Contacts of the helix formed by residues 184 - 196 (chain B) in PDB entry 1YDY
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B MET* 4.2 5.3 - - - +
179B HIS* 4.2 9.2 - - + +
183B LYS* 1.3 72.5 - - - +
185B ILE* 1.3 61.9 + - - +
186B ALA 3.6 2.3 + - - -
187B ALA* 3.1 30.9 + - + +
188B LYS* 3.2 21.1 + - - +
217B ARG* 2.8 46.7 + - - -
222B LEU* 4.9 0.3 - - - +
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Residues in contact with ILE 185 (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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66B LEU* 3.3 31.0 - - + +
67B VAL* 3.8 6.7 - - - -
68B MET* 3.6 15.4 - - + -
74B LEU* 3.7 19.3 - - + -
172B ILE* 3.5 22.0 - - + -
173B LYS 4.1 2.9 - - - +
175B PRO* 3.8 14.6 - - + +
178B HIS* 3.6 42.2 - - + +
179B HIS* 5.5 1.9 - - - +
183B LYS 3.6 3.8 + - - -
184B ASP* 1.3 72.1 - - - +
186B ALA* 1.3 62.6 + - - +
188B LYS* 3.8 1.2 - - - +
189B THR* 2.8 39.6 + - - +
214B GLU* 5.9 0.2 - - - +
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Residues in contact with ALA 186 (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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172B ILE* 3.8 15.0 - - + +
179B HIS* 6.1 0.2 - - - -
184B ASP* 3.3 2.7 + - - +
185B ILE* 1.3 80.5 - - - +
187B ALA* 1.3 64.3 + - - +
189B THR* 3.3 1.9 + - - -
190B LEU* 3.0 27.4 + - - +
214B GLU* 3.4 27.5 + - + +
218B ILE* 3.8 22.7 - - + -
222B LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 187 (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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184B ASP* 3.1 34.2 + - + +
186B ALA* 1.3 78.9 - - - +
188B LYS* 1.3 56.5 + - - +
190B LEU* 3.3 4.6 + - - +
191B GLU* 2.9 45.0 + - - +
222B LEU* 3.9 16.5 - - + +
226B MET* 4.5 5.6 - - - +
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Residues in contact with LYS 188 (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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68B MET* 4.2 18.8 - - + -
72B ASP* 3.6 20.8 + - + +
73B ASN* 5.0 2.1 + - - +
74B LEU* 3.6 27.1 - - + +
149B GLU* 4.6 10.4 + - - -
184B ASP 3.2 14.0 + - - +
185B ILE* 3.8 5.2 - - - +
187B ALA* 1.3 77.3 - - - +
189B THR* 1.3 63.1 + - - +
191B GLU* 3.2 24.6 + - - +
192B VAL* 3.1 38.1 + - - +
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.7 31.4 - - + +
74B LEU* 3.7 12.7 - - - +
148B PHE* 4.2 4.4 - - + -
170B PRO* 5.1 0.2 - - + -
172B ILE* 3.8 14.3 - - + +
185B ILE* 2.8 25.8 + - - +
186B ALA 3.7 4.5 - - - -
188B LYS* 1.3 78.3 - - - +
190B LEU* 1.3 63.1 + - - +
192B VAL* 3.4 2.8 + - - +
193B LEU* 3.0 31.9 + - + +
207B LEU* 4.1 25.6 - - + -
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Residues in contact with LEU 190 (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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186B ALA 3.0 21.1 + - - +
187B ALA 3.8 0.7 - - - +
189B THR* 1.3 73.0 - - - +
191B GLU* 1.3 66.8 + - - +
193B LEU* 3.3 3.5 + - + -
194B LYS* 2.9 26.2 + - - +
207B LEU* 3.9 17.3 - - + -
218B ILE* 4.1 19.5 - - + -
222B LEU* 3.7 35.0 - - + -
223B GLU* 4.5 9.6 - - + +
226B MET* 3.7 22.0 - - + -
228B MET* 3.5 24.4 - - + +
230B LEU* 3.8 18.8 - - + -
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Residues in contact with GLU 191 (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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187B ALA* 2.9 37.0 + - - +
188B LYS* 3.4 27.8 + - + +
189B THR 3.2 0.2 - - - -
190B LEU* 1.3 78.5 - - - +
192B VAL* 1.3 61.8 + - + +
194B LYS* 3.7 3.4 - - - +
195B LYS* 3.0 24.0 + - - +
226B MET* 3.9 19.0 - - + +
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Residues in contact with VAL 192 (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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74B LEU* 4.1 12.6 - - + -
148B PHE* 3.5 27.4 - - + -
149B GLU* 3.7 42.4 - - + +
152B ILE* 5.0 3.1 - - + -
188B LYS* 3.1 25.8 + - - +
189B THR 3.9 5.8 - - - +
190B LEU 3.3 0.2 - - - -
191B GLU* 1.3 73.7 - - + +
193B LEU* 1.3 68.5 + - - +
195B LYS* 3.1 8.7 + - + -
196B TYR* 3.1 32.6 + - + +
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Residues in contact with LEU 193 (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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148B PHE* 3.8 24.0 - - + -
152B ILE* 5.1 2.0 - - + -
168B ILE* 4.7 3.6 - - + -
170B PRO* 4.5 4.9 - - + -
189B THR* 3.0 34.9 + - + +
190B LEU* 3.6 8.1 - - + +
192B VAL* 1.3 76.5 - - - +
194B LYS* 1.3 61.0 + - - +
196B TYR* 3.1 9.2 + - - -
197B GLY 3.3 0.2 + - - -
198B TYR* 2.9 61.3 + - + +
205B VAL* 4.3 14.1 - - + -
207B LEU* 4.5 10.3 - - + -
228B MET* 3.9 2.9 - - + -
230B LEU* 3.7 26.5 - - + -
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Residues in contact with LYS 194 (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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190B LEU 2.9 17.2 + - - +
191B GLU* 3.7 5.2 - - - +
193B LEU* 1.3 75.1 - - - +
195B LYS* 1.3 65.5 + - - +
197B GLY* 3.0 14.0 + - - -
198B TYR 3.7 9.5 + - - -
199B THR* 3.9 16.3 - - + +
226B MET* 2.6 44.7 + - + +
227B GLY 5.5 1.1 - - - -
228B MET* 3.9 14.4 - - + -
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Residues in contact with LYS 195 (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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149B GLU* 5.1 9.0 + - + +
191B GLU 3.0 14.1 + - - +
192B VAL* 3.1 14.6 + - + +
194B LYS* 1.3 77.3 - - - +
196B TYR* 1.3 91.4 + - + +
197B GLY 3.5 0.7 + - - -
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Residues in contact with TYR 196 (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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140A LYS* 6.1 1.6 - - - -
149B GLU* 3.7 36.4 - - + +
152B ILE* 3.6 31.2 - - + -
153B GLU* 2.6 44.7 + - + -
156B GLN* 3.1 32.9 + - - +
192B VAL* 3.1 26.0 + - + +
193B LEU* 3.1 2.0 + - - +
194B LYS 3.1 0.4 - - - -
195B LYS* 1.3 108.0 + - + +
197B GLY* 1.3 60.0 + - - +
198B TYR* 3.5 11.1 - - + -
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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