Contacts of the helix formed by residues 200 - 213 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D GLU* 3.3 27.4 - - - +
196E TYR* 2.8 34.0 + - + +
199E ASN* 1.3 80.6 - - + +
201E ILE* 1.3 74.8 + - + +
202E LEU 3.7 0.2 - - - -
203E PRO* 3.5 1.1 - - - +
204E MET* 3.0 39.9 + - + +
237E PHE* 4.0 16.9 - - + -
240E LEU* 3.9 20.9 - - + -
241E VAL* 3.8 27.8 - - + -
254E THR* 5.6 6.5 - - + -
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Residues in contact with ILE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E PRO* 5.3 4.9 - - + -
120E PHE* 5.2 17.5 - - + -
196E TYR* 2.8 34.1 + - + +
197E ILE* 3.8 15.3 - - + +
200E ILE* 1.3 78.6 - - + +
202E LEU* 1.3 78.0 + - + +
204E MET* 3.4 9.7 - - + +
205E LEU* 2.9 34.5 + - + +
253E TYR* 6.4 1.6 - - + -
254E THR* 4.9 17.5 - - + -
257E ILE* 4.9 13.0 - - + -
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Residues in contact with LEU 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D PHE* 3.4 35.2 - - + -
197E ILE* 2.9 41.4 + - + +
201E ILE* 1.3 82.9 - - + +
203E PRO* 1.4 58.5 - - + +
205E LEU* 3.1 25.9 + - + +
206E PHE* 2.8 47.8 + - + -
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Residues in contact with PRO 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D PHE* 5.3 1.3 - - + -
262D TYR* 3.8 35.0 - - + -
197E ILE 3.3 12.3 - - - +
198E PRO 3.1 20.6 - - - +
199E ASN 3.2 17.3 - - - +
200E ILE 3.5 7.4 - - - +
202E LEU* 1.4 90.6 - - + +
204E MET* 1.3 57.3 + - - +
206E PHE* 3.2 12.3 + - + +
207E ILE* 2.9 35.4 + - - +
237E PHE* 3.9 10.3 - - + -
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Residues in contact with MET 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ILE* 3.0 28.4 + - + +
201E ILE* 3.4 12.3 - - + +
203E PRO* 1.3 76.6 - - - +
205E LEU* 1.3 65.8 + - + +
207E ILE* 3.3 9.9 - - + +
208E LEU* 3.0 24.8 + - - +
234E HIS* 3.8 24.6 - - + -
237E PHE* 4.5 24.6 - - + -
254E THR* 5.6 3.1 - - + -
257E ILE* 4.2 20.6 - - + -
258E ILE* 3.8 32.8 - - + -
261E ILE* 3.6 23.1 - - + -
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E ILE* 2.9 26.5 + - + +
202E LEU* 3.1 36.1 + - + +
204E MET* 1.3 78.4 - - + +
206E PHE* 1.3 57.8 + - + +
208E LEU* 3.2 8.1 + - + +
209E PHE* 2.9 53.4 + - + -
257E ILE* 6.5 1.1 - - + -
261E ILE* 5.6 4.3 - - + -
302E PHE* 3.7 35.2 - - + -
306E ASN* 5.9 1.8 - - - +
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Residues in contact with PHE 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LEU* 6.4 0.4 - - + -
259D PHE* 3.9 13.7 - + - -
262D TYR* 4.3 25.4 - + + -
263D LEU* 3.5 34.1 - - + -
266D PHE* 4.4 29.2 - + + -
202E LEU* 2.8 38.0 + - + -
203E PRO* 3.2 15.0 + - + +
205E LEU* 1.3 70.5 - - + +
207E ILE* 1.3 63.0 + - + +
209E PHE* 3.0 23.5 + + - +
210E ILE* 2.9 37.7 + - + +
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Residues in contact with ILE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LEU* 4.6 13.5 - - + -
235D ILE* 3.9 26.2 - - + -
262D TYR* 5.3 3.4 - - + -
203E PRO* 2.9 18.4 + - + +
204E MET* 3.3 14.4 - - - +
