Contacts of the helix formed by residues 209 - 228 (chain B) in PDB entry 1XAI
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 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B HIS* 3.6 11.7 - - - -
198B PHE* 3.9 2.9 - - - -
207B LEU 3.4 0.4 + - - -
208B ASN* 1.3 81.9 + - - +
210B MET* 1.3 60.5 + - - +
211B ASP* 3.6 1.8 - - - -
212B LYS* 3.8 10.8 + - - +
213B TYR* 2.9 31.8 + - - -
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Residues in contact with MET 210 (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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126B ILE* 4.8 9.9 - - + -
164B LEU* 4.6 9.2 - - + -
172B ILE* 4.8 0.2 - - + -
176B TYR* 3.9 14.6 - - + -
179B VAL* 4.6 11.0 - - - -
198B PHE* 3.7 21.5 - - + -
204B LEU* 3.6 31.2 - - + -
207B LEU* 3.2 41.8 + - + +
208B ASN 3.1 1.4 + - - -
209B GLY* 1.3 76.4 - - - +
211B ASP* 1.3 69.1 + - - +
212B LYS 2.7 6.7 + - - -
213B TYR* 2.7 17.6 + - - +
214B ILE* 3.1 37.7 + - + +
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.6 0.2 - - - +
18B HIS* 2.4 43.0 + - + -
161B LEU* 4.1 26.9 - - + +
164B LEU* 4.3 10.2 - - - +
207B LEU 4.7 1.3 + - - -
209B GLY* 3.6 1.5 - - - +
210B MET* 1.3 78.0 - - - +
212B LYS* 1.3 59.1 + - - +
214B ILE* 3.8 7.2 + - - +
215B ALA* 3.5 20.8 + - - +
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 3.8 8.5 + - - -
209B GLY* 3.8 11.8 + - - +
210B MET 2.7 4.4 + - - -
211B ASP* 1.3 73.7 - - - +
213B TYR* 1.3 108.2 + - + +
214B ILE 3.1 5.2 - - - -
215B ALA* 3.5 5.6 + - - +
216B LYS* 3.2 33.7 + - - +
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.4 30.1 - - + +
190B ALA 5.1 1.3 - - - -
193B ASP* 3.2 31.3 + - - -
194B ILE* 3.6 34.8 - - + -
197B HIS* 3.7 28.2 - + + +
198B PHE* 3.6 15.9 - + + -
209B GLY* 2.9 25.6 - - - +
210B MET* 2.7 11.1 + - - +
212B LYS* 1.3 107.0 + - + +
214B ILE* 1.3 60.2 + - - +
216B LYS* 4.0 20.5 - - + +
217B GLY* 3.5 13.3 + - - -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.2 0.4 - - + -
126B ILE* 3.7 29.2 - - + +
129B HIS* 3.6 13.9 - - + -
159B TYR* 3.5 38.1 - - + +
161B LEU* 4.5 8.7 - - + -
164B LEU* 4.0 21.5 - - + -
179B VAL* 4.3 6.5 - - + -
210B MET* 3.1 28.4 + - + +
211B ASP* 4.0 6.3 - - - +
213B TYR* 1.3 78.7 - - - +
215B ALA* 1.3 59.1 + - - +
216B LYS 3.1 1.1 - - - -
217B GLY* 2.7 19.6 + - - -
218B ILE* 2.8 19.8 + - + +
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Residues in contact with ALA 215 (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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1B MET* 3.5 32.5 - - + -
16B VAL* 5.0 6.2 - - + +
211B ASP 3.5 14.2 + - - +
212B LYS* 3.5 6.8 + - - +
214B ILE* 1.3 78.9 - - - +
216B LYS* 1.3 57.5 + - - +
218B ILE* 3.8 8.3 - - - +
219B GLU* 2.9 39.1 + - - +
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Residues in contact with LYS 216 (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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183B ALA* 6.0 1.6 - - - +
186B ASN* 3.4 29.3 + - - +
190B ALA* 4.0 21.0 - - - +
193B ASP* 5.8 2.5 - - - -
212B LYS* 3.2 25.3 + - - +
213B TYR* 4.1 27.6 - - + +
214B ILE 3.1 0.2 - - - -
215B ALA* 1.3 79.7 - - - +
217B GLY* 1.3 55.3 + - - +
219B GLU* 4.0 11.9 - - - +
220B THR* 2.5 37.6 + - - +
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Residues in contact with GLY 217 (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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129B HIS* 4.0 5.2 - - - -
179B VAL 5.7 0.9 - - - -
182B HIS* 3.3 40.6 + - - -
213B TYR 3.5 8.8 + - - -
214B ILE 2.7 10.5 + - - -
216B LYS* 1.3 78.3 - - - +
218B ILE* 1.3 63.8 + - - -
220B THR* 3.3 2.4 + - - -
221B LYS* 3.1 16.6 + - - +
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Residues in contact with ILE 218 (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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3B LEU* 4.1 18.8 - - + -
14B ILE* 4.4 16.6 - - + -
16B VAL* 3.3 35.9 - - + -
129B HIS* 3.8 26.8 - - + +
133B VAL* 4.3 19.3 - - + +
159B TYR* 3.8 20.4 - - + -
214B ILE* 2.8 22.1 + - + +
215B ALA* 3.8 9.0 - - - +
217B GLY* 1.3 71.9 - - - +
219B GLU* 1.3 64.0 + - - +
221B LYS* 3.0 7.8 + - - +
222B LEU* 2.9 20.8 + - + +
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Residues in contact with GLU 219 (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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1B MET* 4.0 17.3 - - - +
3B LEU* 4.1 24.8 - - + +
215B ALA* 2.9 26.7 + - - +
