Contacts of the helix formed by residues 194 - 216 (chain A) in PDB entry 1L6N
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 HIS 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE* 3.3 15.2 - - + -
193A GLY* 1.3 82.8 + - - +
195A GLN* 1.3 82.6 + - + +
196A ALA* 3.1 9.0 - - + +
197A ALA* 3.0 16.2 + - + +
198A MET* 2.9 24.8 + - - +
277A TYR* 3.9 32.4 - + - -
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 1.3 85.8 - - + +
196A ALA* 1.3 57.8 + - + +
198A MET* 3.2 9.0 + - - +
199A GLN* 2.7 36.1 + - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 3.1 10.5 - - + -
195A GLN* 1.3 86.0 - - + +
197A ALA* 1.3 61.5 + - - +
199A GLN* 3.0 22.1 + - - +
200A MET* 3.1 22.3 + - + +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.7 16.2 - - + -
194A HIS* 3.0 14.5 + - + +
196A ALA* 1.3 79.8 - - - +
198A MET* 1.3 63.2 + - - +
199A GLN 3.2 0.3 + - - -
200A MET* 3.2 16.9 + - + +
201A LEU 2.9 18.9 + - - -
273A ILE* 3.2 42.6 - - + +
277A TYR* 6.3 0.7 - - + -
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Residues in contact with MET 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 5.5 5.6 - - - -
188A LEU* 3.4 37.9 - - + +
191A VAL* 3.3 42.6 - - + -
193A GLY 6.0 1.1 - - - -
194A HIS 2.9 16.3 + - - +
195A GLN* 3.5 12.6 - - - +
197A ALA* 1.3 77.6 - - - +
199A GLN* 1.3 63.5 + - - +
201A LEU* 3.4 17.6 + - + +
202A LYS* 3.0 23.2 + - - +
270A LEU* 4.7 11.9 - - + -
273A ILE* 5.2 1.8 - - - -
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLN 2.7 17.0 + - - +
196A ALA* 3.1 16.3 - - - +
198A MET* 1.3 73.3 - - - +
200A MET* 1.3 71.1 + - - +
202A LYS* 3.0 18.9 + - + +
203A GLU* 3.1 16.3 + - - +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA* 3.1 10.4 + - + +
197A ALA* 3.6 22.2 - - + +
199A GLN* 1.3 84.1 - - + +
201A LEU* 1.3 59.2 + - - +
203A GLU* 2.9 30.9 + - - +
204A THR* 2.9 15.6 + - - -
272A LYS* 6.2 2.0 - - + -
273A ILE* 4.7 9.2 - - + -
276A MET* 3.4 43.1 - - + -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.5 31.4 - - + -
197A ALA 2.9 8.5 + - - +
198A MET* 3.5 28.5 - - + +
199A GLN 3.2 0.2 - - - -
200A MET* 1.3 76.4 - - - +
202A LYS* 1.3 52.9 - - + +
204A THR* 3.2 2.3 + - - -
205A ILE* 2.7 48.5 + - + +
266A ILE* 2.9 42.4 - - + +
269A GLY* 3.3 24.9 - - - +
270A LEU* 3.3 12.3 - - + +
273A ILE* 3.4 18.7 - - + +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A MET 3.0 13.2 + - - +
199A GLN* 3.0 12.8 + - + +
201A LEU* 1.3 78.6 - - + +
203A GLU* 1.3 54.1 + - - +
205A ILE* 4.3 7.4 - - + -
206A ASN* 2.8 58.9 + - - +
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLN* 3.1 12.5 + - - +
200A MET* 2.9 22.9 + - - +
202A LYS* 1.3 75.5 - - - +
204A THR* 1.3 54.4 + - - +
206A ASN* 3.8 3.6 - - - +
207A GLU* 2.7 55.7 + - + +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A MET 2.9 11.0 + - - -
201A LEU 3.7 4.5 - - - -
203A GLU* 1.3 75.0 + - - +
205A ILE* 1.3 56.3 + - - +
207A GLU* 3.5 6.7 + - - +
208A GLU* 2.4 55.7 + - - +
265A TRP 4.1 1.3 - - - +
268A LEU* 3.7 15.4 - - + +
269A GLY* 3.4 35.2 - - - +
272A LYS* 4.8 17.3 + - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 4.9 3.6 - - + -
201A LEU* 2.7 40.1 + - + +
202A LYS* 3.8 7.9 - - + +
204A THR* 1.3 70.3 - - - +
206A ASN* 1.3 66.9 + - - +
208A GLU* 2.9 23.2 + - - +
