Contacts of the helix formed by residues 187 - 209 (chain B) in PDB entry 2XTM
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
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Residue Dist Surf HB Arom Phob DC
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185B ARG 3.7 4.7 + - - +
186B ALA* 1.3 75.8 - - - +
188B GLY* 1.3 67.0 + - - +
189B SER 3.2 3.5 + - - -
190B ASN* 3.3 15.1 + - - +
191B GLN* 3.4 10.7 + - - +
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Residues in contact with GLY 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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187B GLU* 1.3 72.4 - - - +
189B SER* 1.3 57.6 + - - -
191B GLN* 3.6 10.1 + - - +
192B ASP* 3.1 35.9 + - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU 3.2 1.8 + - - -
188B GLY* 1.3 68.5 - - - -
190B ASN* 1.3 61.6 + - - +
192B ASP* 3.1 9.9 + - - +
193B ASP* 3.0 40.0 + - - +
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Residues in contact with ASN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS* 5.7 1.0 + - - -
186B ALA* 4.3 14.5 - - + +
187B GLU 3.3 9.6 + - - +
189B SER* 1.3 76.1 - - - +
191B GLN* 1.3 64.6 + - - +
193B ASP* 3.6 10.5 + - - +
194B GLN* 3.3 24.9 + - - +
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Residues in contact with GLN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN 4.3 3.2 + - - -
41B SER* 3.6 36.8 + - - +
44B ARG* 3.4 28.5 - - + +
184B ASN 5.4 1.2 + - - -
186B ALA* 3.7 23.5 + - - +
187B GLU* 3.4 14.6 + - - -
188B GLY 3.6 17.6 + - - +
189B SER 3.2 0.4 - - - -
190B ASN* 1.3 76.4 - - - +
192B ASP* 1.3 65.6 + - - +
193B ASP 3.3 0.2 + - - -
194B GLN* 3.3 14.8 - - - +
195B VAL* 3.1 30.0 + - + +
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Residues in contact with ASP 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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44B ARG* 2.7 37.2 + - - +
68B TRP* 3.6 13.6 - - + -
188B GLY 3.1 18.9 + - - +
189B SER* 3.1 10.8 + - - +
191B GLN* 1.3 78.4 - - - +
193B ASP* 1.3 60.0 + - - +
195B VAL* 3.6 1.7 + - - -
196B LYS* 3.0 30.2 + - - +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS* 6.2 1.1 - - - +
189B SER* 3.0 27.5 + - - +
190B ASN* 3.7 11.4 - - - +
191B GLN 3.2 0.2 - - - -
192B ASP* 1.3 78.6 - - - +
194B GLN* 1.3 57.5 + - - +
196B LYS* 3.3 12.0 + - - +
197B GLU* 3.0 27.1 + - - +
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Residues in contact with GLN 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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41B SER* 4.1 13.5 - - - -
148B LYS* 4.4 15.6 + - - +
180B CYS* 4.4 1.2 - - - -
181B ALA 4.2 7.1 - - - +
182B PHE* 3.4 38.2 - - + -
183B ASN* 2.8 50.7 + - - +
186B ALA* 4.0 10.6 + - - +
190B ASN 3.3 12.1 + - - +
191B GLN* 3.3 16.9 - - - +
193B ASP* 1.3 75.5 - - - +
195B VAL* 1.3 70.3 + - + +
197B GLU* 3.2 11.7 + - - +
198B LEU 3.0 17.8 + - - -
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Residues in contact with VAL 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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41B SER* 3.3 30.7 - - - +
42B ILE* 4.0 19.1 - - + +
44B ARG* 4.2 6.5 - - - -
68B TRP* 3.7 29.4 - - + -
182B PHE* 4.2 12.8 - - + -
191B GLN* 3.1 19.3 + - + +
192B ASP 3.9 3.4 - - - +
194B GLN* 1.3 75.6 - - + +