216B LYS* 4.0 10.2 - - - +
218B ILE* 1.3 78.8 - - - +
220B THR* 1.3 65.5 + - - +
221B LYS 2.9 1.6 + - - -
222B LEU* 2.9 18.5 + - - +
223B ASP* 3.1 21.0 + - - +
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Residues in contact with THR 220 (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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182B HIS* 4.1 34.3 + - + +
185B LEU* 5.1 8.3 - - + -
186B ASN* 3.5 24.1 + - + +
216B LYS* 2.5 24.2 + - - +
217B GLY* 3.5 6.9 - - - -
219B GLU* 1.3 77.7 - - - +
221B LYS* 1.3 58.8 + - - +
223B ASP* 3.6 13.3 - - - +
224B ILE* 3.1 29.3 - - + +
238B LEU* 6.0 0.4 - - + -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS 5.1 0.7 - - - +
130B ASP* 2.4 60.2 + - - +
131B SER* 4.1 3.2 - - - +
133B VAL* 2.6 31.4 + - + +
182B HIS* 4.3 10.5 - - + +
217B GLY 3.1 10.5 + - - +
218B ILE* 3.0 9.5 + - - +
219B GLU 3.0 0.8 - - - -
220B THR* 1.3 73.4 - - - +
222B LEU* 1.3 56.8 + - - +
223B ASP 2.7 15.7 + - - -
224B ILE* 2.7 18.2 + - - -
225B VAL* 2.9 22.7 + - + +
238B LEU* 3.5 27.4 - - + -
501B CRB 3.3 25.8 + - - +
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Residues in contact with LEU 222 (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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3B LEU* 4.2 13.9 - - + -
4B GLN 3.6 33.7 - - - +
5B THR* 4.1 3.8 - - + +
6B THR* 4.7 6.5 - - + +
14B ILE* 3.6 28.5 - - + -
133B VAL* 4.6 7.7 - - + +
218B ILE 2.9 13.2 + - - +
219B GLU* 2.9 11.9 + - - +
221B LYS* 1.3 75.6 - - - +
223B ASP* 1.3 68.9 + - - +
225B VAL* 3.6 9.4 - - - -
226B VAL* 3.0 48.7 + - + +
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Residues in contact with ASP 223 (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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219B GLU* 3.3 17.3 - - - +
220B THR* 3.6 11.8 - - - +
221B LYS 2.7 4.9 + - - -
222B LEU* 1.3 86.7 - - - +
224B ILE* 1.3 63.7 + - + +
226B VAL* 3.6 1.6 + - - +
227B ALA* 3.0 32.9 + - - +
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Residues in contact with ILE 224 (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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185B LEU* 6.3 4.0 - - + -
220B THR* 3.1 26.9 - - + +
221B LYS 2.7 9.6 + - - +
223B ASP* 1.3 75.3 - - + +
225B VAL* 1.3 56.4 + - - +
227B ALA* 4.2 3.5 - - - +
228B ASP* 3.1 27.7 + - - +
234B VAL* 3.9 20.4 - - + +
235B ARG* 3.4 32.2 - - + +
237B PHE* 5.0 6.5 - - + -
238B LEU* 3.7 31.4 - - + -
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Residues in contact with VAL 225 (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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5B THR* 5.1 1.6 - - + -
7B TYR* 2.6 23.6 + - + +
12B TYR* 4.9 3.4 - - - +
133B VAL* 4.6 4.3 - - + -
134B GLY* 3.8 21.3 - - - +
221B LYS* 2.9 39.3 + - + +
222B LEU* 3.5 15.9 - - + +
224B ILE* 1.3 78.1 - - - +
226B VAL* 1.3 65.3 + - + +
228B ASP 4.4 1.8 - - - +
229B GLU* 2.9 22.2 + - - -
235B ARG* 3.6 38.8 - - - +
238B LEU* 4.0 2.5 - - + -
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Residues in contact with VAL 226 (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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5B THR* 3.9 21.3 - - + -
6B THR* 3.3 58.6 - - - +
7B TYR* 3.2 26.7 - - + +
222B LEU* 3.0 27.4 + - + +
223B ASP* 4.2 2.0 - - - +
225B VAL* 1.3 78.2 - - + +
227B ALA* 1.3 63.9 + - - +
228B ASP 3.4 0.5 + - - -
229B GLU 4.3 1.0 + - - -
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Residues in contact with ALA 227 (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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223B ASP 3.0 20.6 + - - +
224B ILE* 4.2 4.0 - - - +
226B VAL* 1.3 81.0 - - + +
228B ASP* 1.3 60.5 + - + +
234B VAL* 4.8 7.8 - - + +
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Residues in contact with ASP 228 (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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224B ILE 3.1 9.5 + - - +
225B VAL 3.5 2.2 - - - -
227B ALA* 1.3 80.6 - - - +
229B GLU* 1.3 66.5 + - - +
230B LYS 3.3 0.6 + - - -
231B GLU 3.0 7.6 + - - -
232B GLN* 2.6 50.6 + - - +
233B GLY 3.3 0.3 + - - -
234B VAL* 3.1 30.4 + - + -
235B ARG* 2.9 33.0 + - - +
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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
------------------------------------------------------------
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