Contacts of the helix formed by residues 209 - 223 (chain B) in PDB entry 2XH1
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 THR 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B SER* 4.0 23.9 + - - +
207B SER 4.8 2.2 - - - +
208B LEU* 1.3 80.5 - - - +
210B SER* 1.3 64.8 + - - +
211B GLU* 3.6 16.7 + - - +
212B ARG* 3.4 27.5 + - - +
213B LYS* 3.2 22.5 + - - +
243B VAL* 4.3 2.7 - - - -
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Residues in contact with SER 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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209B THR* 1.3 73.6 - - - +
211B GLU* 1.3 73.8 + - - +
213B LYS* 3.4 6.9 + - - +
214B LYS* 3.2 47.5 + - - +
243B VAL* 3.8 23.4 - - - +
244B PRO* 4.1 19.3 - - - +
249B MET* 5.3 0.3 - - - +
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Residues in contact with GLU 211 (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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209B THR* 3.2 20.3 - - - +
210B SER* 1.3 85.8 + - - +
212B ARG* 1.3 65.1 + - + +
214B LYS* 3.6 14.6 + - + +
215B GLU* 3.4 27.0 + - - +
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Residues in contact with ARG 212 (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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162B ASP* 2.8 43.9 + - - -
164B SER* 3.3 26.4 + - - -
165B GLY 2.9 8.7 + - - -
166B ILE 2.9 26.4 + - - -
167B VAL* 3.6 15.5 - - - +
168B PRO* 4.2 13.9 - - + +
208B LEU* 4.0 11.9 - - + -
209B THR* 3.4 20.1 + - - +
211B GLU* 1.3 76.2 - - + +
213B LYS* 1.3 54.8 + - - +
215B GLU* 3.1 12.9 + - - +
216B ILE* 2.8 43.4 + - + +
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Residues in contact with LYS 213 (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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198B PRO* 3.8 30.0 - - - +
199B ASN* 4.6 7.5 + - - +
208B LEU* 3.9 13.3 + - + -
209B THR 3.2 19.6 + - - +
210B SER* 3.6 8.7 - - - +
211B GLU 3.3 0.4 - - - -
212B ARG* 1.3 74.8 - - - +
214B LYS* 1.3 52.8 + - - +
216B ILE* 3.4 1.2 + - - -
217B TYR 2.8 31.0 + - - -
229B GLU* 4.3 6.9 + - - -
243B VAL* 3.5 25.6 + - + +
244B PRO 2.9 30.3 + - - +
245B THR* 3.9 6.3 - - - +
246B PHE* 3.4 37.0 - - + +
249B MET* 3.2 18.4 - - - +
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Residues in contact with LYS 214 (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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210B SER* 3.2 32.1 + - - +
211B GLU* 3.8 13.2 + - - +
212B ARG 3.3 0.2 - - - -
213B LYS* 1.3 77.9 - - - +
215B GLU* 1.3 59.2 + - - +
217B TYR* 3.3 3.1 + - - +
218B GLU* 3.0 37.6 + - - +
244B PRO* 6.3 2.0 - - - -
249B MET* 3.9 19.5 - - + -
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Residues in contact with GLU 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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168B PRO* 3.8 22.6 - - + +
172B ARG* 2.5 37.3 + - - +
211B GLU* 3.4 16.0 + - - +
212B ARG* 3.1 13.4 + - - +
214B LYS* 1.3 75.6 - - + +
216B ILE* 1.3 62.4 + - - +
218B GLU* 3.5 16.8 + - - +
219B LEU* 3.2 28.1 + - - +
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Residues in contact with ILE 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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166B ILE* 3.9 32.1 - - + +
168B PRO* 4.4 7.9 - - + -
171B LEU* 4.2 10.6 - - + +
194B LEU* 3.5 29.2 - - + -
208B LEU* 3.9 29.4 - - + -
212B ARG* 2.8 32.7 + - + +
213B LYS* 3.6 3.8 - - - +
215B GLU* 1.3 70.3 - - - +
217B TYR* 1.3 66.2 + - - +