196B LYS* 1.3 61.2 + - - +
198B LEU* 3.1 3.3 + - - +
199B MET* 2.8 42.6 + - + +
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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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68B TRP* 3.6 23.3 - - + +
192B ASP 3.0 19.4 + - - +
193B ASP* 3.4 11.0 - - - +
195B VAL* 1.3 75.9 - - - +
197B GLU* 1.3 58.4 + - - +
199B MET* 3.3 1.9 + - - +
200B ASP* 2.9 49.9 + - - +
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Residues in contact with GLU 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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148B LYS* 4.8 11.6 + - - -
156B LEU* 5.8 1.0 - - - +
179B ILE 4.8 2.1 - - - +
180B CYS* 3.6 26.5 - - - -
181B ALA* 4.3 6.7 + - - +
193B ASP 3.0 12.8 + - - +
194B GLN* 3.4 12.8 - - - +
195B VAL 3.2 0.2 - - - -
196B LYS* 1.3 78.0 - - - +
198B LEU* 1.3 61.6 + - - +
200B ASP* 3.4 8.2 + - - +
201B CYS* 3.1 27.4 + - - -
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Residues in contact with LEU 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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25B ILE* 5.7 0.2 - - + -
42B ILE* 3.7 33.0 - - + -
110B LEU* 4.0 30.3 - - + -
142B ILE* 4.3 10.8 - - + -
144B LEU* 4.4 1.8 - - + -
180B CYS* 3.8 23.2 - - + -
182B PHE* 3.8 20.4 - - + -
194B GLN 3.0 13.7 + - - +
195B VAL 3.1 6.0 + - - +
197B GLU* 1.3 76.3 - - - +
199B MET* 1.3 62.6 + - + +
201B CYS* 3.0 7.0 + - + +
202B ILE* 2.9 45.2 + - + +
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Residues in contact with MET 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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23B LEU* 5.4 4.5 - - - -
25B ILE* 4.3 7.4 - - + -
42B ILE* 3.7 29.6 - - + -
68B TRP* 3.5 41.5 - - + +
71B ARG* 6.5 0.2 - - - -
73B ILE* 4.0 25.4 - - + -
195B VAL* 2.8 25.7 + - + +
196B LYS 3.8 3.1 - - - +
198B LEU* 1.3 79.9 - - + +
200B ASP* 1.3 59.8 + - - +
202B ILE* 3.3 31.2 + - + +
203B GLU* 2.9 41.6 + - + +
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Residues in contact with ASP 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 LYS* 2.9 35.3 + - - +
197B GLU* 3.6 8.4 - - - +
198B LEU 3.2 0.2 - - - -
199B MET* 1.3 78.7 - - - +
201B CYS* 1.3 56.7 + - - +
203B GLU* 3.3 8.5 + - - +
204B ASP* 3.0 40.0 + - - +
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Residues in contact with CYS 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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142B ILE* 4.1 18.7 - - + -
178B ARG* 5.1 6.6 - - + -
179B ILE 3.9 24.2 - - - -
180B CYS* 4.5 8.7 - - - -
197B GLU* 3.1 24.4 + - - -
198B LEU* 3.0 13.3 + - + +
200B ASP* 1.3 75.0 - - - +
202B ILE* 1.3 62.2 - - - +
204B ASP* 3.3 10.4 - - - +
205B LEU* 3.1 22.5 - - - -
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Residues in contact with ILE 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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23B LEU* 3.8 27.4 - - + -
25B ILE* 4.0 18.8 - - + -
108B VAL* 3.5 28.9 - - + -
110B LEU* 6.1 0.4 - - + -
142B ILE* 3.7 21.8 - - + -
198B LEU* 2.9 26.6 + - + +
199B MET* 3.3 37.4 + - + +
201B CYS* 1.3 77.2 + - - +
203B GLU* 1.3 58.7 + - + +
205B LEU* 3.2 5.1 + - - +
206B LEU* 2.9 32.2 + - + +
