Contacts of the helix formed by residues 203 - 217 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A ASN* 4.7 11.7 - - - -
146B MET* 3.2 56.8 - - + +
147B LEU* 4.4 4.9 - - + -
148B HIS* 4.0 20.9 - - - -
199B ILE 3.9 22.2 - - - -
200B LEU* 2.9 16.1 + - + +
202B PRO* 1.3 97.9 - - + +
204B SER* 1.3 64.7 + - - +
205B ASN 3.3 2.2 - - - -
206B LEU* 3.1 25.8 + - + -
207B ILE* 2.9 23.7 + - + +
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.1 26.6 + - - -
200B LEU 3.7 0.6 + - - -
201B MET* 2.7 25.9 + - - +
202B PRO 3.5 1.8 + - - -
203B PHE* 1.3 76.1 - - - +
205B ASN* 1.3 65.2 + - - +
207B ILE* 3.0 9.8 + - - -
208B THR* 3.2 12.5 + - - +
246B TRP 4.4 2.8 + - - -
247B ALA* 3.4 32.7 - - - +
302B LEU* 5.8 0.2 - - - +
335B LYS* 4.1 17.4 - - - +
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Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO 5.8 1.8 + - - -
203B PHE* 3.3 0.6 - - - +
204B SER* 1.3 78.0 - - - +
206B LEU* 1.3 61.9 + - + +
208B THR* 3.0 23.2 + - - -
209B LYS* 3.1 23.4 - - + +
335B LYS* 2.9 35.6 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PRO 4.5 6.5 - - - +
146B MET* 3.8 30.7 - - + +
147B LEU* 4.0 14.6 - - + +
203B PHE* 3.1 27.4 + - + +
205B ASN* 1.3 78.6 - - + +
207B ILE* 1.3 60.8 + - - +
209B LYS* 3.8 16.6 - - + +
210B LYS* 2.9 30.8 + - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.5 30.1 - - + -
154B PHE* 6.4 0.2 - - + -
168B ALA* 5.6 4.0 - - + -
169B PHE* 6.3 0.2 - - + -
196B TYR* 4.1 14.8 - - + +
200B LEU* 4.4 23.8 - - + -
203B PHE* 2.9 20.4 + - + +
204B SER 3.0 8.0 + - - +
206B LEU* 1.3 74.3 - - - +
208B THR* 1.3 62.4 + - - +
210B LYS* 3.3 4.2 + - + +
211B LEU* 2.8 50.0 + - + +
243B TYR* 4.1 22.7 - - + +
247B ALA* 3.8 17.3 - - + -
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B SER 3.2 5.0 + - - +
205B ASN* 3.0 13.9 + - - +
207B ILE* 1.3 71.3 - - - +
209B LYS* 1.3 77.9 + - - +
211B LEU* 3.0 10.8 + - + +
212B ASP* 2.7 37.7 + - - -
244B ALA* 4.6 4.7 - - - +
247B ALA* 3.5 35.0 - - + +
248B GLU* 4.1 7.9 - - + +
335B LYS* 5.0 3.5 + - - +
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ASN* 3.1 25.2 + - + +
206B LEU* 3.8 17.9 - - + +
208B THR* 1.3 85.5 + - - +
210B LYS* 1.3 58.8 + - - +
212B ASP* 3.2 9.2 + - - +
213B GLU* 2.9 28.7 + - - +
216B LYS* 5.3 0.5 + - - -
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ILE* 4.2 11.2 - - + -
143B GLU 2.7 32.2 + - - +
144B ALA* 3.8 7.9 - - + +
145B PRO* 4.5 4.8 - - - +
147B LEU* 3.7 25.9 - - + +
154B PHE* 4.2 19.5 - - + -
206B LEU 2.9 18.9 + - - +
207B ILE* 3.8 3.4 - - + +
209B LYS* 1.3 76.7 - - - +
211B LEU* 1.3 63.1 + - + +
213B GLU* 2.9 31.5 + - - +
214B ILE* 3.1 29.5 + - + +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PHE* 4.2 21.1 - - + -
207B ILE* 2.8 42.9 + - + +
208B THR* 3.0 8.3 + - + +
210B LYS* 1.3 72.9 - - + +
212B ASP* 1.3 61.7 + - - +
214B ILE* 3.3 14.6 + - + +
215B GLN* 2.9 27.4 + - - +
240B ILE* 3.9 26.7 - - + +
243B TYR* 4.2 2.5 - - + -
244B ALA* 3.7 40.4 - - + +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 2.7 32.3 + - - +
209B LYS* 3.5 8.2 + - - +
211B LEU* 1.3 72.8 - - - +
213B GLU* 1.3 57.1 + - - +
215B GLN* 2.8 13.7 + - + +
216B LYS* 2.7 59.7 + - - +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 3.7 25.5 - - - +
142B ILE* 3.7 13.3 - - - +
209B LYS 2.9 15.6 + - - +
210B LYS* 2.9 36.6 + - - +
211B LEU 3.4 0.2 - - - -
212B ASP* 1.3 75.6 - - - +
214B ILE* 1.3 64.3 + - + +
216B LYS* 3.3 13.4 + - - +
217B ILE* 3.0 49.9 + - + +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ILE* 4.8 7.2 - - + -
154B PHE* 4.2 29.6 - - + -
163B LEU* 4.8 11.4 - - + -
169B PHE* 6.0 2.2 - - + -
210B LYS* 3.1 21.8 + - + +
211B LEU* 3.5 17.5 - - + +
213B GLU* 1.3 80.4 - - + +
215B GLN* 1.3 60.0 + - - +
217B ILE* 4.0 1.9 - - - -
218B ASN 3.3 2.1 + - - -
219B LEU* 3.2 63.3 + - + +
221B ILE* 3.8 20.2 - - + -
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU 2.9 14.5 + - - +
212B ASP* 2.8 22.0 + - - +
214B ILE* 1.3 74.2 - - - +
216B LYS* 1.4 60.0 + - + +
218B ASN* 3.0 30.2 + - - +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LYS 5.3 0.6 + - - -
212B ASP* 2.7 44.5 + - - +
213B GLU* 3.6 11.1 - - - +
215B GLN* 1.4 71.7 - - + +
217B ILE* 1.3 57.5 + - + +
218B ASN* 2.5 24.4 + - - +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 5.6 5.6 - - + -
142B ILE* 6.1 3.6 - - + -
213B GLU* 3.0 39.1 + - + +
214B ILE* 4.3 5.2 - - - +
216B LYS* 1.3 78.0 - - + +
218B ASN* 1.3 65.8 + - - +
219B LEU* 4.0 24.4 - - + -
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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