Contacts of the helix formed by residues 183 - 199 (chain B) in PDB entry 1XPU
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 GLY 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA* 1.3 80.0 - - - +
184B LYS* 1.3 57.1 + - - +
185B THR 3.3 2.2 - - - -
186B MET 2.9 3.3 + - - -
187B LEU* 2.5 36.8 + - - +
345B LEU* 4.0 6.1 - - - -
2600B AGS 2.9 40.0 + - - -
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Residues in contact with LYS 184 (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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176B ILE* 4.8 2.0 - - + -
178B ALA* 3.9 25.4 - - + -
179B PRO 5.2 1.1 - - - +
180B PRO* 6.3 0.2 - - - +
183B GLY* 1.3 75.4 - - - +
185B THR* 1.3 63.2 + - - +
187B LEU* 3.5 3.9 + - - +
188B LEU* 3.0 28.0 + - + +
265B ASP* 3.1 30.1 - - - +
318B THR* 3.7 30.7 - - + +
320B LEU* 3.7 18.6 - - - +
345B LEU* 3.6 11.9 - - - +
2600B AGS 3.2 22.4 + - - +
2601B MG 2.9 13.6 - - - -
2701B FPD 2.7 33.1 + - - -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLY 3.3 0.2 - - - -
184B LYS* 1.3 75.9 + - - +
186B MET* 1.3 57.5 + - + +
188B LEU* 3.6 6.4 + - - +
189B GLN* 2.8 36.0 + - - +
211B GLU* 4.4 3.1 - - - +
215B GLU* 3.5 28.9 + - + +
219B MET* 3.8 21.4 - - + +
265B ASP* 4.3 3.2 + - - +
2600B AGS 2.7 32.2 + - - +
2601B MG 2.2 33.2 - - - -
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Residues in contact with MET 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LYS* 5.7 6.5 - - - +
183B GLY 2.9 1.6 + - - +
185B THR* 1.3 79.2 - - - +
187B LEU* 1.3 54.7 + - - +
189B GLN* 3.4 21.1 - - - +
190B ASN* 2.7 36.3 + - - +
218B GLU* 6.1 0.4 - - - +
2600B AGS 3.0 96.2 + - + +
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Residues in contact with LEU 187 (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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158B THR* 3.7 25.1 - - + -
162B LEU* 4.2 11.9 - - + -
176B ILE* 3.6 27.8 - - + -
183B GLY* 2.5 21.7 + - - +
184B LYS 3.8 2.9 - - - +
186B MET* 1.3 72.2 - - - +
188B LEU* 1.3 57.6 + - - +
190B ASN* 3.3 6.3 + - - +
191B ILE* 3.0 38.5 + - + +
343B LEU* 3.5 33.0 - - + -
345B LEU* 3.8 20.6 - - + -
356B PRO* 5.6 2.7 - - + -
358B ILE* 4.6 9.4 - - + -
2600B AGS 4.6 3.9 + - - +
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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
----------------------------------------------------------
176B ILE* 3.9 22.4 - - + -
184B LYS* 3.0 19.5 + - + +
185B THR* 3.7 4.9 - - - +
187B LEU* 1.3 73.0 - - - +
189B GLN* 1.3 65.4 + - - +
190B ASN 3.1 1.6 - - - -
191B ILE* 3.4 4.3 + - + +
192B ALA* 3.1 24.3 + - - +
206B VAL* 6.0 3.4 - - + -
208B LEU* 5.6 2.0 - - + -
219B MET* 5.1 10.1 - - + -
263B LEU* 3.9 39.9 - - + +
264B LEU 4.1 10.3 - - - +
265B ASP* 4.2 23.3 - - + +
316B ILE 4.2 8.1 - - - +
318B THR* 3.6 25.8 - - + -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 2.8 33.7 + - - +
186B MET* 3.4 24.2 - - + +
188B LEU* 1.3 76.6 - - - +
190B ASN* 1.3 61.2 + - - +
192B ALA* 3.6 16.2 - - - +
193B GLN* 3.7 9.0 + - - +
215B GLU 5.5 0.2 + - - -
218B GLU* 3.1 37.4 + - - +
219B MET* 3.6 28.5 - - - +
222B LEU* 3.4 33.3 - - + +
223B VAL* 5.2 1.0 - - - +
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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
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155B GLU* 3.3 39.5 + - - +
158B THR* 3.4 31.8 + - + +
159B ALA* 4.0 14.9 - - - +
186B MET* 2.7 21.0 + - - +
187B LEU 3.4 6.7 - - - +
188B LEU 3.1 0.2 - - - -
189B GLN* 1.3 72.1 - - - +
191B ILE* 1.3 66.7 + - - +
193B GLN* 3.0 21.9 + - - +
194B SER* 3.4 6.2 + - - -
2600B AGS 4.2 9.1 + - - +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 4.0 15.5 - - + -
158B THR* 5.9 0.9 - - + -
159B ALA* 6.4 0.4 - - - -