209A ALA* 3.2 5.5 + - - +
237A ALA* 6.3 2.2 - - + -
262A TYR* 3.7 20.6 - - + -
265A TRP* 3.3 45.9 - - + +
266A ILE* 3.2 39.0 - - + +
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 2.8 54.8 + - - +
203A GLU* 3.9 4.7 - - - +
205A ILE* 1.3 78.1 - - - +
207A GLU* 1.3 64.2 + - + +
209A ALA* 3.2 17.4 + - - +
210A ALA* 3.2 12.8 + - - +
237A ALA* 5.6 6.7 - - - +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 2.7 45.3 + - + +
204A THR* 3.6 7.8 + - - +
206A ASN* 1.3 73.2 - - + +
208A GLU* 1.3 56.2 + - - +
210A ALA* 3.3 4.9 + - + -
211A GLU* 2.4 64.9 + - - +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A THR* 2.4 44.2 + - - +
205A ILE* 2.9 14.1 + - - +
207A GLU* 1.3 79.5 - - - +
209A ALA* 1.3 50.1 + - - +
211A GLU* 3.5 12.4 + - - +
212A TRP* 2.7 35.7 + - - +
265A TRP* 3.1 39.1 + - + +
268A LEU* 3.4 30.3 - - + +
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ILE 3.2 3.2 + - - +
206A ASN* 3.2 11.3 + - - +
208A GLU* 1.3 77.0 - - - +
210A ALA* 1.3 61.1 + - - +
212A TRP* 3.0 2.5 + - - +
213A ASP* 2.8 32.8 + - - +
233A GLY* 2.9 44.5 - - - +
234A SER* 3.5 8.1 - - - +
237A ALA* 5.2 2.9 - - + -
265A TRP* 3.7 12.5 - - + -
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASN 3.2 10.1 + - - +
207A GLU* 3.7 10.1 - - + +
209A ALA* 1.3 78.7 - - - +
211A GLU* 1.3 59.5 - - - +
213A ASP* 3.4 7.7 + - - +
214A ARG* 2.8 35.5 + - - +
234A SER* 5.5 2.2 + - - -
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU* 2.4 64.0 + - - +
208A GLU* 3.8 14.3 - - - +
210A ALA* 1.3 77.2 - - - +
212A TRP* 1.3 67.5 + - - +
214A ARG* 3.0 19.0 - - + +
215A LEU* 2.9 30.8 + - + +
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Residues in contact with TRP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU 2.7 23.3 + - - +
209A ALA* 3.3 5.6 - - - +
211A GLU* 1.3 72.6 - - - +
213A ASP* 1.3 52.2 + - - +
215A LEU* 2.9 46.1 + - + +
216A HIS* 2.6 78.9 + + - +
231A PRO 4.4 8.5 + - - -
232A ARG* 4.2 0.9 - - - -
233A GLY* 3.4 30.6 - - - +
236A ILE* 4.4 12.7 - - + +
261A ILE* 4.7 19.3 - - + -
265A TRP* 4.6 8.5 - + + +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 2.8 18.6 + - - +
210A ALA* 3.7 6.3 - - - +
212A TRP* 1.3 76.6 - - - +
214A ARG* 1.3 64.1 + - - +
216A HIS* 2.6 36.3 - - - +
218A VAL* 4.0 4.7 - - - +
232A ARG* 3.3 37.2 + - + +
233A GLY 4.5 0.2 - - - +
234A SER* 5.9 1.3 - - - +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ALA 2.8 14.8 + - - +
211A GLU* 3.0 28.3 - - + +
212A TRP 3.0 0.2 - - - -
213A ASP* 1.3 82.9 - - - +
215A LEU* 1.3 58.3 + - - +
216A HIS 3.6 1.4 + - - -
217A PRO* 5.1 0.5 - - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 2.9 18.1 + - + +
212A TRP* 3.1 50.0 - - + +
214A ARG* 1.3 76.9 - - + +
216A HIS* 1.3 60.9 + - + +
217A PRO* 3.2 12.3 - - - +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP* 2.6 60.9 + + + +
213A ASP* 2.6 27.4 + - - +
214A ARG 4.8 0.9 - - - -
215A LEU* 1.3 80.1 + - - +
217A PRO* 1.4 67.4 + - + +
218A VAL* 3.2 29.2 + - + +
230A GLU* 4.2 24.0 + - + +
231A PRO 4.9 9.4 + - - -
232A ARG* 5.6 1.8 - - + -
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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
------------------------------------------------------------
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