Contacts of the helix formed by residues 215 - 234 (chain B) in PDB entry 2CXU
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ILE* 3.7 32.5 - - + -
210B SER* 2.7 28.2 + - - -
211B LYS 5.1 0.5 + - - -
212B THR* 3.7 8.7 + - - -
213B PHE 3.8 0.6 - - - -
214B THR* 1.3 72.5 - - - +
216B GLN* 1.3 62.9 + - - +
217B GLU 3.3 1.0 + - - +
218B THR* 3.9 19.1 - - - +
219B ILE* 2.8 31.8 + - - +
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 3.8 27.3 - - + +
428A ASN* 4.8 3.8 + - - -
214B THR 3.1 8.2 + - - +
215B THR* 1.3 72.4 - - - +
217B GLU* 1.3 59.9 + - + +
219B ILE* 3.9 2.7 - - - +
220B THR* 2.7 45.2 + - - +
522B ALA* 6.1 0.3 - - - +
523B LYS* 3.5 19.1 - - + +
526B GLU* 2.8 41.9 + - - +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A THR* 2.5 34.1 + - - +
388A GLN* 4.4 2.9 - - - +
389A HIS* 2.6 34.6 + - + -
424A ILE* 4.7 8.3 - - + -
428A ASN* 4.5 7.1 + - - +
157B ILE* 3.9 18.1 - - + +
185B SER 4.9 0.4 - - - +
187B ILE* 3.4 40.6 + - + +
215B THR* 3.4 1.8 - - - +
216B GLN* 1.3 80.9 - - + +
218B THR* 1.3 57.6 + - - +
220B THR* 3.4 2.1 + - - -
221B ASN* 3.0 36.1 + - - +
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 3.5 36.7 - - + +
156B GLY* 3.5 2.3 - - - +
157B ILE* 3.4 34.4 + - - +
208B ILE* 4.1 13.5 - - + -
209B ALA 3.6 15.8 + - - +
210B SER* 4.3 5.4 - - - -
215B THR* 3.4 18.1 + - - +
217B GLU* 1.3 78.3 - - - +
219B ILE* 1.3 57.4 + - - +
221B ASN* 3.4 2.2 + - - +
222B ALA* 2.8 29.3 + - - +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.2 15.5 - - + -
210B SER* 4.8 4.3 - - - -
213B PHE* 3.5 59.9 - - + +
214B THR* 3.9 4.7 - - - +
215B THR* 2.8 29.0 + - - +
216B GLN* 4.2 2.0 - - - +
218B THR* 1.3 69.6 - - - +
220B THR* 1.3 60.2 + - - +
222B ALA* 3.3 4.6 + - + +
223B GLU* 2.8 51.7 + - + +
256B PHE* 5.3 5.2 - - + -
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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
----------------------------------------------------------
417A ARG* 3.5 3.9 + - - +
420A LEU* 3.9 25.4 - - + +
421A HIS* 3.8 15.9 - - + +
424A ILE* 3.9 16.2 - - + +
187B ILE* 3.7 20.2 - - + -
216B GLN* 2.7 29.3 + - - +
217B GLU 3.7 3.8 - - - -
219B ILE* 1.3 75.9 - - - +
221B ASN* 1.3 63.5 + - - +
223B GLU* 3.2 9.1 + - - -
224B THR* 3.0 25.8 + - - -
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Residues in contact with ASN 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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421A HIS* 3.1 26.5 + - - -
155B ILE* 3.5 25.0 - - + +
157B ILE* 5.8 0.2 - - - +
184B VAL* 3.8 17.2 - - + +
185B SER* 3.9 9.1 + - - +
186B ASN 3.0 30.8 + - - +
187B ILE* 4.2 2.5 - - - +
188B ASP 5.3 0.2 - - - +
192B ILE* 3.7 16.8 - - + +
217B GLU 3.0 21.2 + - - +
218B THR* 5.0 0.8 - - - +
220B THR* 1.3 75.7 - - - +
222B ALA* 1.3 57.5 + - - +
224B THR* 3.2 3.9 + - - -
225B ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 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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155B ILE* 4.0 11.8 - - - +
208B ILE* 3.6 35.9 - - + -
218B THR 2.8 21.7 + - - +
219B ILE* 3.3 8.3 + - - +
221B ASN* 1.3 74.6 - - - +
223B GLU* 1.3 56.0 + - - +
225B ALA* 3.3 3.8 + - - +
226B LYS 2.9 23.0 + - - -
243B PHE* 4.0 1.0 - - - -
256B PHE* 3.5 23.2 - - + -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG* 3.9 20.8 + - - +
219B ILE* 2.8 39.6 + - + +
220B THR* 3.2 7.4 + - - +
222B ALA* 1.3 69.6 - - - +
224B THR* 1.3 59.9 + - - +
226B LYS* 3.4 15.4 + - - +
227B GLU* 3.0 28.4 + - - +
256B PHE* 3.9 18.5 - - + -
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 4.0 25.6 - - + -
417A ARG* 2.8 33.4 + - + +
421A HIS* 2.7 24.7 + - - +
192B ILE* 4.0 13.0 - - + -
196B LEU* 4.8 5.8 - - + -
220B THR 3.0 5.6 + - - -
221B ASN* 3.2 9.6 + - - -
