Contacts of the helix formed by residues 202 - 212 (chain A) in PDB entry 2A0Y
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 THR 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE 4.8 4.0 - - - +
201A GLU* 1.3 76.5 - - - +
203A VAL* 1.3 59.8 + - - +
204A ALA* 3.7 7.7 + - - +
205A GLU* 3.0 39.0 + - - +
206A CYS* 2.8 27.3 + - - +
246A ILE* 4.8 2.0 - - - -
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Residues in contact with VAL 203 (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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202A THR* 1.3 74.9 - - - +
204A ALA* 1.3 65.0 + - - +
206A CYS* 3.1 3.1 + - - +
207A ARG* 3.0 29.9 + - - +
246A ILE* 3.9 26.2 - - + +
247A MET 3.7 25.1 - - - +
248A ASP 3.9 20.6 - - - +
249A TYR* 3.7 43.5 - - + +
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Residues in contact with ALA 204 (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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202A THR* 3.3 7.0 + - - +
203A VAL* 1.3 80.0 - - - +
205A GLU* 1.3 62.3 + - + +
207A ARG* 3.5 10.0 + - - +
208A VAL* 3.2 26.5 + - - +
249A TYR* 3.8 16.6 + - - +
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Residues in contact with GLU 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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200A PHE 4.4 1.4 - - - +
201A GLU* 3.3 19.8 - - + +
202A THR* 3.0 43.4 + - - +
204A ALA* 1.3 76.5 - - + +
206A CYS* 1.3 64.1 + - - +
208A VAL* 3.1 10.5 + - + +
209A LEU* 3.0 30.6 + - + +
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Residues in contact with CYS 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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120A LEU* 3.8 8.0 - - - +
201A GLU* 4.4 7.8 - - + +
202A THR 2.8 12.9 + - - +
203A VAL 3.4 8.7 - - - +
205A GLU* 1.3 77.0 - - - +
207A ARG* 1.3 60.8 + - - +
209A LEU* 3.2 6.8 + - - +
210A GLN* 3.0 53.6 + - - +
245A VAL* 3.2 34.5 - - + -
246A ILE 3.6 11.9 - - - +
247A MET* 3.6 15.7 - - - -
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Residues in contact with ARG 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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203A VAL* 3.0 26.3 + - - +
204A ALA* 3.7 9.2 - - - +
205A GLU 3.2 0.2 - - - -
206A CYS* 1.3 78.6 - - - +
208A VAL* 1.3 59.6 + - - +
210A GLN* 3.4 17.4 + - - +
211A LYS* 3.0 47.4 + - - +
247A MET* 3.2 30.4 + - + +
248A ASP* 3.9 14.1 - - - +
249A TYR* 4.0 21.8 + - - +
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Residues in contact with VAL 208 (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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138A LEU* 6.3 0.2 - - + -
204A ALA* 3.2 17.8 + - + +
205A GLU* 3.1 13.1 + - + +
207A ARG* 1.3 77.0 - - - +
209A LEU* 1.3 71.2 + - + +
211A LYS* 3.1 12.0 + - + +
212A LEU* 3.0 41.4 + - + +
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Residues in contact with LEU 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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120A LEU* 3.7 19.5 - - + -
138A LEU* 3.9 27.4 - - + -
193A VAL* 4.2 12.6 - - + -
195A VAL* 4.2 7.9 - - + -
201A GLU* 4.1 19.1 - - + -
205A GLU* 3.0 16.1 + - + +
206A CYS* 3.6 6.5 - - - +
208A VAL* 1.3 87.3 - - + +
210A GLN* 1.3 60.0 + - - +
212A LEU* 3.5 11.9 + - + +
213A GLY 3.6 0.2 + - - -
214A ALA* 3.1 26.3 + - - +
217A VAL* 3.8 31.0 - - + -
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Residues in contact with GLN 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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120A LEU* 3.8 28.5 - - + +
122A PRO* 6.0 1.5 - - - +
206A CYS* 3.0 40.9 + - - +
207A ARG* 3.7 16.7 + - - +
208A VAL 3.2 0.2 - - - -
209A LEU* 1.3 73.9 - - - +
211A LYS* 1.3 62.5 + - + +
213A GLY* 2.8 22.2 + - - -
214A ALA 4.0 8.2 + - - +
247A MET* 3.4 31.7 - - - +
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Residues in contact with LYS 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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207A ARG* 3.0 42.9 + - - +
208A VAL* 3.1 9.3 + - + +
210A GLN* 1.3 77.5 - - + +
212A LEU* 1.3 64.5 + - + +
213A GLY 3.1 1.4 + - - -
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Residues in contact with LEU 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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136A ILE* 3.8 25.4 - - + +
138A LEU* 4.3 24.7 - - + -
193A VAL* 5.7 1.1 - - + -
208A VAL* 3.0 36.4 + - + +
209A LEU* 3.8 17.9 - - + +
210A GLN 3.1 0.6 - - - -
211A LYS* 1.3 80.3 - - + +
213A GLY* 1.3 59.3 + - - +
214A ALA* 5.4 0.4 - - + -
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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