Contacts of the helix formed by residues 186 - 205 (chain A) in PDB entry 3P1Q
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 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A HIS* 2.8 29.9 + - - +
184A ALA* 3.1 19.2 + - - +
185A ASN* 1.3 72.6 + - - +
187A PRO* 1.4 66.5 - - - +
188A GLU* 3.2 3.4 - - - +
189A GLU* 3.1 18.8 + - - +
190A ALA 3.0 17.3 + - - -
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A HIS 4.1 0.2 - - - -
181A TYR* 3.7 40.6 - - + +
185A ASN* 3.4 14.6 - - - +
186A SER* 1.4 89.8 - - - +
188A GLU* 1.3 67.8 + - + +
190A ALA* 3.2 2.2 + - + +
191A ILE* 2.9 35.2 + - + +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER 3.2 0.8 - - - -
187A PRO* 1.3 83.3 - - + +
189A GLU* 1.3 57.8 + - - +
191A ILE* 3.4 8.7 + - + +
192A SER* 2.9 34.7 + - - +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A HIS* 3.4 34.4 + - + +
186A SER* 3.1 22.3 + - - +
188A GLU* 1.3 75.3 - - - +
190A ALA* 1.3 67.7 + - - +
192A SER* 3.8 8.2 - - - -
193A LEU* 2.9 32.1 + - + +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 2.7 50.2 + - - +
180A HIS* 3.6 5.1 - - - +
181A TYR* 3.4 29.4 - - + +
186A SER 3.0 6.6 + - - +
187A PRO 3.4 7.9 - - - +
189A GLU* 1.3 78.0 - - - +
191A ILE* 1.3 57.9 + - - +
194A ALA* 3.0 19.2 + - - +
230A TRP* 3.8 6.5 - - + -
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TYR* 5.0 1.1 - - + -
187A PRO* 2.9 30.8 + - + +
188A GLU* 3.8 8.5 - - + +
190A ALA* 1.3 75.4 - - - +
192A SER* 1.3 66.7 + - - +
194A ALA 3.3 0.9 + - - -
195A LYS* 3.0 46.7 + - + +
227A LEU* 3.7 21.1 - - + +
230A TRP* 3.9 35.2 - - + +
231A THR* 3.9 20.4 - - + -
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 2.9 20.2 + - - +
189A GLU* 3.8 11.9 - - - -
191A ILE* 1.3 78.4 - - - +
193A LEU* 1.3 63.1 + - - +
195A LYS* 3.7 7.7 - - - +
196A THR* 3.0 30.6 + - - -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A MET* 4.1 21.5 - - + -
169A ARG* 5.3 1.1 - - - +
173A ALA* 3.7 14.4 - - + +
176A PHE* 3.8 25.4 - - + -
177A SER* 3.7 27.1 - - - +
180A HIS* 4.1 9.2 - - + +
189A GLU* 2.9 24.1 + - - +
190A ALA 3.8 3.4 - - - +
192A SER* 1.3 77.2 - - - +
194A ALA* 1.3 60.1 + - - +
196A THR* 4.8 5.6 - - + -
197A THR* 2.7 47.1 + - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 6.3 0.2 - - + -
177A SER* 3.8 11.4 + - - +
190A ALA 3.0 18.4 + - - +
191A ILE* 3.9 3.8 - - - +
193A LEU* 1.3 78.9 - - - +
195A LYS* 1.3 55.7 + - - +
197A THR* 3.7 1.7 - - - -
198A PHE* 2.9 31.2 + - - +
223A LEU* 4.0 29.9 - - + +
226A ASN* 5.4 1.3 - - + -
227A LEU* 4.0 23.0 - - + +
230A TRP* 4.7 5.4 - - + -
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.0 39.3 + - + +
192A SER* 3.7 7.9 - - - +
194A ALA* 1.3 74.2 - - - +
196A THR* 1.3 62.0 + - - +
198A PHE* 3.2 2.2 + - - +
199A ASP* 2.8 45.2 + - - +
227A LEU* 3.7 24.0 - - + +
231A THR* 4.8 8.4 - - - +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A SER* 3.0 16.5 + - - -
193A LEU* 4.2 6.5 - - + -
195A LYS* 1.3 80.9 - - - +
197A THR* 1.3 66.1 + - - +
199A ASP* 3.9 4.9 - - - +
