Contacts of the helix formed by residues 200 - 213 (chain D) in PDB entry 4LML
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 ILE 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A GLU* 3.2 25.8 - - - +
247A LYS* 5.9 0.4 - - - +
196D TYR* 2.9 33.6 + - + +
199D ASN* 1.3 80.1 - - + +
201D ILE* 1.3 74.8 + - + +
202D LEU 3.6 0.2 - - - -
203D PRO* 3.5 3.1 - - - +
204D MET* 3.2 36.9 + - + +
237D PHE* 4.0 17.8 - - + -
240D LEU* 3.8 23.3 - - + -
241D VAL* 4.1 24.9 - - + -
254D THR* 6.1 4.5 - - + -
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 5.5 8.5 - - + -
120D PHE* 5.2 15.3 - - + -
196D TYR* 2.7 35.9 + - + +
197D ILE* 3.7 15.7 - - + +
200D ILE* 1.3 79.3 - - + +
202D LEU* 1.3 71.9 + - + +
204D MET* 3.5 13.3 - - + +
205D LEU* 3.0 43.3 + - + +
254D THR* 5.8 7.4 - - + -
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PHE* 3.5 36.8 - - + -
197D ILE* 3.0 39.9 + - + +
201D ILE* 1.3 82.7 - - + +
203D PRO* 1.4 64.4 - - + +
205D LEU* 3.2 23.0 + - + +
206D PHE* 2.9 53.4 + - + -
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Residues in contact with PRO 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PHE* 5.2 0.9 - - + -
262A TYR* 3.4 54.1 - - + +
197D ILE 3.6 8.1 - - - +
198D PRO 3.6 8.3 - - - +
199D ASN 3.2 18.8 - - - +
200D ILE 3.5 8.3 - - - +
202D LEU* 1.4 93.6 - - + +
204D MET* 1.3 55.5 + - - +
206D PHE* 3.3 6.8 + - + +
207D ILE* 3.0 34.9 + - - +
237D PHE* 3.9 12.6 - - + -
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Residues in contact with MET 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ILE* 3.2 27.4 + - + +
201D ILE* 3.5 15.0 - - + +
203D PRO* 1.3 74.2 - - - +
205D LEU* 1.3 69.5 + - + +
207D ILE* 3.2 12.0 - - + +
208D LEU* 3.0 23.6 + - - +
234D HIS* 3.7 32.7 - - + -
237D PHE* 4.5 27.9 - - + -
254D THR* 6.1 4.0 - - + -
257D ILE* 5.0 13.0 - - + -
258D ILE* 4.5 16.8 - - + -
261D ILE* 4.1 21.3 - - + +
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 3.0 29.7 + - + +
202D LEU* 3.2 30.3 + - + +
204D MET* 1.3 82.4 - - + +
206D PHE* 1.3 59.7 + - + +
208D LEU* 3.2 10.2 + - + +
209D PHE* 3.0 48.9 + - + -
261D ILE* 5.9 3.1 - - + -
302D PHE* 4.3 26.9 - - + -
306D ASN* 6.0 1.1 - - - +
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Residues in contact with PHE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 6.4 0.4 - - + -
259A PHE* 3.8 12.8 - + - -
262A TYR* 4.1 28.0 - + + +
263A LEU* 3.3 38.1 - - + -
266A PHE* 3.8 35.8 - + + -
202D LEU* 2.9 39.8 + - + -
203D PRO* 3.4 8.7 - - + +
205D LEU* 1.3 79.7 - - + +
207D ILE* 1.3 60.1 + - + +
209D PHE* 3.0 13.1 + + - +
210D ILE* 2.9 34.4 + - + +
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.1 24.7 - - + -
235A ILE* 4.1 17.3 - - + -
262A TYR* 5.4 2.7 - - + -
203D PRO* 3.0 20.3 + - + +
204D MET* 3.2 21.5 - - - +
206D PHE* 1.3 73.3 - - + +
208D LEU* 1.3 57.4 + - - +
