Contacts of the helix formed by residues 186 - 194 (chain A) in PDB entry 2Y01
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ASP* 3.5 21.4 + - - +
185A GLU* 1.3 81.2 - - - +
187A PRO* 1.4 83.1 - - - +
188A GLN* 3.5 25.8 + - + +
189A ALA* 3.6 15.4 - - + +
190A LEU* 3.1 20.3 + - - +
202A VAL* 5.8 1.6 - - + -
205A ARG* 5.0 9.7 + - - -
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Residues in contact with PRO 187 (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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185A GLU 3.7 2.2 - - - +
186A ASP* 1.4 90.8 - - - +
188A GLN* 1.3 62.1 + - - +
190A LEU* 3.2 15.3 + - + +
191A LYS* 3.0 25.5 + - - +
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Residues in contact with GLN 188 (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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186A ASP* 3.5 18.7 - - - +
187A PRO* 1.3 80.4 - - - +
189A ALA* 1.3 60.7 + - - +
191A LYS* 3.5 9.5 - - - +
192A CYS* 3.4 20.3 + - - +
202A VAL* 4.5 26.0 - - + +
317A ARG* 5.4 8.5 - - - +
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Residues in contact with ALA 189 (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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184A ASP* 3.7 30.3 - - + +
186A ASP* 3.2 12.7 + - + +
188A GLN* 1.3 76.0 - - - +
190A LEU* 1.3 60.1 + - - +
192A CYS* 3.3 2.2 + - - -
193A TYR* 3.1 46.8 + - + +
202A VAL* 3.8 26.5 - - + -
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Residues in contact with LEU 190 (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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184A ASP 5.0 2.9 - - - +
185A GLU* 3.4 27.8 - - + +
186A ASP 3.1 18.7 + - - +
187A PRO* 3.2 14.3 + - + +
189A ALA* 1.3 72.5 - - - +
191A LYS* 1.3 60.5 + - - +
193A TYR* 4.5 6.9 - - + +
194A GLN* 2.9 35.5 + - - +
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Residues in contact with LYS 191 (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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187A PRO 3.0 13.2 + - - +
188A GLN* 3.5 15.3 - - - +
190A LEU* 1.3 77.9 - - - +
192A CYS* 1.3 61.6 + - - +
194A GLN* 3.4 7.8 - - - +
195A ASP* 3.3 20.6 - - + +
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Residues in contact with CYS 192 (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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188A GLN 3.4 9.5 + - - +
189A ALA 3.3 7.7 + - - +
190A LEU 3.3 0.6 - - - -
191A LYS* 1.3 77.6 - - - +
193A TYR* 1.3 77.0 + - + +
194A GLN 3.4 0.2 + - - -
195A ASP* 3.1 21.6 + - - +
198A CYS* 2.1 61.2 - - - +
200A ASP* 3.9 21.1 - - - +
202A VAL* 4.6 9.4 - - + -
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Residues in contact with TYR 193 (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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182A TRP* 3.5 25.0 - + - -
183A ARG* 3.6 45.0 - - + +
184A ASP 3.4 32.8 + - - -
189A ALA* 3.1 27.9 + - + +
190A LEU* 4.5 6.3 - - + +
192A CYS* 1.3 87.9 - - + +
194A GLN* 1.3 58.0 + - - +
195A ASP 3.3 4.8 + - - +
200A ASP 5.4 1.1 - - - -
202A VAL* 2.6 37.5 + - + -
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Residues in contact with GLN 194 (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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190A LEU 2.9 16.8 + - - +
191A LYS* 3.4 6.0 - - - +
193A TYR* 1.3 76.2 - - - +
195A ASP* 1.3 60.3 + - - +
196A PRO* 4.6 1.9 - - - +
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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