Contacts of the helix formed by residues 212 - 230 (chain B) in PDB entry 2HXO
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 ASP 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLY 3.6 4.6 + - - +
211B HIS* 1.3 77.8 + - - +
213B ASP* 1.3 67.2 + - - +
214B ARG* 3.4 13.7 + - - +
215B GLU* 2.9 45.8 + - + +
216B GLN* 3.1 21.5 + - - +
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Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 5.8 3.6 - - - -
98B TRP* 3.8 19.5 - - + -
163B ASN* 4.0 13.3 - - - +
166B ASN* 4.5 4.1 + - - +
179B ARG* 2.6 52.7 + - - +
183B LEU* 5.0 0.2 - - - +
211B HIS* 3.7 16.1 + - - +
212B ASP* 1.3 74.4 + - - +
214B ARG* 1.3 56.9 + - - +
216B GLN* 3.2 7.7 + - - +
217B PHE* 2.9 29.1 + - - +
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.6 33.5 - - + +
98B TRP* 3.7 29.5 - - + +
99B ASP* 2.9 41.0 + - - -
102B GLU* 4.4 4.8 + - - -
212B ASP* 3.4 13.1 + - - +
213B ASP* 1.3 77.4 - - - +
215B GLU* 1.3 63.1 + - - +
217B PHE* 3.2 5.7 + - + +
218B LEU* 3.1 30.7 + - + +
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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
----------------------------------------------------------
212B ASP* 2.9 31.8 + - - +
213B ASP 3.3 0.2 - - - -
214B ARG* 1.3 71.9 - - - +
216B GLN* 1.3 60.2 + - - +
218B LEU* 3.3 8.5 + - - +
219B ALA* 2.9 30.3 + - + +
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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
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146A PHE 4.4 0.2 - - - +
147A THR* 3.2 48.8 + - - +
150A SER* 3.6 14.2 - - - -
151A ALA* 3.6 20.6 - - - +
154A HIS* 4.3 18.9 + - + +
155B TYR* 3.6 2.5 + - - -
211B HIS* 3.3 40.9 + - + +
212B ASP 3.1 5.6 + - - +
213B ASP* 3.2 8.5 + - - +
215B GLU* 1.3 75.5 - - - +
217B PHE* 1.3 57.9 + - - +
219B ALA* 3.3 3.7 + - - +
220B GLY* 2.9 26.0 + - - +
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Residues in contact with PHE 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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154A HIS* 6.0 0.2 - - - -
94B ALA* 3.6 49.1 - - + -
95B LEU* 4.1 8.3 - - + -
98B TRP* 3.5 42.2 - + + -
155B TYR* 2.9 32.2 + + - -
156B ILE* 3.9 20.4 - - + -
159B ALA* 3.5 29.8 - - + -
213B ASP 2.9 13.6 + - - +
214B ARG 3.2 9.9 - - - +
216B GLN* 1.3 77.8 - - - +
218B LEU* 1.3 70.8 + - + +
221B ILE* 3.0 23.3 + - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 4.5 25.1 + - + +
95B LEU* 3.8 44.9 - - + -
214B ARG* 3.1 26.4 + - + +
215B GLU* 3.3 7.6 + - - +
217B PHE* 1.3 84.2 - - + +
219B ALA* 1.3 60.4 + - - +
221B ILE* 3.4 8.4 + - + +
222B THR* 3.0 30.8 + - - -
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.6 28.5 - - + -
215B GLU* 2.9 19.9 + - + +
216B GLN* 3.6 4.5 - - - +
217B PHE 3.3 0.2 - - - -
218B LEU* 1.3 73.4 - - - +
220B GLY* 1.3 61.7 + - - +
222B THR* 3.2 9.1 + - - -
223B LEU* 2.9 34.4 + - - +
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Residues in contact with GLY 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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151A ALA* 4.2 17.4 - - - +
155B TYR* 3.0 28.4 - - - -
216B GLN* 2.9 12.4 + - - +
219B ALA* 1.3 77.0 - - - +
221B ILE* 1.3 61.0 + - - +
223B LEU* 3.2 5.1 + - - +
224B VAL* 3.0 27.4 + - - +
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Residues in contact with ILE 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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90B VAL* 4.4 8.7 - - + -
91B ARG* 4.0 19.1 - - + -
94B ALA* 3.9 11.9 - - + -
152B LEU* 4.7 9.0 - - + -
155B TYR* 3.4 14.6 - - + -
156B ILE* 3.2 37.0 - - + -
217B PHE* 3.0 26.6 + - + +
218B LEU* 3.5 13.9 - - + +
220B GLY* 1.3 77.0 - - - +
222B THR* 1.3 58.7 + - - +
224B VAL* 3.2 5.3 + - - +
225B LEU* 2.8 48.8 + - + +
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Residues in contact with THR 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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91B ARG* 3.1 32.7 + - - +