210D ILE* 4.2 8.3 - - - -
211D SER* 2.9 27.7 + - - -
230D THR* 3.4 36.3 - - + +
233D ALA* 4.1 8.5 - - + -
234D HIS* 3.7 28.9 - - + +
237D PHE* 4.6 5.8 - - + -
265D TYR* 3.3 6.4 + - - +
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D MET* 3.0 18.6 + - + +
205D LEU* 3.3 8.5 - - + +
206D PHE 3.1 0.2 - - - -
207D ILE* 1.3 76.5 - - - +
209D PHE* 1.3 73.2 + - + +
211D SER* 2.4 25.2 + - - +
212D TRP* 3.5 21.6 + - + -
234D HIS* 6.1 0.2 - - + -
261D ILE* 3.8 21.8 - - + -
264D PHE* 4.9 9.0 - - + -
265D TYR* 3.6 34.1 - - + +
302D PHE* 3.6 42.0 - - + -
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Residues in contact with PHE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PHE* 3.5 31.4 - + + -
270A ILE* 6.6 0.2 - - - -
205D LEU* 3.0 37.7 + - + -
206D PHE* 3.0 8.7 + + - +
208D LEU* 1.3 84.5 - - + +
210D ILE* 1.3 65.3 + - - +
211D SER 3.1 1.1 - - - -
212D TRP* 2.9 54.9 - + - +
213D THR* 3.0 9.3 + - - -
302D PHE* 4.5 16.8 - + - -
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A VAL* 4.6 5.4 - - + -
231A LEU* 3.7 26.9 - - + -
265A TYR 4.3 0.7 - - - +
266A PHE* 3.5 32.9 - - + +
269A VAL* 3.6 44.0 - - + -
270A ILE* 6.5 0.4 - - - -
206D PHE* 2.9 22.6 + - + +
207D ILE* 3.9 5.8 - - - +
209D PHE* 1.3 74.2 - - - +
211D SER* 1.3 64.7 + - - +
213D THR* 3.1 28.8 - - - +
226D LEU* 3.1 19.8 - - + +
230D THR* 4.1 8.3 - - + -
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Residues in contact with SER 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ILE 2.9 16.9 + - - -
208D LEU* 2.4 27.1 + - - +
210D ILE* 1.3 78.8 - - - +
212D TRP* 1.3 68.5 + - - +
213D THR 3.5 0.3 + - - -
214D ALA* 3.8 9.0 + - - +
226D LEU* 4.1 5.2 - - - +
227D VAL* 4.0 22.1 - - - +
230D THR* 3.2 29.6 - - - +
265D TYR* 3.7 17.2 - - - -
268D ALA* 6.2 0.7 - - - -
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Residues in contact with TRP 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D LEU* 3.8 20.4 - - + -
209D PHE* 2.9 64.7 + + - +
211D SER* 1.3 79.1 + - - +
213D THR* 1.3 57.9 + - - +
214D ALA* 2.8 13.0 + - - +
215D PHE* 3.2 41.5 + + + +
216D TRP* 4.3 5.4 - + - -
227D VAL* 5.9 0.4 - - - -
264D PHE* 4.2 19.7 - + + -
268D ALA* 5.4 6.5 - - + -
298D PHE* 3.3 60.1 - + + -
299D PRO* 4.0 20.7 - - + +
302D PHE* 3.8 21.1 - + + -
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Residues in contact with THR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TYR* 4.2 5.4 + - - +
269A VAL* 4.0 13.9 - - + +
270A ILE* 4.2 13.6 - - - +
273A THR* 3.0 46.0 + - - +
209D PHE 3.0 11.2 + - - -
210D ILE* 3.1 25.4 + - - +
212D TRP* 1.3 77.3 - - - +
214D ALA* 1.3 57.9 + - - +
215D PHE 3.1 6.3 + - - -
216D TRP* 3.3 18.2 + - - +
217D SER 4.5 0.5 + - - -
226D LEU* 3.9 18.8 - - + -
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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