200A GLU* 2.8 64.6 + - - +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO 4.8 2.2 - - - +
169A ARG* 4.9 11.7 + - + +
170A LEU* 3.6 25.6 - - + -
173A ALA* 3.4 34.2 - - + +
193A LEU* 2.7 31.2 + - - +
194A ALA* 3.7 4.7 - - - -
196A THR* 1.3 80.1 - - - +
198A PHE* 1.3 62.4 + - - +
200A GLU* 4.0 5.2 - - - +
201A ALA* 3.0 23.4 + - - +
223A LEU* 3.7 11.7 - - + -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA 2.9 18.4 + - - +
195A LYS* 3.6 5.4 - - - +
197A THR* 1.3 76.2 - - - +
199A ASP* 1.3 70.6 + - - +
201A ALA* 3.3 5.1 + - - +
202A MET* 2.8 55.9 + - + +
220A MET* 3.4 44.2 - - + +
221A GLN* 5.4 0.2 - - - -
223A LEU* 4.2 14.6 - - + +
224A ARG* 3.3 45.5 - - + -
227A LEU* 4.7 3.4 - - + -
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Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 2.8 29.1 + - - +
196A THR* 3.9 5.5 - - - +
198A PHE* 1.3 93.4 - - - +
200A GLU* 1.3 63.6 + - + +
202A MET* 3.3 8.0 + - - +
203A ALA* 3.2 22.3 + - - +
224A ARG* 4.7 4.0 + - - -
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.7 26.0 - - + +
169A ARG* 5.6 3.8 + - - -
196A THR* 2.8 46.3 + - - +
197A THR* 4.1 3.9 - - - +
199A ASP* 1.3 75.7 - - + +
201A ALA* 1.3 66.5 + - - +
203A ALA* 3.5 8.4 + - - +
204A ASP* 3.5 14.2 + - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.6 19.8 - - - +
165A THR* 3.2 20.2 - - + +
170A LEU* 3.8 12.1 - - + -
197A THR 3.0 17.7 + - - +
198A PHE 3.6 3.8 - - - +
200A GLU* 1.3 76.4 - - - +
202A MET* 1.4 64.5 + - - +
204A ASP 2.9 11.6 + - - -
205A LEU* 3.1 10.9 + - - +
220A MET* 3.7 23.6 - - + -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 2.8 46.2 + - + +
199A ASP* 3.3 10.7 + - - +
201A ALA* 1.4 76.4 - - - +
203A ALA* 1.3 60.0 + - - +
204A ASP 3.3 0.9 + - - -
205A LEU* 3.4 30.6 + - + +
206A HIS 4.8 0.7 + - - -
213A TYR* 6.1 0.4 - - - +
217A THR* 6.2 0.2 - - - -
220A MET* 3.4 19.0 - - + +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASP 3.2 12.2 + - - +
200A GLU* 3.8 8.5 - - - +
201A ALA 3.2 1.0 - - - -
202A MET* 1.3 78.6 - - - +
204A ASP* 1.3 55.5 + - - +
205A LEU 3.5 0.2 - - - -
206A HIS* 3.1 24.0 + - - -
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.7 7.7 - - - +
164A PRO* 3.6 27.3 - - + +
165A THR* 2.6 31.5 + - + +
200A GLU 3.5 10.8 + - - +
201A ALA 2.9 9.1 + - - +
203A ALA* 1.3 74.5 - - - +
205A LEU* 1.3 63.8 + - - +
206A HIS* 3.1 6.7 + - - -
207A THR* 2.8 49.4 + - - +
208A LEU* 4.0 2.3 - - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR* 3.9 9.9 - - + -
201A ALA 3.1 13.1 + - - +
202A MET* 3.4 41.3 + - + +
204A ASP* 1.3 79.1 - - - +
206A HIS* 1.3 62.5 + - - +
207A THR 3.0 0.2 - - - -
208A LEU* 3.0 39.4 + - + +
213A TYR* 3.6 48.1 - - + +
216A SER* 4.1 5.2 - - - -
217A THR* 4.0 17.7 - - + -
220A MET* 4.0 14.4 - - + -
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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
------------------------------------------------------------
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