Contacts of the helix formed by residues 203 - 217 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A MET* 3.1 51.6 - - + +
147A LEU* 4.5 4.0 - - + -
148A HIS* 4.1 22.2 - - - -
199A ILE 4.0 17.9 - - - -
200A LEU* 2.9 19.2 + - + +
202A PRO* 1.3 97.5 - - + +
204A SER* 1.3 66.5 + - - +
205A ASN* 3.2 3.1 - - - +
206A LEU* 3.1 28.3 + - + -
207A ILE* 3.0 22.7 + - + +
315B ASN* 4.5 11.4 - - - -
711B FMN 6.6 0.2 - + - -
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 3.4 24.7 - - - -
200A LEU 3.6 0.8 + - - -
201A MET* 3.0 17.0 + - - -
202A PRO 3.5 2.2 + - - -
203A PHE* 1.3 75.4 - - - +
205A ASN* 1.3 63.5 + - - +
207A ILE* 3.1 13.5 + - - +
208A THR* 3.2 14.0 + - - -
246A TRP 4.7 2.5 - - - -
247A ALA* 3.4 26.4 - - - +
333A ARG 5.2 0.9 + - - -
335A LYS* 3.9 21.4 - - - +
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Residues in contact with ASN 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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203A PHE* 3.2 0.8 - - - -
204A SER* 1.3 76.4 + - - +
206A LEU* 1.3 63.7 + - + +
208A THR* 3.1 18.5 + - - -
209A LYS* 3.2 25.4 + - - +
335A LYS* 3.4 30.8 + - - +
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Residues in contact with LEU 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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145A PRO 4.4 7.2 - - - +
146A MET* 3.8 28.3 - - + +
147A LEU* 3.8 12.7 - - + +
203A PHE* 3.1 32.8 + - + +
205A ASN* 1.3 75.3 - - + +
207A ILE* 1.3 60.2 + - - +
209A LYS* 3.4 17.7 + - + +
210A LYS* 2.9 32.1 + - - +
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Residues in contact with ILE 207 (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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147A LEU* 3.7 29.8 - - + -
168A ALA* 5.9 2.0 - - + -
196A TYR* 4.0 13.0 - - + +
200A LEU* 4.5 26.5 - - + +
203A PHE* 3.0 24.6 + - + +
204A SER 3.1 8.0 + - - +
206A LEU* 1.3 77.1 - - - +
208A THR* 1.3 58.6 + - - +
210A LYS* 3.4 4.6 + - - +
211A LEU* 2.8 53.8 + - + +
243A TYR* 4.1 21.5 - - + +
247A ALA* 3.7 13.9 - - + -
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER 3.2 6.6 + - - -
205A ASN* 3.1 18.5 + - - -
207A ILE* 1.3 74.9 - - - +
209A LYS* 1.3 65.7 + - - +
211A LEU* 3.1 6.8 + - + +
212A ASP* 2.8 37.2 + - - +
244A ALA* 4.2 17.7 - - + +
247A ALA* 3.8 21.9 + - + -
248A GLU* 4.3 10.5 - - + +
335A LYS* 5.1 2.5 + - - +
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Residues in contact with LYS 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 ASN* 3.2 21.7 + - - +
206A LEU* 3.6 20.9 - - + +
208A THR* 1.3 76.7 - - - +
210A LYS* 1.3 57.7 + - - +
212A ASP* 3.0 10.8 + - - +
213A GLU* 2.9 29.3 + - - +
216A LYS* 4.9 1.6 + - - +
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Residues in contact with LYS 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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128A THR* 5.6 0.8 + - - -
142A ILE* 4.4 6.1 - - + -
143A GLU 2.8 29.1 + - - +
144A ALA* 4.1 12.1 - - + +
145A PRO* 4.7 4.6 - - - +
147A LEU* 3.6 29.6 - - + -
154A PHE* 4.1 14.8 - - + -
206A LEU 2.9 18.4 + - - +
207A ILE 3.7 3.6 - - - +
209A LYS* 1.3 76.4 - - - +
211A LEU* 1.3 63.7 + - + +
213A GLU* 2.9 37.1 + - - +
214A ILE* 3.1 34.4 + - + +
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Residues in contact with LEU 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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169A PHE* 4.2 19.7 - - + -
207A ILE* 2.8 43.2 + - + +
208A THR* 3.1 8.5 + - + +
210A LYS* 1.3 77.1 - - + +
212A ASP* 1.3 59.1 + - - +
214A ILE* 3.4 15.2 + - + +
215A GLN* 2.9 27.2 + - - +
240A ILE* 3.8 27.4 - - + +
243A TYR* 4.0 5.8 - - + -
244A ALA* 3.8 32.5 - - + +
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Residues in contact with ASP 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 THR* 2.8 25.4 + - - +
209A LYS* 3.3 11.3 - - - +
211A LEU* 1.3 74.8 - - - +
213A GLU* 1.3 57.0 + - - +
214A ILE 3.1 1.6 - - - -
215A GLN* 2.7 12.6 + - - +
216A LYS* 2.7 58.8 + - - +
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Residues in contact with GLU 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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128A THR* 3.7 25.6 + - - +
142A ILE* 3.7 12.2 - - - +
209A LYS 2.9 17.4 + - - +
210A LYS* 2.9 36.3 + - - +
212A ASP* 1.3 72.5 - - - +
214A ILE* 1.3 62.0 + - - +
216A LYS* 3.3 14.9 + - - +
217A ILE* 3.0 48.2 + - + +
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Residues in contact with ILE 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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142A ILE* 4.6 15.3 - - + -
154A PHE* 4.4 27.4 - - + -
163A LEU* 4.8 11.9 - - + -
169A PHE* 6.1 2.0 - - + -
210A LYS* 3.1 21.9 + - + +
211A LEU* 3.6 17.9 - - + +
212A ASP 3.1 0.4 - - - -
213A GLU* 1.3 77.7 - - + +
215A GLN* 1.3 59.9 + - - +
217A ILE* 4.1 3.9 - - + -
218A ASN* 3.4 1.9 + - - -
219A LEU* 3.2 56.4 + - + +
221A ILE* 4.0 18.4 - - + -
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Residues in contact with GLN 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 LEU 2.9 15.2 + - - +
212A ASP* 2.7 21.9 + - - +
214A ILE* 1.3 75.6 - - - +
216A LYS* 1.3 60.4 + - + +
218A ASN* 3.0 31.7 + - - +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 4.9 1.4 + - - +
212A ASP* 2.7 45.0 + - - +
213A GLU* 3.8 14.3 - - - +
215A GLN* 1.3 71.7 - - + +
217A ILE* 1.3 56.0 + - + +
218A ASN* 2.5 23.3 + - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 5.5 5.2 - - + -
142A ILE* 5.3 6.1 - - + -
213A GLU* 3.0 45.9 + - + +
214A ILE* 4.2 8.7 - - - +
216A LYS* 1.3 73.2 - - + +
218A ASN* 1.3 65.0 + - - +
219A LEU* 3.4 25.0 + - + -
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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