Contacts of the helix formed by residues 186 - 200 (chain U) in PDB entry 5A0Q
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 186 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41U CYS* 3.2 13.2 - - - -
43U ASP* 3.3 37.6 + - - +
44U GLY* 4.7 7.9 - - - -
46U VAL* 3.5 24.2 - - - -
185U THR* 1.3 73.0 - - - +
187U ARG* 1.3 56.7 + - - +
189U ILE* 3.1 4.8 + - - +
190U VAL* 3.0 28.8 + - - +
215U TRP* 4.3 15.3 - - - -
217U GLY* 4.8 9.6 - - - -
219U LEU* 6.4 2.0 - - + -
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Residues in contact with ARG 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185U THR* 3.1 12.3 - - - +
186U CYS* 1.3 76.4 - - - +
188U ASP* 1.3 62.0 + - - +
190U VAL* 3.2 11.9 - - - +
191U LYS* 3.5 26.1 - - - +
215U TRP* 4.2 18.2 - - - -
219U LEU* 5.9 10.1 - - + -
231U ILE* 4.2 24.4 - - - +
234U GLU* 5.1 3.2 + - - -
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Residues in contact with ASP 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184U MET* 4.0 27.0 - - + +
185U THR* 3.1 30.8 + - - +
186U CYS 3.3 0.4 - - - -
187U ARG* 1.3 76.7 - - - +
189U ILE* 1.3 58.2 + - - +
191U LYS* 3.1 19.4 + - - +
192U GLU* 2.8 36.9 + - - +
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Residues in contact with ILE 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39U ILE* 3.9 24.5 - - + +
41U CYS* 4.1 11.9 - - + -
46U VAL* 3.8 16.2 - - + -
179U LEU* 3.5 30.7 - - + -
181U MET* 4.9 1.8 - - + -
184U MET* 3.7 25.1 - - + -
185U THR 3.4 14.6 - - - +
186U CYS* 3.1 11.6 + - - +
188U ASP* 1.3 71.8 - - - +
190U VAL* 1.3 63.5 + - - +
191U LYS 3.1 2.0 - - - -
192U GLU* 3.8 8.7 - - + +
193U VAL* 2.9 43.1 + - + +
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Residues in contact with VAL 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U VAL* 4.0 5.4 - - - -
186U CYS 3.0 9.0 + - - +
187U ARG* 3.2 26.0 - - - +
189U ILE* 1.3 75.1 - - - +
191U LYS* 1.3 59.8 + - - +
213U LEU* 3.3 27.0 - - + +
215U TRP* 2.3 72.0 - - + +
227U VAL* 3.6 26.5 - - + -
231U ILE* 4.0 13.2 - - + -
235U ALA* 4.9 0.7 - - + -
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Residues in contact with LYS 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187U ARG* 3.5 34.1 - - - +
188U ASP* 3.1 16.0 + - - +
190U VAL* 1.3 81.2 - - + +
192U GLU* 1.4 69.7 + - - +
194U ALA* 3.3 7.6 + - - +
195U LYS* 3.0 34.4 + - + +
231U ILE* 4.9 0.7 - - + -
234U GLU* 3.4 37.7 - - - +
235U ALA* 4.2 10.2 - - + +
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Residues in contact with GLU 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179U LEU* 4.1 17.6 - - + +
184U MET* 4.0 15.2 - - + +
188U ASP* 2.8 38.6 + - - +
189U ILE* 3.0 27.1 + - + +
191U LYS* 1.4 88.5 - - - +
193U VAL* 1.3 58.6 + - - +
195U LYS* 3.2 33.3 + - - +
196U ILE* 2.9 33.8 + - + +
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Residues in contact with VAL 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U ILE* 3.5 27.5 - - + +
39U ILE* 3.4 26.2 - - + -
46U VAL* 3.6 23.3 - - + +
48U GLY* 3.5 22.0 - - - -
189U ILE* 2.9 19.3 + - + +
192U GLU* 1.3 73.2 - - - +
194U ALA* 1.4 57.7 + - - +
196U ILE* 3.3 10.4 + - - +
197U ILE* 3.0 30.0 + - + +
213U LEU* 3.6 13.9 - - + -
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Residues in contact with ALA 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191U LYS 3.3 9.3 + - - +
193U VAL* 1.4 78.3 - - - +
195U LYS* 1.3 59.0 + - - +
197U ILE* 3.4 4.9 - - - +
198U TYR* 2.9 27.7 + - - +
209U PHE* 4.5 3.3 - - + -
211U LEU* 3.6 42.4 - - + -
213U LEU* 3.8 6.7 - - + +
235U ALA* 3.8 23.3 - - + +
236U GLU* 5.2 0.4 - - - -
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Residues in contact with LYS 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175U GLU* 3.9 10.3 - - - +
191U LYS* 3.0 22.7 + - + +
192U GLU* 3.2 38.7 + - - +
194U ALA* 1.3 76.6 - - - +
196U ILE* 1.4 55.4 + - - +
198U TYR* 3.1 8.8 + - + +
199U ILE* 3.1 32.5 + - + +
235U ALA 5.1 6.7 - - - +
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Residues in contact with ILE 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U ILE* 3.6 35.7 - - + -
39U ILE* 3.7 20.9 - - + -
172U ALA* 3.9 27.4 - - + +
175U GLU* 3.1 36.1 - - + +
176U ILE* 4.5 4.9 - - + -
179U LEU* 3.8 18.6 - - + -
192U GLU 2.9 20.7 + - - +
193U VAL* 3.6 5.2 - - - +
195U LYS* 1.4 70.0 - - - +
197U ILE* 1.4 60.0 + - - +
199U ILE* 3.3 1.6 + - - +
200U VAL* 3.0 30.1 + - + +
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Residues in contact with ILE 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U THR* 4.6 7.2 - - - +
37U ILE* 3.7 24.5 - - + -
48U GLY* 4.5 0.2 - - - -
49U VAL 4.1 7.6 - - - +
50U GLU* 3.4 48.0 - - + +
193U VAL* 3.0 28.2 + - + +
194U ALA 3.4 6.3 - - - +
196U ILE* 1.4 75.9 - - - +
198U TYR* 1.4 57.4 + - - +
200U VAL* 3.6 7.3 - - + +
201U HIS* 3.0 30.8 + - - +
209U PHE* 3.6 22.9 - - + -
211U LEU* 3.9 16.4 - - + -
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Residues in contact with TYR 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194U ALA 2.9 14.2 + - - +
195U LYS* 3.1 12.5 + - + +
197U ILE* 1.4 76.3 - - - +
199U ILE* 1.4 69.9 + - + +
201U HIS* 3.0 29.4 - - - +
209U PHE* 3.3 40.6 - + + -
236U GLU 5.9 2.0 - - - -
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Residues in contact with ILE 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175U GLU* 3.3 30.7 - - + +
195U LYS* 3.1 14.1 + - + +
196U ILE 3.3 1.3 + - - +
198U TYR* 1.4 89.5 - - + +
200U VAL* 1.4 66.4 + - + +
201U HIS 3.4 4.9 + - - +
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Residues in contact with VAL 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U THR* 3.7 23.6 - - - +
50U GLU* 5.2 2.2 - - - +
168U ALA* 3.9 18.8 - - + +
171U ALA* 3.3 30.7 - - + +
172U ALA* 3.7 18.2 - - + -
175U GLU* 5.4 2.2 - - + +
196U ILE* 3.0 22.2 + - + +
197U ILE* 3.6 10.5 - - - +
199U ILE* 1.4 76.1 - - + +
201U HIS* 1.3 65.3 + - - +
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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