Contacts of the helix formed by residues 226 - 245 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.0 36.5 - - + +
4A LYS* 4.9 1.6 - - - -
173C ILE* 4.3 25.1 - - + -
176C LYS* 3.4 51.6 - - + +
177C LEU* 4.3 15.7 - - + -
200C TRP* 3.0 33.8 - + + -
213C LEU* 4.9 8.9 - - + +
218C GLY* 4.5 5.8 - - - -
220C ASP* 3.2 45.4 + - - +
224C GLN 3.6 9.6 + - - -
225C HIS* 1.3 81.3 + - - +
227C LYS* 1.3 59.0 - - - +
228C ASN* 2.8 9.6 - - - +
229C VAL* 2.7 30.9 + - + +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C TRP* 4.1 10.7 - - - +
221C LYS* 4.5 26.0 - - - +
223C LYS* 5.3 9.1 + - - +
225C HIS* 4.0 25.1 - - + +
226C TRP* 1.3 86.8 - - - +
228C ASN* 1.3 88.8 + - - +
230C HIS* 2.7 15.5 + - - +
231C LYS* 2.7 68.8 + - - +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C LYS* 5.8 2.2 - - - +
225C HIS* 5.4 2.2 - - + -
226C TRP 2.8 4.0 - - - +
227C LYS* 1.3 105.5 + - + +
229C VAL* 1.3 57.7 + - - +
230C HIS 2.9 1.6 - - - -
231C LYS* 3.1 23.8 - - - +
232C GLN* 2.4 54.1 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PHE* 3.4 21.3 - - + +
172C LEU* 3.2 30.3 - - + +
173C ILE* 3.6 19.7 - - + +
176C LYS* 3.5 28.1 - - - +
200C TRP* 3.2 21.3 - - + -
226C TRP* 2.7 26.8 + - + +
228C ASN* 1.3 71.6 - - - +
230C HIS* 1.3 55.9 + - - +
232C GLN* 3.2 8.7 + - - +
233C VAL* 2.6 39.7 + - - +
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Residues in contact with HIS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PHE* 5.0 0.2 - - - -
188C VAL* 3.7 10.5 - - + +
196C SER* 2.3 51.2 + - - -
198C PRO* 3.5 35.4 - - + +
200C TRP* 4.6 5.2 - - + +
226C TRP 4.5 1.8 - - - +
227C LYS* 2.7 16.8 + - - +
229C VAL* 1.3 82.8 - - + +
231C LYS* 1.3 65.0 + - + -
233C VAL* 3.2 13.4 + - + +
234C VAL* 3.1 33.4 + - + +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LYS* 2.7 77.9 + - - +
228C ASN* 2.8 17.1 + - - +
230C HIS* 1.3 77.0 - - + +
232C GLN* 1.3 56.7 + - - +
234C VAL* 3.3 10.7 - - + +
235C GLU* 3.1 36.2 + - + +
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Residues in contact with GLN 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 2.9 38.1 - - + +
175C GLU* 3.7 17.8 + - - -
176C LYS* 5.8 3.5 + - - +
228C ASN* 2.4 39.1 + - - +
229C VAL* 3.2 8.9 - - - +
231C LYS* 1.3 72.0 - - - +
233C VAL* 1.3 59.8 + - - +
235C GLU* 4.2 3.3 - - - +
236C GLY* 2.8 27.2 + - - -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP* 4.2 31.4 - - + +
168C ARG* 3.9 15.7 - - + +
169C PHE* 3.7 36.8 - - + +
172C LEU* 3.4 17.7 - - + -
188C VAL* 5.0 4.3 - - + -
196C SER* 5.7 1.3 - - - -
229C VAL 2.6 27.1 + - - +
230C HIS* 3.2 22.4 + - + +
232C GLN* 1.3 71.0 - - - +
234C VAL* 1.3 72.9 + - + +
236C GLY* 2.9 16.1 + - - -
237C GLY 3.4 2.9 + - - -
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Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP* 5.9 2.0 - - - -
193C GLY 3.1 27.8 - - - +
194C ASP* 3.4 30.5 - - + +
196C SER* 5.3 2.2 - - - -
230C HIS* 3.1 30.5 - - + +
231C LYS* 3.3 17.0 - - + +
233C VAL* 1.3 75.8 - - + +
235C GLU* 1.3 74.9 + - + +
237C GLY* 2.7 17.8 + - - -
238C TYR* 3.9 7.8 + - + -
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 3.1 18.1 + - + +
232C GLN* 4.2 3.1 - - - +
234C VAL* 1.3 83.2 - - + +
236C GLY* 1.3 52.5 + - - +
237C GLY 2.8 0.5 + - - -
238C TYR* 2.6 44.7 + - - +
239C GLU* 3.1 31.8 + - + +
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.1 23.6 - - - -
168C ARG* 4.5 0.9 - - - -
