Contacts of the helix formed by residues 226 - 245 (chain B) in PDB entry 2LDX
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 TRP 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ILE* 4.3 24.2 - - + -
176B LYS* 3.4 53.4 - - + +
177B LEU* 4.3 15.9 - - + -
200B TRP* 3.0 33.5 - + + -
213B LEU* 4.9 8.3 - - + -
218B GLY* 4.5 6.0 - - - -
220B ASP* 3.2 44.4 + - - +
224B GLN 3.6 10.0 + - - -
225B HIS* 1.3 80.2 + - - +
227B LYS* 1.3 59.0 - - - +
228B ASN* 2.8 9.3 - - - +
229B VAL* 2.7 30.5 + - + +
3D VAL* 4.0 35.9 - - + +
4D LYS* 4.9 1.3 - - - -
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TRP* 4.1 10.0 - - - +
221B LYS* 4.5 26.9 - - - +
223B LYS* 5.3 8.5 + - - +
225B HIS* 4.0 26.3 - - + +
226B TRP* 1.3 86.8 - - - +
228B ASN* 1.3 89.7 + - - +
230B HIS* 2.7 14.7 + - - +
231B LYS* 2.7 69.7 + - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LYS* 5.8 1.8 - - - +
225B HIS* 5.4 2.5 - - + -
226B TRP 2.8 4.5 - - - +
227B LYS* 1.3 106.9 + - + +
229B VAL* 1.3 57.1 + - - +
230B HIS 2.9 1.8 - - - -
231B LYS* 3.1 24.3 - - - +
232B GLN* 2.4 53.4 + - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.4 21.3 - - + +
172B LEU* 3.2 29.7 - - + +
173B ILE* 3.6 20.4 - - + +
176B LYS* 3.5 27.7 - - - +
200B TRP* 3.2 21.8 - - + -
226B TRP* 2.7 26.2 + - + +
228B ASN* 1.3 71.5 - - - +
230B HIS* 1.3 54.4 + - - +
232B GLN* 3.2 9.1 + - - +
233B VAL* 2.6 39.9 + - - +
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 5.0 0.2 - - - -
188B VAL* 3.7 10.8 - - + +
196B SER* 2.3 52.5 + - - -
198B PRO* 3.5 35.0 - - + +
200B TRP* 4.6 4.7 - - + +
226B TRP 4.5 1.6 - - - +
227B LYS* 2.7 16.2 + - - +
229B VAL* 1.3 82.7 - - + +
231B LYS* 1.3 64.4 + - + -
233B VAL* 3.2 13.4 + - + +
234B VAL* 3.1 33.9 + - + +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LYS* 2.7 77.1 + - - +
228B ASN* 2.8 16.7 + - - +
230B HIS* 1.3 77.4 - - + +
232B GLN* 1.3 57.8 + - - +
234B VAL* 3.3 10.4 - - + +
235B GLU* 3.1 36.1 + - + +
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Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 2.9 37.0 - - + +
175B GLU* 3.7 18.0 + - - -
176B LYS* 5.8 2.9 + - - +
228B ASN* 2.4 38.5 + - - +
229B VAL* 3.2 8.4 - - - +
231B LYS* 1.3 72.4 - - - +
233B VAL* 1.3 59.5 + - - +
235B GLU* 4.7 2.9 - - - -
236B GLY* 2.8 28.1 + - - -
66D HIS* 5.6 0.2 + - - -
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Residues in contact with VAL 233 (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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165B ASP* 4.2 30.7 - - + +
168B ARG* 3.9 15.4 - - + +
169B PHE* 3.7 37.5 - - + +
172B LEU* 3.4 17.0 - - + -
188B VAL* 5.0 3.8 - - + -
196B SER* 5.7 1.8 - - - -
229B VAL 2.6 26.0 + - - +
230B HIS* 3.2 22.9 + - + +
232B GLN* 1.3 70.9 - - - +
234B VAL* 1.3 71.0 + - - +
236B GLY* 2.9 16.6 + - - -
237B GLY 3.4 3.1 + - - -
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Residues in contact with VAL 234 (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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165B ASP* 5.9 1.8 - - - -
193B GLY 3.1 26.9 - - - +
194B ASP* 3.4 30.3 - - + +
196B SER* 5.3 2.5 - - - -
230B HIS* 3.1 31.2 - - + +
231B LYS* 3.3 16.4 - - + +
233B VAL* 1.3 75.6 - - + +
235B GLU* 1.3 75.0 + - + +
237B GLY* 2.7 17.8 + - - -
238B TYR* 3.9 8.0 + - + -
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Residues in contact with GLU 235 (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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231B LYS* 3.1 17.0 + - + +
232B GLN* 4.2 3.6 - - - +
234B VAL* 1.3 83.2 - - + +
236B GLY* 1.3 51.5 + - - +
237B GLY 2.8 0.5 + - - -
238B TYR* 2.6 44.0 + - - +
239B GLU* 3.1 30.8 + - - +
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Residues in contact with GLY 236 (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 ARG* 4.5 0.7 - - - -
232B GLN* 2.8 18.6 + - - -
233B VAL 3.1 10.1 - - - -
234B VAL 2.8 0.6 + - - -
235B GLU* 1.3 75.3 - - - +
237B GLY* 1.3 56.2 + - - +
