Contacts of the helix formed by residues 185 - 200 (chain B) in PDB entry 3A4T
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 TYR 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B ASP 3.3 8.7 + - - -
183B ILE 3.7 1.3 + - - -
184B LYS* 1.4 81.8 + - - +
186B CYS* 1.3 61.7 + - - +
187B SER* 3.1 15.5 - - - +
188B LEU* 2.7 74.0 - - + +
189B ARG* 3.6 13.7 + - - +
191B LYS* 3.9 12.6 + - - -
217B GLU* 2.7 30.6 + - + -
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Residues in contact with CYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO* 4.6 8.2 - - - +
166B CYS* 3.6 11.2 - - - -
167B SER* 3.6 21.8 - - - +
183B ILE 3.0 24.7 + - - +
184B LYS* 3.4 0.6 - - - +
185B TYR* 1.3 71.6 - - - +
187B SER* 1.3 56.8 + - - +
189B ARG* 3.3 13.4 + - - +
190B GLN* 3.0 37.5 + - - +
218B GLU* 3.5 23.1 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LYS* 3.9 8.1 - - - +
185B TYR* 2.9 27.4 - - - +
186B CYS* 1.3 78.9 - - - +
188B LEU* 1.3 54.9 + - - +
190B GLN* 3.1 15.2 + - - +
191B LYS* 2.9 37.3 + - - +
217B GLU* 2.9 43.1 + - - -
218B GLU* 4.2 0.4 - - - +
222B VAL* 4.1 1.0 - - - +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 2.7 64.9 - - + +
187B SER* 1.3 73.4 - - - +
189B ARG* 1.3 59.9 + - + +
191B LYS* 3.7 12.6 - - + +
192B GLU* 3.2 27.9 + - - +
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.7 3.0 - - - +
144B ARG* 3.3 35.6 - - - +
165B PRO* 4.2 12.5 - - + +
185B TYR 3.7 13.7 - - - +
186B CYS* 3.3 14.2 + - - +
188B LEU* 1.3 74.1 - - + +
190B GLN* 1.3 61.0 + - + +
192B GLU* 3.7 11.6 - - - +
193B LEU* 2.9 59.0 + - + +
501B SFG 3.0 43.3 + - - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 4.4 1.6 - - - +
164B ALA* 3.7 17.3 - - + -
165B PRO* 2.9 20.2 + - + +
186B CYS* 3.0 20.0 + - - +
187B SER* 3.1 20.2 - - - +
188B LEU 3.4 0.2 - - - -
189B ARG* 1.3 74.8 - - + +
191B LYS* 1.3 57.7 + - - +
193B LEU* 3.7 7.0 - - - +
194B ILE* 2.8 32.6 + - - +
209B TYR* 2.9 28.6 + - + +
211B THR* 4.0 4.4 + - - -
218B GLU* 2.8 49.8 + - - +
222B VAL* 3.5 8.6 - - + +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.9 19.0 + - + -
187B SER* 2.9 27.3 + - - +
188B LEU* 3.7 13.2 - - + +
189B ARG 3.2 0.2 - - - -
190B GLN* 1.3 74.3 - - - +
192B GLU* 1.3 65.5 + - - +
194B ILE* 3.2 11.6 - - - +
195B ASP* 3.1 19.1 + - - +
217B GLU* 4.2 0.6 + - - -
221B GLU* 2.9 52.3 + - - +
222B VAL* 4.5 8.5 - - - +
225B TYR* 3.7 51.6 - - + +
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Residues in contact with GLU 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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144B ARG* 3.4 44.8 + - - +
188B LEU 3.2 15.1 + - - +
189B ARG* 3.7 10.1 - - - +
191B LYS* 1.3 78.6 - - - +
193B LEU* 1.3 63.0 + - - +
195B ASP* 3.1 6.9 + - - +
196B ILE* 3.0 34.1 + - + +
225B TYR* 5.0 3.3 + - - -
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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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90B MET* 3.6 9.3 - - + +
91B CYS* 4.4 15.7 - - - -
143B MET* 4.1 31.6 - - + -
144B ARG* 4.5 13.2 - - + -
162B LEU* 3.5 24.5 - - + +
164B ALA* 5.2 0.2 - - + -
165B PRO* 4.6 8.5 - - + -
189B ARG* 2.9 51.2 + - + +
190B GLN* 3.7 6.7 - - - +
192B GLU* 1.3 76.4 - - - +
194B ILE* 1.3 57.5 + - - +
196B ILE* 3.1 8.6 + - + +
197B GLY 2.8 24.8 + - - -
501B SFG 4.2 11.7 - - + +
