Contacts of the helix formed by residues 186 - 195 (chain B) in PDB entry 1Y67
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 ARG 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B ASN 3.4 23.4 + - - -
183B TYR* 2.9 36.0 + - - +
184B GLN* 3.1 24.2 + - - +
185B ASN* 1.3 91.8 + - - +
187B ARG* 1.3 65.6 + - - +
188B PRO* 3.3 7.6 - - + -
189B ASP* 3.1 39.5 + - + +
190B TYR 3.3 8.3 + - - -
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Residues in contact with ARG 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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175A TRP* 5.7 3.6 - - - -
126B ALA 2.7 36.8 + - - -
127B LYS* 3.7 13.3 + - - +
129B ARG 2.8 21.0 + - - -
131B GLY 3.3 25.9 + - - +
174B VAL* 3.6 29.0 + - + +
176B GLU* 5.4 3.8 + - - +
179B TYR* 3.1 49.9 + - + +
185B ASN 2.9 13.0 + - - +
186B ARG* 1.3 71.2 - - - +
188B PRO* 1.4 64.3 - - + +
190B TYR* 3.1 5.4 + - + +
191B LEU* 2.9 40.3 + - + +
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Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU* 4.6 3.5 - - - +
127B LYS* 3.8 34.3 - - + +
185B ASN 4.5 2.5 - - - +
186B ARG* 3.3 7.6 - - + -
187B ARG* 1.4 92.8 - - + +
189B ASP* 1.3 60.3 + - - +
191B LEU* 3.4 11.6 + - + +
192B ALA* 3.0 27.5 + - - +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.7 18.2 - - + -
186B ARG* 3.1 41.4 + - - +
188B PRO* 1.3 77.1 - - - +
190B TYR* 1.3 66.5 + - - +
192B ALA* 3.5 6.8 + - - +
193B ALA* 3.1 23.9 + - - +
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Residues in contact with TYR 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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18B HIS 5.1 0.7 - - - -
19B ILE* 4.6 21.1 - - + -
84B PHE* 3.8 13.9 - - - -
172B VAL* 3.6 24.0 - - + +
173B ASP 2.7 29.2 + - - -
174B VAL* 4.5 1.6 - - + -
178B ALA* 3.6 25.0 - - + +
179B TYR* 3.4 34.5 - + + -
183B TYR* 3.6 35.3 - + + -
186B ARG 3.3 5.1 + - - +
187B ARG* 3.1 12.5 + - + +
189B ASP* 1.3 77.8 - - - +
191B LEU* 1.3 66.9 + - + +
193B ALA* 3.2 3.3 + - - +
194B PHE* 3.0 29.8 + + + +
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Residues in contact with LEU 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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122B PHE* 5.4 3.6 - - + -
123B GLU* 4.0 19.5 - - + +
126B ALA* 3.6 34.3 - - + -
127B LYS* 3.9 27.1 - - + +
172B VAL* 3.9 22.4 - - + -
174B VAL* 3.9 13.9 - - + -
187B ARG* 2.9 34.7 + - + +
188B PRO* 3.7 5.6 - - + +
189B ASP 3.3 0.2 - - - -
190B TYR* 1.3 77.9 - - + +
192B ALA* 1.3 64.4 + - - +
194B PHE* 3.5 16.8 - - + +
195B TRP* 3.5 17.6 + - - -
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Residues in contact with ALA 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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123B GLU* 4.5 10.2 + - - +
188B PRO 3.0 17.2 + - - +
189B ASP* 3.9 7.9 - - - +
191B LEU* 1.3 76.7 - - - +
193B ALA* 1.3 60.5 + - - +
194B PHE 3.5 0.3 + - - -
195B TRP* 3.6 25.0 + - - +
196B ASN* 3.9 6.3 + - - -
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Residues in contact with ALA 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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18B HIS* 3.8 25.5 - - + +
183B TYR* 3.3 26.7 - - + +
189B ASP 3.1 14.4 + - - +
190B TYR* 3.2 3.3 + - + +
192B ALA* 1.3 75.5 - - - +
194B PHE* 1.3 63.8 + - - +
195B TRP 3.2 0.2 - - - -
196B ASN* 3.1 30.6 + - - +
197B VAL 4.1 0.9 + - - -
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Residues in contact with PHE 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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19B ILE* 5.2 5.2 - - + -
84B PHE* 3.8 24.2 - + - -
87B ILE* 4.0 9.6 - - + -
88B MET* 4.0 17.5 - - + -
122B PHE* 4.2 16.4 - + - -
170B LEU* 4.2 8.3 - - + -
171B GLY 3.6 19.7 - - - -
172B VAL* 3.8 28.5 - - + -
190B TYR* 3.0 19.3 + + + +
191B LEU* 3.5 17.3 - - + +
192B ALA 3.3 0.2 - - - -
193B ALA* 1.3 72.6 - - - +
195B TRP* 1.3 72.2 + + - +
196B ASN 3.0 2.2 - - - -
197B VAL* 3.0 31.3 + - + +
198B VAL* 3.4 29.2 + - + +
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Residues in contact with TRP 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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98B ASN* 2.8 31.5 + - - +
115B PHE* 4.7 0.7 - + + -
118B PHE* 3.6 31.4 - + - -
119B LYS* 3.5 55.6 - - + +
122B PHE* 3.4 37.0 - + + -
123B GLU* 2.9 26.9 + - + -
170B LEU* 4.2 9.2 - - + -
191B LEU 3.5 20.7 + - - -
192B ALA* 3.6 14.8 + - - +
193B ALA 3.2 1.0 - - - -
194B PHE* 1.3 80.3 - + - +
196B ASN* 1.3 58.9 + - - +
197B VAL 3.3 0.2 - - - -
198B VAL* 3.8 12.1 + - + +
200B TRP* 3.9 25.4 + + - -
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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