 3.6 5.4 - - - +
196B LYS* 1.3 76.7 - - + +
198B ALA* 1.4 64.5 - - - +
200B THR* 2.8 26.3 + - - +
201B TYR* 3.2 31.5 + - + -
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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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140B PHE* 3.6 13.6 - - + -
173B LYS* 5.1 1.2 - - + +
176B LEU* 3.9 29.4 - - + +
177B TYR* 4.1 14.8 - - + -
180B CYS* 4.4 2.9 - - - -
194B CYS 2.7 19.6 + - - +
195B ARG* 3.6 12.6 - - - +
197B ILE* 1.4 73.4 - - - +
199B ASN* 1.3 55.9 + - - +
201B TYR* 3.3 2.6 + - - +
202B TYR* 3.0 30.1 + - - +
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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
----------------------------------------------------------
173B LYS* 3.4 19.6 + - - +
177B TYR* 2.6 28.3 + - - -
195B ARG* 3.0 20.8 + - - +
196B LYS* 3.7 9.4 - - - +
197B ILE 3.3 0.2 - - - -
198B ALA* 1.3 76.6 - - - +
200B THR* 1.3 58.1 + - + +
202B TYR* 3.6 4.1 + - - +
203B ASP* 2.9 43.6 + - - +
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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
----------------------------------------------------------
196B LYS* 3.3 22.9 - - + +
197B ILE* 2.8 23.4 + - - +
199B ASN* 1.3 78.5 - - + +
201B TYR* 1.3 68.4 + - - +
203B ASP* 4.0 7.4 - - - +
204B ALA* 3.1 24.4 + - - +
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Residues in contact with TYR 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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128B CYS* 4.2 14.6 - - + -
130B LYS* 4.6 8.1 + - - +
131B SER* 3.6 24.2 - - - -
132B PRO* 2.6 46.9 + - - +
135B PRO* 3.5 12.8 - - + +
140B PHE* 3.8 17.9 - + - -
144B CYS* 4.8 0.2 - - - -
172B PHE* 4.4 14.8 - + + -
176B LEU* 4.1 12.8 - - + -
197B ILE* 3.2 38.3 + - + +
198B ALA 3.3 7.2 + - - +
200B THR* 1.3 86.4 + - - +
202B TYR* 1.3 63.5 + - - +
204B ALA* 3.4 6.1 + - - +
205B VAL* 3.1 27.2 + - - +
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Residues in contact with TYR 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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166B LYS* 4.9 5.0 + - - -
169B ASP* 3.5 28.9 - - + -
170B ASP* 2.9 24.9 + - - -
172B PHE* 4.5 7.7 - + + -
173B LYS* 3.5 50.3 - - + -
176B LEU* 5.3 0.4 - - + -
198B ALA 3.0 17.0 + - - +
199B ASN* 3.8 3.8 - - - +
201B TYR* 1.3 73.8 - - - +
203B ASP* 1.3 73.8 + - - +
205B VAL* 3.2 7.3 + - - +
206B ARG* 2.9 62.4 + - + +
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Residues in contact with ASP 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* 2.9 32.9 + - - +
200B THR* 4.0 7.7 - - - +
202B TYR* 1.3 92.5 - - - +
204B ALA* 1.3 56.0 - - - +
206B ARG* 3.5 6.3 + - - +
207B THR* 2.8 34.1 + - - +
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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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130B LYS* 4.0 24.2 - - + +
200B THR 3.1 18.9 + - - +
201B TYR* 3.6 5.2 - - - +
203B ASP* 1.3 75.2 - - - +
205B VAL* 1.3 52.9 + - - +
207B THR* 3.2 5.1 + - - -
208B PHE* 2.8 53.4 + - + +
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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
----------------------------------------------------------
130B LYS* 4.3 18.6 - - - +
147B HIS* 3.4 28.7 - - + +
151B TYR* 4.0 0.9 - - - +
165B ARG* 2.8 25.9 + - - -
169B ASP* 3.3 36.8 - - + +
172B PHE* 4.1 18.2 - - + -
201B TYR 3.1 15.7 + - - +
202B TYR* 3.7 5.6 - - + +
204B ALA* 1.3 76.0 - - - +
206B ARG* 1.3 53.3 + - - +
209B GLY* 2.8 21.4 + - - +
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Residues in contact with ARG 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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162B GLU* 4.8 6.5 + - - -
165B ARG* 2.8 47.8 + - - +
166B LYS* 3.4 47.8 - - - +
169B ASP* 2.7 44.8 + - - -
202B TYR* 2.9 54.2 + - + +
203B ASP* 3.7 8.7 - - - +
205B VAL* 1.3 77.7 - - - +
207B THR* 1.3 63.3 + - + +
210B TRP* 4.3 0.7 - - - -
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Residues in contact with THR 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 ASP 2.8 17.8 + - - +
204B ALA* 3.2 4.9 + - - -
206B ARG* 1.3 83.0 - - + +
208B PHE* 1.4 76.7 + - - +
210B TRP* 2.7 26.7 + - - -
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 5.6 10.1 - - + -
204B ALA* 2.8 40.2 + - + +
207B THR* 1.4 89.6 - - - +
209B GLY* 1.3 60.9 + - - +
210B TRP* 3.2 5.8 - - - +
211B LEU* 3.1 47.4 + - + +
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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
----------------------------------------------------------
151B TYR* 3.4 28.9 - - - -
155B LYS* 5.2 1.4 + - - -
160B PHE* 4.1 4.7 - - - -
165B ARG* 3.4 12.8 - - - +
204B ALA 4.1 0.2 + - - -
205B VAL* 2.8 31.7 + - - +
208B PHE* 1.3 71.1 - - - +
210B TRP* 1.3 58.8 + - - +
211B LEU* 3.2 6.1 + - - +
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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
------------------------------------------------------------
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