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Residues in contact with GLU 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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23B LEU* 4.3 9.1 - - - +
71B ARG* 3.6 36.3 + - - +
199B MET* 2.9 34.6 + - + +
200B ASP* 3.3 10.5 + - - +
202B ILE* 1.3 75.9 - - + +
204B ASP* 1.3 59.1 + - - +
206B LEU* 3.4 5.9 + - - +
207B MET* 2.9 29.6 + - - +
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Residues in contact with ASP 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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100A LEU* 5.9 0.4 - - + +
200B ASP* 3.0 24.0 + - - +
201B CYS* 3.6 11.3 - - - +
202B ILE 3.2 0.2 - - - -
203B GLU* 1.3 77.0 - - - +
205B LEU* 1.3 64.8 + - - +
207B MET* 3.3 9.2 + - - +
208B GLU* 3.0 30.6 + - - +
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Residues in contact with LEU 205 (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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107B HIS 4.2 5.4 - - - +
108B VAL* 4.2 20.0 - - + -
139B GLY 3.7 20.9 - - - +
140B HIS* 3.8 31.0 - - - +
142B ILE* 4.3 9.0 - - + -
178B ARG* 3.8 35.9 - - - +
201B CYS 3.1 13.8 - - - -
202B ILE* 3.2 7.8 + - - +
204B ASP* 1.3 75.5 - - - +
206B LEU* 1.3 65.7 + - + +
208B GLU* 3.1 13.3 + - - +
209B LYS* 3.0 40.1 + - + +
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Residues in contact with LEU 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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23B LEU* 3.8 28.0 - - + -
71B ARG* 4.1 16.8 - - - +
107B HIS* 4.0 41.1 - - + +
108B VAL* 5.1 0.7 - - + -
140B HIS* 4.8 3.4 - - + -
202B ILE* 2.9 27.6 + - + +
203B GLU* 3.9 6.5 - - - +
205B LEU* 1.3 79.3 - - + +
207B MET* 1.3 62.0 + - - +
209B LYS* 3.2 2.3 + - + +
210B ASN 3.0 4.3 + - - -
211B GLY* 2.8 37.2 + - - +
212B ASP 3.4 25.8 - - - +
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Residues in contact with MET 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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93A LYS* 3.4 43.7 - - + +
96A GLN* 4.2 5.4 - - + -
97A ARG* 3.1 46.0 + - + +
100A LEU* 4.1 22.7 - - + -
203B GLU 2.9 17.1 + - - +
204B ASP* 3.6 8.5 - - - +
205B LEU 3.2 0.2 - - - -
206B LEU* 1.3 76.8 - - - +
208B GLU* 1.3 67.1 + - - +
210B ASN* 3.1 11.1 + - - +
211B GLY 4.9 0.9 - - - +
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Residues in contact with GLU 208 (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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97A ARG* 3.0 21.8 + - - +
100A LEU* 3.6 45.0 - - + +
101A LEU* 3.6 16.9 - - + +
1232A GOL 2.8 22.0 + - - +
178B ARG* 4.7 13.2 + - - -
204B ASP* 3.0 22.8 + - - +
205B LEU* 3.1 12.5 + - + +
207B MET* 1.3 83.3 - - - +
209B LYS* 1.3 56.9 + - + +
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Residues in contact with LYS 209 (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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1232A GOL 3.5 31.8 + - - +
139B GLY* 3.2 33.0 + - - -
140B HIS* 3.7 28.4 - - + +
178B ARG* 5.9 0.4 - - - +
205B LEU* 3.0 26.6 + - + +
206B LEU* 3.2 5.8 + - - +
208B GLU* 1.3 77.8 - - + +
210B ASN* 1.3 71.2 + - - +
211B GLY 3.1 1.3 - - - -
212B ASP* 2.9 36.0 + - + +
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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