Contacts of the helix formed by residues 214 - 226 (chain M) in PDB entry 6LTJ
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 THR 214 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206M TRP* 4.0 2.9 - - - -
211M LYS 4.7 5.4 - - - +
212M LEU 3.5 14.1 - - - +
213M MET* 1.3 77.1 - - - +
215M PRO* 1.3 74.3 - - - +
216M GLU* 2.9 25.0 + - - +
217M MET* 2.9 37.2 + - + +
218M PHE* 3.0 11.6 + - - +
242M ARG* 4.4 2.9 - - - -
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Residues in contact with PRO 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M TRP* 3.9 22.0 - - + -
213M MET 4.5 0.2 - - - +
214M THR* 1.3 85.1 - - - +
216M GLU* 1.3 56.5 + - - +
218M PHE* 3.7 3.1 - - + +
219M SER* 2.9 30.1 + - - -
238M ALA* 4.0 23.6 - - + +
241M ILE* 3.8 33.1 - - + +
242M ARG* 3.7 30.3 - - + +
245M ILE* 4.9 4.9 - - + -
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Residues in contact with GLU 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214M THR* 2.9 11.5 + - - +
215M PRO* 1.3 76.2 - - - +
217M MET* 1.3 60.4 + - + +
219M SER* 2.8 19.2 + - - +
220M GLU* 2.9 18.8 + - - +
234M VAL* 4.1 11.7 - - + +
235M PRO* 6.3 0.7 - - + -
238M ALA* 3.5 13.7 - - + +
242M ARG* 2.3 52.0 + - - -
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Residues in contact with MET 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M LEU 3.3 27.4 - - - +
213M MET* 4.1 13.7 - - + -
214M THR* 2.9 27.2 + - + +
216M GLU* 1.3 73.7 - - + +
218M PHE* 1.3 66.6 + - - +
220M GLU* 3.2 5.5 + - - +
221M ILE* 2.9 38.6 + - + +
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Residues in contact with PHE 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M PHE* 3.6 36.6 - + - -
206M TRP* 3.6 27.6 - + + -
213M MET* 4.1 10.3 - - - +
214M THR 3.0 8.3 + - - +
215M PRO 3.7 6.7 - - - +
217M MET* 1.3 77.5 - - - +
219M SER* 1.3 62.5 + - - +
221M ILE* 3.3 2.6 + - - +
222M LEU* 2.9 49.6 + - + +
237M ILE* 4.8 0.9 - - + -
241M ILE* 3.6 17.5 - - + -
484N THR* 6.2 0.2 - - + -
487N ARG* 3.9 24.0 - - - -
494N VAL* 3.7 17.3 - - + -
498N MET* 3.4 35.5 - - + +
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Residues in contact with SER 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215M PRO 2.9 17.0 + - - -
216M GLU* 2.8 21.0 + - - -
218M PHE* 1.3 81.0 - - - +
220M GLU* 1.3 56.4 + - - +
222M LEU* 3.8 4.8 - - - +
223M CYS* 2.9 32.2 + - - +
234M VAL* 3.2 27.2 + - - +
237M ILE* 3.6 34.9 - - - +
238M ALA 4.2 0.4 - - - -
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Residues in contact with GLU 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216M GLU 2.9 18.1 + - - +
217M MET* 3.6 7.4 - - - +
218M PHE 3.2 0.2 - - - -
219M SER* 1.3 74.1 + - - +
221M ILE* 1.3 66.8 + - + +
223M CYS* 3.1 8.2 - - - -
224M ASP* 2.9 28.8 + - + +
230M PRO* 3.9 18.1 - - - +
234M VAL* 3.2 26.9 - - - +
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Residues in contact with ILE 221 (chain M).
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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213M MET* 5.1 5.2 - - + -
217M MET* 2.9 31.3 + - + +
218M PHE 3.8 3.1 - - - +
220M GLU* 1.3 77.5 - - + +
222M LEU* 1.3 54.3 + - - +
224M ASP* 3.3 7.0 + - - +
225M ASP* 2.7 52.8 + - - +
483N SER* 4.5 8.7 - - - -
484N THR* 5.2 0.4 - - + -
498N MET* 3.7 31.4 - - + -
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Residues in contact with LEU 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M LEU* 4.3 9.2 - - + -
200M LEU* 4.1 16.4 - - + -
202M ASP* 5.5 0.9 - - + -
218M PHE* 2.9 39.9 + - + +
219M SER 3.8 2.5 - - - +
220M GLU 3.2 0.2 - - - -
221M ILE* 1.3 77.8 - - - +
223M CYS* 1.3 59.2 + - - +
225M ASP* 3.2 1.0 + - - +
226M LEU* 3.0 50.6 + - + +
228M LEU* 5.4 0.7 - - + -
237M ILE* 3.9 25.8 - - + -
484N THR* 3.6 28.5 - - + -
487N ARG* 3.8 16.2 - - - +
488N ARG* 4.6 1.3 - - - +
498N MET* 6.3 0.2 - - + -
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Residues in contact with CYS 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219M SER 2.9 17.4 + - - +
220M GLU* 3.1 25.6 - - - -
222M LEU* 1.3 77.3 - - - +
224M ASP* 1.3 58.2 + - - +
227M ASP* 3.0 6.6 + - - -
228M LEU* 2.7 57.3 + - + +
230M PRO* 3.6 27.8 - - + +
233M PHE* 4.6 6.5 - - + -
234M VAL* 3.5 22.7 - - + -
237M ILE* 5.1 1.6 - - + -
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Residues in contact with ASP 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220M GLU* 2.9 22.2 + - + +
221M ILE* 3.6 7.6 - - - +
222M LEU 3.2 0.2 - - - -
223M CYS* 1.3 78.8 - - - +
225M ASP* 1.3 72.7 + - - +
227M ASP* 3.1 18.3 - - - +
230M PRO* 6.3 0.9 - - - -
480N TYR* 5.7 3.6 - - - -
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Residues in contact with ASP 225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221M ILE* 2.7 36.8 + - - +
222M LEU 3.7 4.0 - - - +
224M ASP* 1.3 81.3 - - - +
226M LEU* 1.3 61.3 + - - +
227M ASP* 3.1 15.5 + - - +
480N TYR* 4.3 7.3 + - - -
482N THR* 3.1 42.4 - - - +
483N SER 3.9 3.2 + - - -
484N THR* 3.2 36.9 + - + +
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Residues in contact with LEU 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M LEU* 3.6 25.8 - - + -
222M LEU* 3.0 24.1 + - + +
225M ASP* 1.3 74.2 - - - +
227M ASP* 1.3 70.4 + - - +
228M LEU* 3.3 20.4 - - + +
482N THR* 6.0 0.2 - - - +
484N THR* 4.0 16.8 - - - +
488N ARG* 3.4 37.2 - - - +
45R GLN* 5.9 1.6 - - + -
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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