Contacts of the helix formed by residues 203 - 217 (chain C) in PDB entry 1YCH
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 PHE 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C MET* 3.4 55.9 - - + +
147C LEU* 4.2 4.3 - - + -
148C HIS* 4.1 16.4 - - - -
199C ILE 3.8 19.5 - - - -
200C LEU* 2.9 23.9 + - + +
202C PRO* 1.3 94.6 - - + +
204C SER* 1.3 64.8 + - - +
205C ASN* 3.2 3.1 - - - -
206C LEU* 3.1 24.9 + - + +
207C ILE* 3.0 23.0 + - + +
315D ASN* 4.5 11.7 - - - -
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C TYR* 2.8 28.4 + - - -
200C LEU 3.6 0.2 + - - -
201C MET* 2.9 24.1 + - - +
202C PRO 3.5 1.4 + - - -
203C PHE* 1.3 77.2 - - - +
205C ASN* 1.3 62.8 + - - +
207C ILE* 3.2 10.0 + - - -
208C THR* 3.2 15.1 + - - -
246C TRP 4.2 3.3 + - - -
247C ALA* 3.5 28.7 - - - +
302C LEU* 5.7 0.2 - - - +
335C LYS* 4.6 13.9 - - - +
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Residues in contact with ASN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PRO 5.4 2.6 + - - -
203C PHE* 3.2 0.8 - - - -
204C SER* 1.3 76.9 - - - +
206C LEU* 1.3 64.3 + - + +
208C THR* 3.2 16.3 + - - -
209C LYS* 3.3 23.8 + - - +
335C LYS* 3.6 28.5 + - - +
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Residues in contact with LEU 206 (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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145C PRO 3.8 9.0 - - - +
146C MET* 3.6 33.4 - - + +
147C LEU* 3.6 18.2 - - + +
203C PHE* 3.1 21.6 + - + +
205C ASN* 1.3 78.6 - - + +
207C ILE* 1.3 59.3 + - - +
209C LYS* 3.4 19.1 + - + +
210C LYS* 2.8 31.5 + - - +
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Residues in contact with ILE 207 (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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147C LEU* 3.9 26.2 - - + -
154C PHE* 6.4 0.2 - - + -
168C ALA* 5.6 4.7 - - + -
169C PHE* 6.4 0.2 - - + -
196C TYR* 4.1 13.7 - - + +
200C LEU* 4.3 27.6 - - + -
203C PHE* 3.0 20.4 + - + +
204C SER 3.2 7.8 + - - +
206C LEU* 1.3 76.9 - - - +
208C THR* 1.3 57.2 + - - +
210C LYS* 3.4 4.6 + - - +
211C LEU* 2.8 44.4 + - + +
243C TYR* 4.2 22.7 - - + +
247C ALA* 3.9 16.8 - - + -
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Residues in contact with THR 208 (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 SER 3.2 14.6 + - - -
205C ASN* 3.2 12.5 + - - -
207C ILE* 1.3 72.2 - - - +
209C LYS* 1.3 63.7 + - - +
211C LEU* 3.1 6.1 + - + +
212C ASP* 2.8 36.7 + - - +
244C ALA* 4.2 16.6 - - + +
247C ALA* 3.7 22.6 + - + -
248C GLU* 4.3 11.0 - - + +
335C LYS* 5.5 2.1 + - - -
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Residues in contact with LYS 209 (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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205C ASN* 3.3 22.8 + - - +
206C LEU* 3.6 22.8 - - + +
208C THR* 1.3 76.1 - - - +
210C LYS* 1.3 57.7 + - - +
212C ASP* 3.1 10.7 + - - +
213C GLU* 2.9 27.8 + - - +
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Residues in contact with LYS 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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128C THR* 5.4 0.4 + - - -
142C ILE* 4.4 6.7 - - + -
143C GLU 2.9 29.1 + - - +
144C ALA* 4.3 4.1 - - + +
145C PRO* 4.9 4.6 - - - +
147C LEU* 3.7 24.2 - - + +
154C PHE* 3.9 27.6 - - + -
206C LEU 2.8 21.2 + - - +
207C ILE* 3.8 3.1 - - - +
209C LYS* 1.3 72.8 - - - +
211C LEU* 1.3 63.7 + - + +
213C GLU* 2.8 39.6 + - - +
214C ILE* 3.1 29.3 + - + +
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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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169C PHE* 4.2 19.7 - - + -
207C ILE* 2.8 37.4 + - + +
208C THR* 3.1 8.9 + - + +
210C LYS* 1.3 75.1 - - + +
212C ASP* 1.3 60.9 + - - +
214C ILE* 3.5 19.0 + - + +
215C GLN* 2.9 25.3 + - - +
240C ILE* 4.0 29.6 - - + +
243C TYR* 4.2 4.9 - - + -
244C ALA* 3.8 36.1 - - + +
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Residues in contact with ASP 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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208C THR* 2.8 25.9 + - - +
209C LYS* 3.5 10.1 - - - +
211C LEU* 1.3 77.8 - - - +
213C GLU* 1.3 56.1 + - - +
215C GLN* 2.9 12.9 + - + +
216C LYS* 2.7 51.6 + - + +
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Residues in contact with GLU 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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128C THR* 3.7 17.5 + - - +
142C ILE* 3.7 20.0 - - + +
209C LYS 2.9 11.7 + - - +
210C LYS* 2.8 44.7 + - - +
212C ASP* 1.3 75.3 - - - +
214C ILE* 1.3 65.2 + - + +
216C LYS* 3.2 8.1 + - - +
217C ILE* 3.0 43.3 + - + +
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Residues in contact with ILE 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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142C ILE* 4.7 10.1 - - + -
154C PHE* 4.3 19.7 - - + -
163C LEU* 4.8 12.1 - - + -
169C PHE* 5.8 2.2 - - + -
210C LYS* 3.1 30.1 + - + +
211C LEU* 3.5 21.8 - - + +
213C GLU* 1.3 80.9 - - + +
215C GLN* 1.3 60.9 + - - +
217C ILE* 4.1 5.4 - - - -
218C ASN 3.4 2.3 + - - -
219C LEU* 3.3 45.4 + - + +
221C ILE* 3.8 26.9 - - + -
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Residues in contact with GLN 215 (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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211C LEU 2.9 15.4 + - - +
212C ASP* 2.9 24.6 + - + +
214C ILE* 1.3 74.5 - - - +
216C LYS* 1.3 61.4 + - + +
218C ASN* 3.0 25.7 + - - +
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Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ASP* 2.7 31.4 + - + +
213C GLU* 3.7 6.1 - - - +
215C GLN* 1.3 71.9 - - + +
217C ILE* 1.3 57.0 + - + +
218C ASN* 2.5 22.2 + - - +
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Residues in contact with ILE 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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128C THR* 5.3 7.4 - - + -
142C ILE* 6.0 6.5 - - + -
213C GLU* 3.0 42.9 + - + +
214C ILE* 4.3 4.5 - - - +
216C LYS* 1.3 74.0 - - + +
218C ASN* 1.3 64.1 + - - +
219C LEU* 3.9 28.7 - - + -
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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