239B GLU* 4.2 8.4 - - - +
240B VAL* 2.8 28.6 + - - +
66D HIS* 3.1 23.0 - - - -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 4.4 19.7 - - - -
233B VAL 3.4 3.4 + - - -
234B VAL 2.7 16.3 + - - -
236B GLY* 1.3 73.4 - - - -
238B TYR* 1.3 64.1 + - - +
240B VAL* 3.1 21.9 - - - +
241B LEU* 4.0 7.3 + - - +
247B THR* 5.3 5.1 + - - -
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Residues in contact with TYR 238 (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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102B GLY 5.4 3.8 - - - -
104B THR* 3.2 54.7 + - + +
105B ARG* 3.7 12.0 - - + +
193B GLY* 5.3 5.8 - - - -
194B ASP* 3.1 40.0 + - - -
234B VAL* 4.3 9.4 - - + -
235B GLU* 2.6 31.6 + - - +
237B GLY* 1.3 69.6 - - - +
239B GLU* 1.3 62.1 + - - +
240B VAL 3.0 3.5 + - - -
241B LEU* 3.1 23.3 + - + +
242B ASP* 3.2 20.8 + - - +
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Residues in contact with GLU 239 (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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235B GLU* 3.1 27.3 + - - +
236B GLY* 4.4 9.6 - - - +
237B GLY 3.6 0.2 - - - -
238B TYR* 1.3 75.1 - - - +
240B VAL* 1.3 61.7 + - - +
242B ASP* 3.7 13.0 + - - +
243B MET* 3.1 45.2 + - + +
62D LEU* 5.7 5.4 - - + -
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Residues in contact with VAL 240 (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 ARG* 4.6 3.8 - - - +
236B GLY 2.8 28.9 - - - +
237B GLY* 3.1 14.8 - - - +
239B GLU* 1.3 77.7 - - - +
241B LEU* 1.3 68.9 + - + +
243B MET* 3.0 14.4 + - - +
244B LYS* 3.0 16.3 + - + +
246B TYR 3.9 15.3 - - - +
247B THR* 4.9 8.1 - - - +
59D GLY* 4.1 17.3 - - - +
62D LEU* 5.5 3.8 - - + -
63D ASP* 4.1 28.9 - - + +
66D HIS* 3.9 15.7 - - + +
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Residues in contact with LEU 241 (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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99B MET* 3.7 25.4 - - + -
100B VAL* 4.1 4.3 - - - +
101B SER* 3.5 29.6 - - - +
102B GLY 6.0 0.2 - - - +
104B THR* 4.1 26.5 - - + +
237B GLY 4.0 7.2 + - - +
238B TYR* 3.1 16.1 + - + +
240B VAL* 1.3 76.0 - - + +
242B ASP* 1.3 83.1 + - - +
243B MET 2.6 3.9 + - - -
245B GLY* 2.7 27.6 + - - -
246B TYR* 3.5 28.9 - - - +
247B THR* 4.6 6.3 - - + +
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Residues in contact with ASP 242 (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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101B SER* 3.6 26.5 + - - +
102B GLY 4.6 1.7 + - - -
238B TYR* 3.2 18.4 + - - +
239B GLU* 3.9 19.9 - - + +
240B VAL 3.2 0.6 - - - -
241B LEU* 1.3 89.1 - - - +
243B MET* 1.3 62.9 + - + +
245B GLY* 4.4 2.4 + - - -
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Residues in contact with MET 243 (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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239B GLU* 3.1 31.0 - - + +
240B VAL* 3.0 6.2 + - - +
241B LEU 2.6 5.7 + - - -
242B ASP* 1.3 81.0 - - + +
244B LYS* 1.3 58.9 + - - +
245B GLY 3.1 4.9 - - - -
55D ASP* 4.3 18.8 - - - +
56D LYS* 3.7 17.7 + - - +
58D ARG* 2.9 44.6 - - + +
59D GLY* 3.4 11.2 - - - -
62D LEU* 4.2 12.3 - - + -
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Residues in contact with LYS 244 (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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240B VAL* 3.0 17.1 + - + +
243B MET* 1.3 75.1 - - - +
245B GLY* 1.3 58.8 + - - +
246B TYR* 3.0 62.2 + - + +
248B SER* 2.5 29.4 + - - -
249B TRP* 4.1 6.5 - - - +
56D LYS* 4.2 15.4 - - + +
59D GLY* 4.4 0.2 - - - -
60D GLU* 2.3 65.5 + - + +
63D ASP* 2.8 21.8 + - - +
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET* 4.8 3.5 - - - +
241B LEU* 2.7 23.3 + - - -
242B ASP 4.6 2.2 - - - -
243B MET 3.1 1.6 - - - -
244B LYS* 1.3 80.5 - - - +
246B TYR* 1.3 71.9 + - - +
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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