Contacts of the helix formed by residues 202 - 217 (chain L) in PDB entry 6O81
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 GLU 202 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198L CYS* 5.1 0.3 - - - +
200L GLY* 4.9 0.4 - - - -
201L TYR* 1.3 89.0 - - + +
203L GLY* 1.3 59.0 + - - +
204L ILE 3.6 1.6 - - - -
205L ASP* 3.7 21.5 - - + +
206L ALA* 3.0 28.5 + - + +
342S LYS* 5.1 5.4 - - - -
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Residues in contact with GLY 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L CYS* 3.3 35.7 + - - +
200L GLY* 4.3 5.1 + - - -
201L TYR 3.3 7.5 + - - -
202L GLU* 1.3 76.0 - - - +
204L ILE* 1.3 58.7 + - - +
206L ALA* 3.8 1.9 - - - +
207L VAL* 2.9 27.8 + - - +
342S LYS 4.5 3.4 + - - -
343S ILE* 6.1 0.2 - - - -
344S ASP* 5.0 9.4 - - - -
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Residues in contact with ILE 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L GLY* 1.3 72.9 - - - +
205L ASP* 1.3 59.5 + - - +
207L VAL* 3.7 7.5 - - - +
208L LYS* 2.9 30.3 + - - +
274S LEU 5.7 4.3 - - - +
276S GLY* 5.6 5.2 - - - +
342S LYS* 4.4 15.8 + - + +
343S ILE 3.6 24.0 - - - +
344S ASP* 4.6 8.7 - - - +
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Residues in contact with ASP 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202L GLU* 3.6 23.6 + - + +
203L GLY 3.3 0.4 - - - -
204L ILE* 1.3 78.8 - - - +
206L ALA* 1.3 57.5 + - - +
208L LYS* 3.4 5.3 + - - +
209L GLU* 2.9 29.0 + - - +
342S LYS* 5.5 6.0 + - + +
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Residues in contact with ALA 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L CYS* 4.4 13.5 - - + -
202L GLU* 3.0 20.5 + - + +
203L GLY 3.9 2.9 - - - +
205L ASP* 1.3 73.2 - - - +
207L VAL* 1.3 60.3 + - - +
209L GLU* 3.7 7.7 - - - +
210L ALA* 2.9 30.1 + - - +
260L LYS 5.3 1.9 - - - +
261L ILE* 5.8 2.0 - - - -
264L LYS* 3.8 30.3 - - + +
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Residues in contact with VAL 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL* 5.2 10.3 - - - +
197L ALA* 5.4 8.5 - - - +
198L CYS* 5.3 1.9 - - - +
203L GLY 2.9 18.7 + - - +
204L ILE* 3.7 8.7 - - - +
205L ASP 3.3 0.2 - - - -
206L ALA* 1.3 77.2 - - - +
208L LYS* 1.3 56.1 + - - +
210L ALA* 3.4 6.2 + - - +
211L LEU* 2.9 28.8 + - - +
234L TYR* 5.5 10.3 - - + -
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Residues in contact with LYS 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L ILE 2.9 17.8 + - - +
205L ASP* 3.8 6.1 - - - +
207L VAL* 1.3 77.2 - - - +
209L GLU* 1.3 58.2 + - - +
211L LEU* 3.7 6.9 - - - +
212L ARG* 2.9 29.1 + - - +
271S VAL 4.7 13.1 - - - +
272S ASP* 5.6 4.7 - - - +
274S LEU* 6.2 2.5 - - + -
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Residues in contact with GLU 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L ASP 2.9 18.1 + - - +
206L ALA* 3.7 7.9 - - - +
208L LYS* 1.3 74.1 - - - +
210L ALA* 1.3 60.6 + - - +
212L ARG* 3.4 6.2 + - - +
213L ALA* 2.9 29.3 + - - +
260L LYS* 5.4 0.9 - - - -
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Residues in contact with ALA 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L VAL* 5.7 6.3 - - + -
206L ALA 2.9 17.8 + - - +
207L VAL* 3.8 6.3 - - - +
208L LYS 3.4 0.2 - - - -
209L GLU* 1.3 72.4 - - - +
211L LEU* 1.3 60.8 + - - +
213L ALA* 3.4 1.8 + - - +
214L GLY* 2.9 25.3 + - - -
257L ILE* 4.2 22.3 - - + +
260L LYS* 4.1 26.4 - - + +
261L ILE* 4.5 11.0 - - + +
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Residues in contact with LEU 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L VAL 2.9 18.3 + - - +
208L LYS* 3.7 8.1 - - - +
210L ALA* 1.3 77.6 - - - +
212L ARG* 1.3 56.0 + - - +
214L GLY* 3.4 1.9 + - - -
215L LEU* 2.9 29.8 + - - +
226L ILE* 5.4 9.5 - - + +
271S VAL* 4.2 29.2 - - + +
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Residues in contact with ARG 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L LYS 2.9 18.1 + - - +
209L GLU* 3.8 6.1 - - - +
210L ALA 3.3 0.2 - - - -
211L LEU* 1.3 76.7 - - - +
213L ALA* 1.3 58.6 + - - +
215L LEU* 3.8 5.8 - - - +
216L ASN* 2.9 30.5 + - - +
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Residues in contact with ALA 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L GLU 2.9 17.0 + - - +
210L ALA* 3.8 7.6 - - - +
211L LEU 3.3 0.2 - - - -
212L ARG* 1.3 76.2 - - - +
214L GLY* 1.3 62.0 + - - +
216L ASN* 3.6 6.5 + - - +
217L CYS* 3.4 21.3 + - - +
256L VAL* 5.1 9.2 - - + +
260L LYS* 4.4 15.3 - - + -
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Residues in contact with GLY 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L ALA 2.9 16.6 + - - -
211L LEU* 3.8 1.8 - - - -
212L ARG 3.3 0.2 - - - -
213L ALA* 1.3 78.1 - - - +
215L LEU* 1.3 60.6 + - - +
217L CYS* 3.5 14.9 + - - +
218L SER 3.9 4.3 + - - -
224L ILE* 4.6 7.7 - - - +
253L ALA* 4.3 26.0 - - - +
256L VAL* 5.5 0.4 - - - -
257L ILE* 4.9 7.5 - - - +
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Residues in contact with LEU 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L LEU 2.9 17.9 + - - +
212L ARG* 4.0 6.3 - - - +
214L GLY* 1.3 76.5 - - - +
216L ASN* 1.3 63.8 + - - +
218L SER* 3.5 17.8 + - - +
224L ILE 4.5 16.6 - - - +
226L ILE* 6.1 4.0 - - + +
271S VAL* 6.0 4.5 - - + -
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Residues in contact with ASN 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L ARG 2.9 18.4 + - - +
213L ALA* 3.9 8.3 - - - +
214L GLY 3.3 0.4 - - - -
215L LEU* 1.3 77.7 - - - +
217L CYS* 1.3 56.7 + - - +
218L SER 3.2 6.6 + - - +
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Residues in contact with CYS 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ALA 3.4 14.3 + - - +
214L GLY* 3.5 10.0 + - - +
215L LEU 3.3 0.6 - - - -
216L ASN* 1.3 76.5 - - - +
218L SER* 1.3 61.9 + - - +
219L THR* 3.4 4.3 + - - -
249L VAL 5.7 0.7 - - - +
252L GLN 5.7 0.7 - - - +
253L ALA* 4.9 17.2 - - - +
256L VAL* 4.9 9.2 - - + -
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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