Contacts of the helix formed by residues 208 - 222 (chain C) in PDB entry 3HUU
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 ASP 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ASN* 2.7 34.2 + - - +
39C PHE* 5.7 0.9 - - - +
150C GLU* 3.5 27.4 - - - +
160C ARG* 4.5 5.9 + - - +
206C THR* 3.2 3.3 + - - -
207C SER* 1.3 82.4 + - - +
209C VAL* 1.3 76.5 + - - +
210C MET* 3.4 13.1 + - - +
211C LEU* 3.3 10.4 + - + +
212C ASN 3.0 20.8 + - - -
234C THR* 3.1 12.7 + - - -
235C PHE 4.0 5.9 - - - +
236C ASN* 4.3 6.6 + - - +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 5.2 0.9 - - - +
38C PRO* 5.0 3.6 - - + -
208C ASP* 1.3 78.0 - - - +
210C MET* 1.3 60.1 + - + +
212C ASN* 3.2 6.9 + - + +
213C MET* 3.0 28.6 + - + +
234C THR* 3.4 7.2 + - + -
235C PHE 2.8 21.8 - - - +
236C ASN* 3.1 34.5 - - + +
238C SER* 4.3 2.0 - - - +
240C LEU* 3.9 28.5 - - + -
241C THR* 3.6 23.6 - - + +
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Residues in contact with MET 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.8 20.0 - - + +
36C GLN* 3.7 34.1 - - + +
37C ASN* 3.7 30.1 - - - +
38C PRO* 4.3 2.0 - - - -
208C ASP* 3.4 6.0 + - - +
209C VAL* 1.3 73.5 - - - +
211C LEU* 1.3 65.8 + - - +
213C MET* 3.5 3.3 + - - +
214C GLN* 3.4 15.9 + - - +
240C LEU* 3.9 24.7 - - - -
239D PHE* 3.5 56.8 - - + -
240D LEU* 4.5 5.2 - - + -
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 3.7 31.9 - - + +
149C GLN 3.8 4.9 - - - +
150C GLU* 3.7 32.3 - - + +
180C ILE* 4.0 26.5 - - + -
186C LEU* 4.7 9.9 - - + -
206C THR* 4.1 11.9 - - + -
207C SER* 4.2 4.3 - - - +
208C ASP* 3.3 14.8 + - + +
210C MET* 1.3 77.8 - - - +
212C ASN* 1.3 57.4 + - - +
214C GLN* 3.2 23.3 + - - +
215C LEU* 3.0 24.3 + - + +
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Residues in contact with ASN 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ILE 5.4 0.2 - - - +
206C THR* 2.8 35.2 + - - +
208C ASP 3.0 9.0 + - - +
209C VAL* 3.2 13.7 - - + +
211C LEU* 1.3 74.7 - - - +
213C MET* 1.3 65.3 + - - +
215C LEU* 3.0 8.9 + - - +
216C LEU* 2.9 36.9 + - - +
232C THR* 4.5 1.7 - - - -
233C ALA 4.1 4.2 - - - +
234C THR* 3.7 18.2 - - - +
241C THR* 5.7 0.6 - - - +
244C ALA* 5.4 0.4 - - - +
248C GLN* 3.1 42.5 + - - +
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Residues in contact with MET 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C VAL* 3.0 22.2 + - + +
210C MET* 3.8 9.4 - - - +
211C LEU 3.3 0.4 - - - -
212C ASN* 1.3 75.9 - - - +
214C GLN* 1.3 62.3 + - - +
216C LEU* 3.4 13.5 + - + +
217C ASN 3.0 18.0 + - - -
240C LEU* 3.9 17.7 - - + +
213D MET* 4.0 22.9 - - + -
239D PHE* 4.3 14.6 - - + -
240D LEU* 3.4 56.5 - - + +
243D ASN* 3.3 25.9 - - + +
244D ALA* 4.4 4.9 - - + -
245D THR* 4.9 0.3 - - - +
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Residues in contact with GLN 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ILE* 5.4 3.6 - - - +
182C SER 5.5 0.8 - - - -
183C MET* 3.7 37.7 + - + +
186C LEU* 4.4 5.8 - - + +
210C MET 3.4 5.9 + - - +
211C LEU* 3.2 35.0 + - + +
212C ASN 3.1 0.2 - - - -