219B LEU* 3.2 8.6 + - - +
220B ALA* 2.9 20.8 + - + +
227B ILE* 4.5 4.7 - - + -
246B PHE* 3.8 15.9 - - + -
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Residues in contact with TYR 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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213B LYS 2.8 11.2 + - - +
214B LYS 3.8 2.5 - - - +
216B ILE* 1.3 73.0 - - - +
218B GLU* 1.3 60.4 + - + +
220B ALA* 3.2 2.1 + - - +
221B ARG* 2.9 36.7 + - + +
227B ILE* 4.0 20.2 - - + -
246B PHE* 4.2 3.6 - + + -
249B MET* 3.0 48.7 - - + -
250B ASP* 2.7 37.3 + - - -
251B VAL* 3.2 4.1 + - + -
252B ASP* 2.8 41.1 + - - +
254B ARG* 3.7 17.2 - - + +
255B VAL* 3.9 8.3 - - + -
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Residues in contact with GLU 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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214B LYS* 3.0 32.3 + - - +
215B GLU* 3.6 17.2 - - - +
216B ILE 3.2 0.2 - - - -
217B TYR* 1.3 77.6 - - + +
219B LEU* 1.3 59.7 + - + +
221B ARG* 3.4 8.8 + - - +
222B LYS* 2.9 29.9 + - - +
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Residues in contact with LEU 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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168B PRO* 4.1 13.0 - - + +
171B LEU* 4.2 15.0 - - + -
172B ARG* 3.5 50.3 - - + +
175B LEU* 4.0 19.1 - - + -
215B GLU 3.2 26.3 + - - +
216B ILE 3.2 7.4 + - - +
218B GLU* 1.3 78.7 - - + +
220B ALA* 1.3 63.6 + - - +
222B LYS* 4.4 11.4 - - + +
223B TYR* 3.0 46.1 + - + -
225B PHE* 3.7 5.1 - - - -
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Residues in contact with ALA 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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216B ILE 2.9 8.2 + - - +
217B TYR 3.2 7.8 + - - +
219B LEU* 1.3 78.0 - - - +
221B ARG* 1.3 56.2 + - - +
224B ASP* 2.8 22.7 + - - -
225B PHE* 2.9 45.4 + - + +
227B ILE* 3.6 26.2 - - + -
254B ARG* 3.4 15.2 + - - -
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Residues in contact with ARG 221 (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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217B TYR* 2.9 24.4 + - + +
218B GLU* 3.6 7.9 - - - +
220B ALA* 1.3 75.5 - - - +
222B LYS* 1.3 68.4 + - + +
224B ASP* 3.1 14.6 + - - +
251B VAL* 3.7 24.9 - - - +
252B ASP* 2.7 43.0 + - - +
254B ARG* 3.7 14.4 + - - +
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Residues in contact with LYS 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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180B PRO* 3.4 43.9 - - + +
218B GLU 2.9 17.2 + - - +
219B LEU* 3.9 12.8 - - + +
221B ARG* 1.3 79.3 - - - +
223B TYR* 1.3 91.4 + - + +
224B ASP* 3.7 1.0 + - - +
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Residues in contact with TYR 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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5B ARG* 5.3 0.3 + - - -
172B ARG* 4.8 3.5 + - - -
175B LEU* 3.4 57.7 + - + -
176B SER* 4.3 6.6 + - - -
178B TRP* 3.7 19.7 + + + -
179B LYS 4.3 3.8 - - - -
180B PRO* 3.8 28.7 - - + +
183B ALA* 3.5 13.3 - - - +
190B THR* 5.3 4.8 - - - -
191B PRO* 5.2 4.0 - - + +
219B LEU* 3.0 27.4 + - + +
220B ALA 3.8 0.4 - - - -
222B LYS* 1.3 110.9 + - + +
224B ASP* 1.3 70.6 + - - +
225B PHE* 3.4 19.4 + - + +
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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
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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