218B LEU 3.0 15.3 + - - -
219B ALA* 3.2 10.7 + - - -
221B ILE* 1.3 77.6 - - - +
223B LEU* 1.3 56.2 + - - +
225B LEU* 3.3 5.4 + - + +
226B THR* 2.8 42.3 + - - +
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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
----------------------------------------------------------
147A THR* 4.6 9.4 - - + +
148A ALA* 4.4 10.8 - - + -
151A ALA* 3.8 26.9 - - + -
223A LEU 4.2 2.2 - - - +
224A VAL* 4.8 12.6 - - + +
227A GLY* 3.4 40.3 - - - +
228A ILE* 3.7 19.5 - - + +
231A LEU* 4.2 18.4 - - + -
219B ALA* 2.9 18.9 + - + +
220B GLY* 3.2 8.7 + - - +
222B THR* 1.3 77.7 - - - +
224B VAL* 1.3 61.6 + - - +
226B THR* 3.3 4.4 + - - +
227B GLY* 3.2 16.6 + - - -
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 5.8 0.2 - - + -
223A LEU* 4.6 11.1 - - + +
224A VAL* 4.0 25.4 - - + +
151B ALA* 4.7 9.6 - - + +
152B LEU* 3.6 37.9 - - + +
155B TYR* 4.1 26.0 - - + -
220B GLY 3.0 14.8 + - - +
221B ILE* 3.6 6.7 - - - +
223B LEU* 1.3 72.9 - - + +
225B LEU* 1.3 59.8 + - - +
227B GLY* 3.0 3.6 + - - -
228B ILE* 2.9 35.6 + - + +
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Residues in contact with LEU 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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87B GLN* 3.7 42.2 - - + +
90B VAL* 4.1 22.0 - - + -
91B ARG* 4.3 11.9 - - - +
138B MSE 3.6 26.5 - - + +
152B LEU* 4.3 14.1 - - + -
221B ILE* 2.8 38.9 + - + +
222B THR* 3.7 4.9 - - + +
224B VAL* 1.3 76.2 - - - +
226B THR* 1.3 57.8 + - - +
228B ILE* 3.3 5.6 + - + +
229B THR* 2.8 35.3 + - - -
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Residues in contact with THR 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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226A THR* 4.8 1.7 - - + +
227A GLY* 3.9 18.4 - - - +
230A ALA* 4.0 20.9 - - + -
222B THR* 2.8 33.3 + - - +
223B LEU* 3.5 8.3 - - - +
225B LEU* 1.3 74.6 - - - +
227B GLY* 1.3 64.0 + - - +
229B THR* 3.4 8.2 + - - -
230B ALA* 3.2 20.8 + - + +
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Residues in contact with GLY 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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223A LEU* 3.4 38.0 - - - +
226A THR* 4.0 17.5 - - - +
227A GLY* 4.1 1.1 - - - -
223B LEU 3.2 4.8 + - - -
224B VAL 3.0 5.9 + - - -
226B THR* 1.3 80.2 - - - +
228B ILE* 1.3 60.6 + - - +
230B ALA* 3.3 15.1 + - - +
231B LEU* 3.7 6.2 + - - +
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Residues in contact with ILE 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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223A LEU* 4.0 13.9 - - + -
135B VAL* 4.6 3.8 - - + -
138B MSE 3.8 16.4 - - + -
140B VAL* 3.5 28.5 - - + +
148B ALA* 3.7 41.5 - - + +
152B LEU* 3.8 26.9 - - + -
224B VAL* 2.9 22.5 + - + +
225B LEU* 3.3 11.2 + - + +
227B GLY* 1.3 77.3 - - - +
229B THR* 1.3 62.3 + - - +
231B LEU* 3.1 26.4 + - + +
232B HIS 4.1 0.5 + - - -
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Residues in contact with THR 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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87B GLN* 3.6 13.6 + - - +
138B MSE 2.9 28.0 - - + +
140B VAL* 5.6 0.4 - - - -
225B LEU 2.8 24.2 + - - -
226B THR* 3.7 8.6 - - - -
227B GLY 3.3 0.2 - - - -
228B ILE* 1.3 76.9 - - - +
230B ALA* 1.3 60.4 + - - +
231B LEU 3.1 0.7 - - - -
232B HIS* 3.2 22.9 - - + +
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Residues in contact with ALA 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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226A THR* 3.9 20.2 - - + -
226B THR 3.2 12.4 + - - +
227B GLY 3.5 10.8 - - - +
228B ILE 3.1 0.4 - - - -
229B THR* 1.3 72.8 - - - +
231B LEU* 1.3 62.2 + - + +
232B HIS* 3.1 9.2 + - - +
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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