223B GLU* 1.3 73.4 - - - +
225B ALA* 1.3 63.5 + - - +
227B GLU* 3.3 5.7 + - - +
228B TRP* 3.1 22.5 + - + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 4.1 7.0 - - + -
192B ILE* 4.5 4.9 - - + +
196B LEU* 4.5 7.6 - - - -
206B PHE* 3.7 34.5 - - + -
221B ASN 2.9 13.5 + - - +
222B ALA 3.5 8.5 - - - +
224B THR* 1.3 77.4 - - - +
226B LYS* 1.3 56.3 + - - +
228B TRP* 3.4 11.2 + - - +
229B PHE* 2.9 29.3 + - - +
243B PHE* 3.8 8.7 - - + -
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Residues in contact with LYS 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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222B ALA 2.9 15.6 + - - +
223B GLU* 3.7 13.5 + - - +
224B THR 3.3 0.2 - - - -
225B ALA* 1.3 77.4 - - - +
227B GLU* 1.3 55.9 + - - +
229B PHE* 3.3 1.6 + - - +
230B LEU* 2.8 47.8 + - + +
239B VAL* 4.0 19.3 - - + -
243B PHE* 3.6 13.6 - - + -
255B GLU 4.6 2.2 + - - -
256B PHE* 2.7 66.5 + - + +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG* 3.5 32.1 + - - -
223B GLU 3.0 18.9 + - - +
224B THR* 3.6 7.3 - - - +
226B LYS* 1.3 75.5 - - - +
228B TRP* 1.3 62.6 + - - +
230B LEU* 3.4 5.6 + - - +
231B GLU* 3.1 43.6 + - - +
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Residues in contact with TRP 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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196B LEU* 3.7 52.0 + - + +
199B LEU* 3.6 31.0 - - + -
200B SER 3.7 5.2 - - - -
201B PRO* 3.4 45.1 - - + +
204B SER* 4.6 1.1 - - - -
206B PHE* 3.6 26.2 - + - -
224B THR* 3.1 12.7 + - + +
225B ALA 3.5 12.6 - - - +
227B GLU* 1.3 76.1 + - - +
229B PHE* 1.3 79.1 - - + +
231B GLU* 3.4 24.0 + - - +
232B ALA* 3.7 6.2 + - - +
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Residues in contact with PHE 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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144B TYR* 3.6 11.2 - + - -
201B PRO* 3.6 26.5 - - + -
206B PHE* 5.2 2.0 - + + -
225B ALA 2.9 18.7 + - - +
226B LYS 3.5 2.9 - - - +
228B TRP* 1.3 89.4 - + + +
230B LEU* 1.3 70.3 + - + +
232B ALA* 3.1 6.8 + - - +
233B ALA* 2.9 43.1 + - + -
238B ALA* 3.6 11.7 - - + -
239B VAL* 3.7 28.7 - - + -
242B HIS* 3.3 42.4 - + + -
243B PHE* 4.1 20.2 - + + -
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Residues in contact with LEU 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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226B LYS* 2.8 41.0 + - + +
227B GLU* 4.1 5.2 - - - +
229B PHE* 1.3 80.3 - - + +
231B GLU* 1.3 61.6 + - - +
233B ALA 4.2 1.8 - - - +
234B LYS* 2.8 29.8 + - - +
235B ASP 3.4 41.1 - - - +
236B PRO* 3.9 14.4 - - + -
239B VAL* 3.9 14.4 - - + -
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Residues in contact with GLU 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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227B GLU* 3.1 36.7 + - - +
228B TRP* 3.5 18.4 - - - +
230B LEU* 1.3 77.9 - - - +
232B ALA* 1.3 59.0 + - - +
234B LYS* 3.8 17.5 + - - +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR* 3.5 21.5 + - - +
201B PRO* 3.7 25.6 - - + -
228B TRP 3.7 2.8 + - - +
229B PHE 3.1 8.3 + - - +
231B GLU* 1.3 79.9 - - - +
233B ALA* 1.3 59.4 + - - +
234B LYS* 2.8 25.0 + - - +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR* 3.6 30.0 - - + -
229B PHE* 2.9 47.2 + - + +
230B LEU* 4.5 1.1 - - - -
232B ALA* 1.3 75.2 - - - +
234B LYS* 1.3 71.8 + - - +
235B ASP* 3.1 10.5 + - - +
238B ALA* 4.2 7.9 - - + -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 2.8 22.6 + - - +
231B GLU 3.8 18.5 + - - +
232B ALA* 2.8 25.1 + - - +
233B ALA* 1.3 71.9 + - - +
235B ASP* 1.3 58.0 + - - +
236B PRO* 4.4 4.1 - - - +
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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