Contacts of the helix formed by residues 215 - 231 (chain B) in PDB entry 2XWU
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 PRO 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B GLN* 4.5 14.6 - - + +
213B SER 3.4 8.5 - - - +
214B SER* 1.3 88.4 - - - +
216B SER* 1.3 67.9 + - - +
217B CYS* 3.2 16.8 - - - -
218B VAL* 2.9 37.5 + - + +
219B ARG* 3.0 11.1 + - - +
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Residues in contact with SER 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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214B SER 4.1 0.4 + - - -
215B PRO* 1.3 71.8 - - - +
217B CYS* 1.3 57.8 + - - +
219B ARG* 3.1 15.2 + - - +
220B GLN* 3.0 27.9 + - - +
252B ASP* 5.0 4.9 - - - -
254B GLU* 3.6 25.4 - - - +
255B LEU* 3.9 7.4 - - - +
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Residues in contact with CYS 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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160B GLN* 2.9 38.4 - - - +
164B LEU* 3.9 10.3 - - + +
215B PRO* 3.9 14.8 - - - -
216B SER* 1.3 79.0 + - - +
218B VAL* 1.3 68.9 + - - +
220B GLN* 3.5 7.3 + - - +
221B LYS* 3.3 26.5 + - - +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN* 4.5 7.6 - - + -
163B CYS* 4.2 30.5 - - + -
164B LEU* 3.6 27.8 - - + -
167B LEU* 4.1 1.5 - - + +
208B LEU* 4.5 7.6 - - + -
214B SER* 4.2 17.9 - - - +
215B PRO* 2.9 31.1 + - + +
217B CYS* 1.3 76.0 - - - +
219B ARG* 1.3 68.7 + - - +
221B LYS* 3.3 3.3 + - - +
222B VAL* 2.9 33.8 + - + +
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Residues in contact with ARG 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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208B LEU 5.3 1.1 - - - +
209B LEU* 2.4 47.1 + - + +
210B GLN 5.0 0.2 - - - -
211B GLN 3.6 11.5 + - - -
212B PRO* 4.5 6.5 + - - +
214B SER* 2.6 46.8 + - - +
215B PRO 3.0 14.9 + - - +
216B SER* 3.1 13.0 + - - +
218B VAL* 1.3 77.4 - - - +
220B GLN* 1.3 62.3 + - - +
222B VAL* 3.1 9.0 + - - +
223B LEU* 3.0 28.3 + - + +
252B ASP* 5.2 2.9 - - - -
255B LEU* 3.6 31.8 - - + +
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Residues in contact with GLN 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 SER 3.0 15.2 + - - +
217B CYS* 3.8 8.5 - - - +
218B VAL 3.3 0.2 - - - -
219B ARG* 1.3 76.3 - - - +
221B LYS* 1.3 63.1 + - + +
223B LEU* 3.2 12.7 + - - +
224B LYS* 3.0 44.2 + - - +
254B GLU 5.6 3.6 - - - +
255B LEU* 4.6 8.0 - - + +
258B SER* 4.5 5.9 - - - -
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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
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164B LEU* 3.7 35.9 + - + +
167B LEU* 3.7 26.2 - - + +
168B GLU* 4.1 24.1 + - - +
171B THR* 4.4 4.0 + - - +
217B CYS 3.3 14.0 + - - +
218B VAL 3.8 2.5 - - - +
220B GLN* 1.3 77.6 - - + +
222B VAL* 1.3 58.2 + - - +
224B LYS* 3.2 25.2 + - + +
225B CYS* 2.8 30.6 + - - +
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Residues in contact with VAL 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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167B LEU* 4.1 10.1 - - + -
205B LEU* 3.9 22.0 - - + +
208B LEU* 3.7 33.2 - - + -
209B LEU* 3.0 41.7 - - + -
218B VAL* 2.9 19.3 + - + +
219B ARG 3.1 7.6 + - - +
221B LYS* 1.3 78.1 - - - +
223B LEU* 1.3 64.3 + - + +
225B CYS* 3.2 7.6 + - - +
226B PHE* 2.9 21.6 + - + +
242B LEU* 4.8 2.5 - - + -
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Residues in contact with LEU 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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209B LEU* 5.0 13.7 - - + -
219B ARG* 3.0 18.8 + - + +
220B GLN* 3.6 5.8 - - - +
222B VAL* 1.3 77.6 - - + +
224B LYS* 1.3 65.1 + - - +
226B PHE* 3.1 10.6 + - + +
227B SER* 3.0 24.6 + - - -
242B LEU* 5.7 0.4 - - + +
246B ALA* 4.0 31.2 - - + -
249B ALA* 4.7 5.2 - - + -
255B LEU* 3.9 25.8 - - + +
258B SER* 3.4 33.7 - - - +
259B SER* 3.7 19.5 - - - +
262B ALA* 4.5 6.5 - - + +