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Residues in contact with ILE 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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162B LEU* 3.2 19.4 - - + +
190B GLN 2.8 19.7 + - - +
191B LYS* 3.2 22.0 + - - +
193B LEU* 1.3 73.1 - - - +
195B ASP* 1.3 61.7 + - - +
197B GLY* 3.4 1.0 + - - +
198B ILE* 3.1 28.7 + - + +
207B LEU* 4.3 13.9 - - + -
209B TYR* 4.3 7.4 - - + -
222B VAL* 4.1 17.3 - - + +
223B ILE* 3.8 28.3 - - + -
225B TYR* 4.4 2.5 - - + -
226B ILE* 4.0 37.0 - - + -
271B LEU* 4.0 9.4 - - + -
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Residues in contact with ASP 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 LYS 3.1 15.6 + - - +
192B GLU* 4.0 4.5 - - - +
194B ILE* 1.3 77.8 - - - +
196B ILE* 1.3 63.8 + - - +
198B ILE 3.5 0.3 + - - -
199B ASP* 3.1 28.5 + - - +
225B TYR* 4.6 11.7 - - + +
226B ILE* 3.8 13.5 - - + +
229B LYS* 4.5 13.5 - - - +
230B ARG* 2.8 40.5 + - - +
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Residues in contact with ILE 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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90B MET* 3.8 12.8 - - + -
143B MET* 4.3 3.6 - - + -
144B ARG* 3.8 39.7 - - + +
147B LYS* 3.6 47.8 - - + +
192B GLU* 3.0 27.4 + - + +
193B LEU* 3.3 11.7 - - + +
195B ASP* 1.3 77.7 - - + +
197B GLY* 1.3 62.7 + - - +
199B ASP* 3.1 20.7 + - - +
200B LEU* 3.2 20.1 + - + +
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Residues in contact with GLY 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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90B MET* 3.7 17.7 - - - +
160B ILE* 3.3 20.6 - - - +
193B LEU 2.8 14.5 + - - -
194B ILE 3.4 1.5 + - - -
195B ASP 3.4 0.2 - - - -
196B ILE* 1.3 73.0 - - - +
198B ILE* 1.3 61.0 + - - +
200B LEU* 3.1 11.3 + - - -
201B LEU* 3.4 5.7 + - - +
207B LEU* 3.6 23.8 - - - +
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Residues in contact with ILE 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 ILE* 3.1 17.3 + - + +
195B ASP 3.8 1.8 - - - +
197B GLY* 1.3 69.7 - - - +
199B ASP* 1.3 57.0 + - - +
200B LEU 3.1 3.1 + - - -
201B LEU* 3.3 26.0 + - + +
207B LEU* 4.3 8.3 - - + -
226B ILE* 3.9 17.9 - - + -
230B ARG* 3.3 37.7 - - - +
232B ASP* 4.8 1.3 - - - +
233B VAL* 3.6 28.3 - - + -
271B LEU* 3.9 21.1 - - + -
273B LYS* 2.5 40.1 + - + +
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Residues in contact with ASP 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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147B LYS* 4.9 7.3 + - + +
151B LEU* 3.5 29.4 - - + +
156B PHE* 3.5 21.5 - - - -
195B ASP* 3.1 22.1 + - - +
196B ILE* 3.1 15.6 + - + +
198B ILE* 1.3 75.1 - - - +
200B LEU* 1.4 61.3 + - + +
201B LEU 3.4 0.8 + - - -
230B ARG* 2.9 27.4 + - - +
273B LYS* 4.1 6.6 + - - +
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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
----------------------------------------------------------
88B LEU* 3.7 23.1 - - + -
90B MET* 5.2 0.2 - - + -
143B MET* 3.9 11.4 - - + -
147B LYS* 4.0 4.7 - - + +
150B LEU* 3.6 31.6 - - + -
151B LEU* 3.8 25.4 - - + -
155B ILE 4.0 10.1 - - - +
156B PHE* 3.4 8.5 - - + -
157B PHE* 2.9 30.9 + - + -
160B ILE* 3.7 10.0 - - + +
196B ILE* 3.5 31.9 - - + +
197B GLY* 3.1 11.0 + - - +
198B ILE 3.1 1.2 - - - -
199B ASP* 1.4 77.4 - - + +
201B LEU* 1.3 60.5 + - - +
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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