162B LEU* 3.8 35.0 - - + -
168B ILE* 6.1 7.4 - - + -
176B ILE* 4.3 23.3 - - + -
187B LEU* 3.0 22.8 + - + +
188B LEU* 3.4 9.2 + - + +
190B ASN* 1.3 69.9 - - + +
192B ALA* 1.3 58.1 + - - +
193B GLN 2.9 10.8 + - - -
194B SER* 3.0 19.0 + - - +
195B ILE* 3.0 24.6 + - + +
263B LEU* 4.2 18.8 - - + -
316B ILE* 5.0 9.9 - - + -
343B LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU 3.1 17.6 + - - +
189B GLN 3.6 8.5 - - - +
190B ASN 3.2 0.2 - - - -
191B ILE* 1.3 75.6 - - - +
193B GLN* 1.3 62.6 + - - +
195B ILE* 4.0 1.8 - - - -
196B ALA* 3.5 22.9 + - - +
204B LEU* 3.8 11.0 - - + +
206B VAL* 4.8 0.2 - - + -
223B VAL* 3.6 35.2 - - + -
224B LYS 4.9 2.6 + - - -
263B LEU* 4.0 17.2 - - + +
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 5.1 17.4 - - - +
189B GLN 3.7 7.7 + - - +
190B ASN* 3.0 12.7 + - - +
191B ILE 3.0 1.0 - - - -
192B ALA* 1.3 83.0 + - - +
194B SER* 1.3 61.3 + - - +
195B ILE 3.0 5.7 + - - -
196B ALA* 3.4 5.0 + - - +
197B TYR* 3.2 31.9 + - + +
222B LEU* 3.6 27.1 + - - +
223B VAL* 5.2 0.2 - - - +
224B LYS* 4.2 22.7 - - - +
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Residues in contact with SER 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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147B MET* 3.4 46.7 - - - +
159B ALA* 3.7 14.7 - - - +
190B ASN* 3.4 8.4 + - - -
191B ILE* 3.0 9.2 + - - -
193B GLN* 1.3 76.7 - - - +
195B ILE* 1.3 58.3 + - - +
197B TYR* 4.8 2.7 - - - -
198B ASN* 3.3 33.1 - - - +
199B HIS* 3.6 6.1 + - - -
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Residues in contact with ILE 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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145B LEU* 4.7 6.7 - - + -
147B MET* 3.7 22.7 - - + -
168B ILE* 6.1 1.6 - - + -
191B ILE* 3.0 26.8 + - + +
192B ALA 4.1 4.7 - - - +
193B GLN 3.0 1.0 - - - -
194B SER* 1.3 75.6 - - - +
196B ALA* 1.3 59.4 + - - +
197B TYR 3.0 5.1 + - - -
199B HIS* 2.9 57.1 + - + +
202B CYS* 5.0 3.8 - - + +
204B LEU* 3.8 41.1 - - + -
261B ILE* 4.4 31.2 - - + -
263B LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 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 ALA 3.5 15.7 + - - +
193B GLN* 3.4 8.1 + - - +
195B ILE* 1.3 80.0 - - - +
197B TYR* 1.3 58.0 + - - +
199B HIS 4.9 1.3 - - - -
200B PRO* 4.0 17.5 - - - +
204B LEU* 4.8 2.7 - - + -
224B LYS* 3.5 47.8 + - + +
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Residues in contact with TYR 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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193B GLN* 3.2 20.5 + - + +
194B SER* 4.7 1.6 - - - +
195B ILE 3.0 2.4 + - - -
196B ALA* 1.3 78.1 - - - +
198B ASN* 1.3 89.8 + - - +
199B HIS 3.4 0.9 - - - -
200B PRO* 3.5 14.6 - - - +
224B LYS* 5.8 5.8 - - - -
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Residues in contact with ASN 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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146B ARG* 3.0 19.3 - - - +
147B MET* 3.7 16.3 - - - +
194B SER* 3.3 19.4 + - - +
197B TYR* 1.3 105.5 - - - +
199B HIS* 1.3 81.2 + - + +
200B PRO* 3.5 5.8 - - - +
201B ASP* 4.5 0.9 - - - +
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Residues in contact with HIS 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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144B ARG 4.7 2.7 - - - -
145B LEU* 3.7 30.5 - - + +
146B ARG* 3.1 37.2 + - + -
147B MET* 4.7 0.7 - - + -
170B ARG* 4.2 7.0 + - - -
194B SER 3.6 15.5 - - - -
195B ILE* 2.9 33.1 + - + +
196B ALA* 4.9 0.2 - - - -
198B ASN* 1.3 91.7 + - + +
200B PRO* 1.3 60.8 - - - +
201B ASP* 3.1 19.3 + - - +
202B CYS* 3.4 30.2 + - + +
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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