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Residues in contact with LYS 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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48A LYS* 6.1 2.2 - - - +
171B THR* 4.3 10.9 - - + +
220B GLN* 3.0 35.9 + - - +
221B LYS* 3.2 27.9 + - + +
223B LEU* 1.3 78.3 - - - +
225B CYS* 1.3 60.9 + - - +
227B SER* 3.3 8.8 + - - +
228B SER* 3.2 19.9 + - - -
258B SER* 4.8 13.9 - - - -
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Residues in contact with CYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 4.4 6.3 - - + -
170B LEU* 3.9 27.1 - - - -
171B THR* 3.2 26.7 + - - +
201B VAL* 4.6 1.1 - - - -
205B LEU* 4.0 24.5 - - + -
221B LYS 2.8 15.3 + - - +
222B VAL* 3.4 7.0 - - - +
223B LEU 3.1 0.2 - - - -
224B LYS* 1.3 73.3 - - - +
226B PHE* 1.3 67.3 + - - +
228B SER* 3.0 12.1 + - - -
229B TRP* 3.3 32.1 - - - -
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.6 24.7 - + - -
205B LEU* 4.0 12.3 - - + +
222B VAL* 2.9 13.0 + - + +
223B LEU* 3.4 14.4 - - + +
225B CYS* 1.3 77.7 - - - +
227B SER* 1.3 60.7 + - - +
229B TRP* 3.4 2.9 + - - +
230B VAL* 3.0 48.7 + - + +
239B CYS* 3.9 21.1 - - + -
242B LEU* 3.3 47.6 - - + -
243B ILE* 4.0 15.9 - - + -
246B ALA* 5.2 2.0 - - + -
262B ALA* 3.8 33.9 - - + -
263B ILE* 5.7 0.2 - - - -
266B ALA* 4.4 1.3 - - + -
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Residues in contact with SER 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 LEU 3.0 10.6 + - - -
224B LYS* 3.7 10.9 - - - -
225B CYS 3.2 0.4 - - - -
226B PHE* 1.3 77.6 - - - +
228B SER* 1.3 61.7 + - - +
230B VAL* 3.3 15.9 + - - +
231B GLN* 3.2 22.5 + - - +
258B SER 4.7 1.2 + - - -
261B GLU* 4.1 2.8 - - - +
262B ALA* 3.3 33.4 + - - +
265B ASN* 4.1 14.5 + - - -
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Residues in contact with SER 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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171B THR* 3.0 35.5 + - - -
174B PRO* 3.3 20.6 - - - +
175B GLU* 3.5 15.5 - - - +
178B GLN* 6.1 0.5 - - - +
224B LYS 3.2 11.0 + - - -
225B CYS 3.0 11.3 + - - -
227B SER* 1.3 78.2 - - - +
229B TRP* 1.3 61.7 + - - +
231B GLN* 3.2 21.8 + - - +
232B LEU* 3.8 2.8 + - - +
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Residues in contact with TRP 229 (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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170B LEU* 3.1 24.0 + - + -
173B LEU* 4.0 22.9 - - + -
174B PRO* 3.3 19.3 - - + +
191B ARG* 6.0 0.2 - - - -
194B LEU* 3.6 32.1 - - + -
197B GLU* 4.6 3.6 - - + -
198B CYS* 3.7 27.6 - - + -
201B VAL* 3.4 43.4 - - + +
202B PHE* 3.9 24.0 - + + -
225B CYS* 3.3 27.7 + - - -
226B PHE 4.0 1.6 - - - +
228B SER* 1.3 74.3 - - - +
230B VAL* 1.3 61.8 + - - +
232B LEU* 2.9 50.4 + - + +
233B GLU 3.8 2.1 + - - -
234B VAL* 4.1 10.3 - - + +
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Residues in contact with VAL 230 (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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202B PHE* 5.2 0.7 - - + -
226B PHE* 3.0 59.7 + - + +
227B SER* 3.5 9.6 - - - +
228B SER 3.1 0.4 - - - -
229B TRP* 1.3 78.4 - - - +
231B GLN* 1.3 62.6 + - - +
233B GLU* 3.1 7.8 + - - +
234B VAL* 4.8 1.8 - - - -
239B CYS* 4.7 3.6 - - - -
262B ALA 4.9 0.9 - - - +
265B ASN* 3.5 18.4 - - + +
266B ALA* 3.5 26.9 - - + +
269B GLN* 3.0 42.9 + - + +
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Residues in contact with GLN 231 (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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104A ARG* 6.1 0.9 - - - +
111A GLN* 3.7 23.9 - - - +
178B GLN* 4.2 24.5 + - + +
227B SER* 3.2 17.6 + - - +
228B SER* 3.6 10.8 - - - +
229B TRP 3.1 1.0 - - - -
230B VAL* 1.3 74.5 - - - +
232B LEU* 1.3 57.6 + - - +
233B GLU* 3.0 18.1 + - - +
265B ASN* 4.3 29.9 + - - +
269B GLN* 6.1 0.2 - - - +
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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
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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