213C MET* 1.3 78.8 - - - +
215C LEU* 1.3 61.9 + - - +
217C ASN* 3.3 4.0 + - - +
218C VAL* 3.1 27.4 + - - +
239D PHE* 3.8 20.3 - - + -
243D ASN* 3.4 25.6 - - - +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 4.1 9.9 - - + -
186C LEU* 4.2 9.2 - - + +
190C ILE* 3.4 33.4 - - + -
204C ILE* 3.6 31.4 - - + +
206C THR* 3.7 18.8 - - + -
211C LEU 3.0 12.5 + - - +
212C ASN* 3.0 12.5 + - - +
214C GLN* 1.3 77.7 - - - +
216C LEU* 1.3 59.6 + - + +
218C VAL* 3.1 2.9 + - - -
219C LEU* 2.8 51.3 + - + +
232C THR* 4.0 19.7 - - + -
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ASN* 2.9 38.0 + - - +
213C MET* 3.8 9.9 - - + +
215C LEU* 1.3 76.3 - - + +
217C ASN* 1.3 57.5 + - - +
219C LEU* 3.9 5.1 - - + +
220C TYR* 3.0 30.1 + - - +
226C ILE* 3.7 23.5 - - + +
232C THR* 3.9 11.0 - - + +
244C ALA* 3.8 27.6 - - + -
245C THR 4.0 14.0 - - - +
248C GLN* 3.5 25.1 - - - +
245D THR* 3.6 15.9 - - + +
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C MET* 3.9 18.2 - - + +
187C ARG* 4.7 4.5 + - - -
213C MET 3.0 13.9 + - - +
214C GLN* 3.4 12.1 - - - +
215C LEU 3.1 0.2 - - - -
216C LEU* 1.3 77.4 - - - +
218C VAL* 1.3 61.1 + - - +
220C TYR* 3.4 5.2 + - - +
221C GLU* 3.1 33.1 + - - +
242D GLU 4.4 4.0 + - - -
243D ASN* 3.8 11.1 - - - +
244D ALA 2.8 25.5 + - - +
245D THR* 3.8 10.0 - - - +
246D PRO* 4.2 3.2 - - - +
247D SER* 3.7 15.6 - - - +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C MET* 3.7 18.4 - - - -
186C LEU* 3.4 20.0 - - + -
187C ARG* 4.1 18.4 - - + +
190C ILE* 3.5 28.5 - - + -
214C GLN 3.1 13.7 + - - +
215C LEU 3.1 6.6 + - - +
217C ASN* 1.3 78.9 - - - +
219C LEU* 1.3 64.4 + - - +
221C GLU* 3.3 6.6 + - + +
222C TYR* 3.0 45.5 + - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE* 4.1 16.6 - - + -
204C ILE* 4.7 8.5 - - + -
215C LEU* 2.8 42.9 + - + +
216C LEU* 4.0 4.7 - - + +
218C VAL* 1.3 72.5 - - - +
220C TYR* 1.3 60.9 + - - +
222C TYR* 3.3 3.6 + - - -
223C GLN 3.1 4.0 + - - -
224C LEU* 2.9 65.8 + - + +
226C ILE* 3.7 26.9 - - + -
230C ILE* 4.1 13.0 - - + -
232C THR* 3.7 20.6 - - + -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU 3.0 19.2 + - - +
217C ASN* 3.5 6.1 - - - +
219C LEU* 1.3 78.0 - - - +
221C GLU* 1.3 56.8 + - - +
223C GLN* 3.1 10.9 + - - +
224C LEU 5.0 1.8 - - - +
245C THR* 4.7 0.2 - - + -
220D TYR* 3.8 39.0 - + + -
224D LEU 4.3 1.6 + - - -
225D ARG* 2.7 60.7 + - - -
226D ILE* 2.9 43.2 + - - +
245D THR* 4.2 22.9 - - + -
246D PRO* 3.6 34.1 - - + -
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ARG* 3.8 30.6 + - - -
217C ASN* 3.1 22.2 + - - +
218C VAL* 3.3 8.1 + - - +
220C TYR* 1.3 79.7 - - - +
222C TYR* 1.3 85.3 + - + +
223C GLN* 3.3 4.5 + - - +
225D ARG* 3.9 11.8 + - - +
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ARG* 3.1 38.7 + - + +
190C ILE* 3.6 20.6 - - + -
191C LYS* 3.5 35.0 - - + +
218C VAL* 3.0 34.1 + - + +
219C LEU* 4.1 3.1 - - - +
220C TYR 3.2 0.2 - - - -
221C GLU* 1.3 97.2 + - + +
223C GLN* 1.3 68.7 + - - +
224C LEU* 3.3 20.4 + - + +
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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