232C GLN 2.8 17.9 + - - -
233C VAL 3.1 10.1 - - - -
234C VAL 2.8 0.4 + - - -
235C GLU* 1.3 74.6 - - - +
237C GLY* 1.3 56.8 + - - +
239C GLU* 4.2 8.7 - - - +
240C VAL* 2.8 27.7 + - - +
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Residues in contact with GLY 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ARG* 4.4 20.0 - - - -
233C VAL 3.4 3.2 + - - -
234C VAL 2.7 16.5 + - - -
236C GLY* 1.3 73.4 - - - -
238C TYR* 1.3 63.6 - - - +
240C VAL* 3.1 21.4 - - - +
241C LEU* 4.0 7.7 + - - +
247C THR* 5.3 5.2 + - - -
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLY 5.4 3.1 - - - -
104C THR* 3.1 54.9 + - + +
105C ARG* 3.7 11.9 - - + +
193C GLY* 5.3 5.7 - - - -
194C ASP* 3.1 39.4 + - - -
234C VAL* 4.3 10.5 - - + -
235C GLU* 2.6 32.9 + - - +
237C GLY* 1.3 69.3 - - - -
239C GLU* 1.3 62.8 + - - +
240C VAL 3.0 2.9 + - - -
241C LEU* 3.1 24.0 + - + +
242C ASP* 3.2 19.6 + - - +
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 5.7 5.2 - - + -
235C GLU* 3.1 26.9 + - + +
236C GLY* 4.3 9.4 - - - +
237C GLY 3.6 0.2 - - - -
238C TYR* 1.3 75.0 - - - +
240C VAL* 1.3 61.9 + - - +
242C ASP* 3.7 14.5 + - - +
243C MET* 3.1 44.8 + - + +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY* 4.1 17.2 - - - +
62A LEU* 5.5 4.0 - - + -
63A ASP* 4.1 29.2 - - + +
66A HIS* 3.9 15.7 - - + +
168C ARG* 4.6 4.0 - - - +
236C GLY 2.8 28.9 - - - +
237C GLY* 3.1 14.4 - - - +
239C GLU* 1.3 76.6 - - - +
241C LEU* 1.3 67.8 - - + +
243C MET* 3.0 15.0 + - - +
244C LYS* 3.0 16.8 + - + +
246C TYR 3.9 15.3 - - - +
247C THR* 4.9 8.3 - - - +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C MET* 3.7 25.1 - - + -
100C VAL* 4.1 4.7 - - - +
101C SER* 3.5 28.7 - - - +
102C GLY 6.0 0.2 - - - +
104C THR* 4.1 26.0 - - + +
237C GLY 4.5 7.4 - - - +
238C TYR* 3.1 15.8 + - + +
240C VAL* 1.3 76.1 - - + +
242C ASP* 1.3 82.4 + - - +
243C MET 2.6 4.5 + - - -
245C GLY* 2.7 27.2 + - - -
246C TYR* 3.5 28.7 - - - +
247C THR* 4.6 6.3 - - + +
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Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C SER* 3.6 25.7 + - - +
102C GLY 4.6 1.6 + - - -
238C TYR* 3.2 20.2 + - - +
239C GLU* 3.9 19.5 - - + +
240C VAL 3.2 0.4 - - - -
241C LEU* 1.3 89.8 - - - +
243C MET* 1.3 63.1 + - + +
245C GLY* 4.4 2.4 + - - -
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Residues in contact with MET 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 4.3 18.6 - - - +
56A LYS* 3.7 17.4 + - - +
58A ARG* 2.9 46.0 - - + +
59A GLY* 3.4 10.8 - - - -
62A LEU* 4.2 12.1 - - + -
239C GLU* 3.1 31.2 - - + +
240C VAL* 3.0 4.9 + - - +
241C LEU 2.6 5.1 + - - -
242C ASP* 1.3 80.3 - - + +
244C LYS* 1.3 60.5 + - - +
245C GLY 3.1 4.9 - - - -
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 4.2 15.3 - - + +
60A GLU* 2.3 65.0 + - + +
63A ASP* 2.8 21.1 + - - +
240C VAL* 3.0 16.8 + - + +
243C MET* 1.3 74.9 - - - +
245C GLY* 1.3 58.6 - - - +
246C TYR* 3.0 60.0 + - + +
248C SER* 2.5 30.3 + - - -
249C TRP* 4.1 6.7 - - - +
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Residues in contact with GLY 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET* 4.8 3.6 - - - +
241C LEU* 2.7 22.0 + - - -
242C ASP 4.6 2.0 - - - -
243C MET 3.1 2.0 - - - -
244C LYS* 1.3 80.2 - - - +
246C TYR* 1.3 72.5 + - - +
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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