206E PHE* 1.3 72.8 - - + +
208E LEU* 1.3 60.5 + - + +
210E ILE* 4.2 8.3 - - - -
211E SER* 2.9 21.7 + - - -
230E THR* 3.4 36.0 - - + +
233E ALA* 3.8 10.1 - - + +
234E HIS* 3.5 26.7 - - + +
237E PHE* 4.4 9.2 - - + -
265E TYR* 3.2 14.4 + - - +
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Residues in contact with LEU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E MET 3.0 19.1 + - - +
205E LEU* 3.3 6.1 - - - +
206E PHE 3.0 0.2 - - - -
207E ILE* 1.3 76.4 - - + +
209E PHE* 1.3 70.4 + - + +
211E SER* 3.2 16.1 - - - +
212E TRP* 3.5 30.1 + - + -
261E ILE* 3.6 22.2 - - + -
264E PHE* 4.8 7.9 - - + -
265E TYR* 3.5 32.1 - - + +
302E PHE* 3.4 46.4 - - + -
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Residues in contact with PHE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D PHE* 3.9 22.2 - + + -
205E LEU* 2.9 48.6 + - + -
206E PHE* 3.0 22.0 + + - +
208E LEU* 1.3 76.8 - - + +
210E ILE* 1.3 66.6 + - - +
211E SER 3.1 1.1 - - - -
212E TRP* 3.1 36.8 - + - +
213E THR* 3.0 21.3 + - - -
302E PHE* 4.3 21.5 - + - -
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Residues in contact with ILE 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D VAL* 5.2 5.8 - - + -
231D LEU* 3.9 27.8 - - + -
265D TYR 4.9 0.4 - - - +
266D PHE* 3.6 35.8 - - + +
269D VAL* 4.1 33.9 - - + -
206E PHE* 2.9 26.1 + - + +
207E ILE* 3.9 5.6 - - - +
209E PHE* 1.3 75.5 - - - +
211E SER* 1.3 62.8 + - - +
213E THR* 3.2 25.1 - - - +
226E LEU* 3.2 18.5 - - + +
230E THR* 4.3 9.2 - - + -
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Residues in contact with SER 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ILE 2.9 17.3 + - - -
208E LEU* 3.2 14.5 + - - +
209E PHE 3.1 0.6 - - - -
210E ILE* 1.3 78.6 - - - +
212E TRP* 1.3 61.7 + - - +
213E THR 3.6 0.5 + - - -
214E ALA* 4.0 8.3 + - - +
226E LEU* 4.3 5.4 - - - +
227E VAL* 3.9 25.6 - - - +
230E THR* 3.3 24.8 + - - +
265E TYR* 3.5 26.5 - - - -
268E ALA* 5.0 4.5 - - - +
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Residues in contact with TRP 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E LEU* 4.0 24.5 - - + -
209E PHE* 3.1 45.1 + + - +
211E SER* 1.3 79.3 - - - +
213E THR* 1.3 62.2 + - - +
214E ALA* 2.9 8.0 + - - +
215E PHE* 3.4 42.7 + + + +
216E TRP* 4.3 4.6 - + - -
227E VAL* 5.8 0.4 - - - -
264E PHE* 3.9 23.3 - + + -
268E ALA* 5.4 5.6 - - + -
298E PHE* 3.5 47.8 - + + -
299E PRO* 3.7 29.8 - - + +
302E PHE* 3.7 22.4 - + + -
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Residues in contact with THR 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D TYR* 5.1 6.1 + - - +
269D VAL* 4.4 14.0 - - + +
270D ILE* 4.7 9.0 - - - +
273D THR* 3.6 32.2 + - - +
209E PHE 3.0 11.8 + - - -
210E ILE* 3.2 24.0 - - - +
211E SER 3.3 0.2 - - - -
212E TRP* 1.3 77.9 - - - +
214E ALA* 1.3 58.2 + - - +
215E PHE 3.0 7.3 + - - -
216E TRP* 3.3 25.8 + - - +
217E SER 4.8 0.3 + - - -
226E LEU* 4.0 14.8 - - + -
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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