Contacts of the helix formed by residues 253 - 263 (chain A) in PDB entry 2DO0
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 SER 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LEU* 6.4 2.0 - - - -
202A GLY 4.3 17.3 - - - -
203A SER* 4.6 4.5 - - - -
252A GLN* 1.3 77.5 + - - +
254A ILE* 1.3 79.5 + - - +
256A ALA* 3.0 11.1 + - - +
257A VAL* 2.9 32.4 + - - +
277A MET* 6.0 1.3 - - - -
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Residues in contact with ILE 254 (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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252A GLN* 3.1 30.0 - - + +
253A SER* 1.3 89.8 + - - +
255A GLU* 1.3 67.8 + - + +
257A VAL* 3.2 9.0 + - + +
258A GLN* 3.1 38.8 + - + +
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Residues in contact with GLU 255 (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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226A ALA* 3.1 48.6 - - - +
227A GLY* 3.8 3.8 - - - -
228A VAL* 3.2 23.0 + - - +
250A PHE* 3.9 10.5 - - + -
251A GLU* 3.8 20.5 + - - +
252A GLN* 3.1 33.9 + - + +
254A ILE* 1.3 81.8 - - + +
256A ALA* 1.3 64.4 + - - +
258A GLN* 3.2 7.9 + - - +
259A ALA 3.2 4.7 + - - -
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Residues in contact with ALA 256 (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 GLY 5.0 0.4 - - - +
203A SER* 3.3 46.2 - - - +
205A VAL* 4.3 2.3 - - + +
250A PHE* 3.5 18.9 - - + -
252A GLN 3.2 3.5 + - - +
253A SER* 3.0 9.5 + - - +
255A GLU* 1.3 79.9 - - - +
257A VAL* 1.3 63.8 + - + +
259A ALA* 3.3 3.5 + - - +
260A ILE* 3.1 28.9 + - + +
277A MET* 5.5 1.6 - - + -
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Residues in contact with VAL 257 (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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253A SER* 2.9 27.6 + - - +
254A ILE* 3.5 9.9 - - + +
256A ALA* 1.3 72.7 - - - +
258A GLN* 1.3 67.9 + - + +
260A ILE* 3.0 21.9 + - + +
261A SER* 3.1 14.1 + - - -
277A MET* 3.9 23.3 - - + -
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Residues in contact with GLN 258 (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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226A ALA* 3.6 28.4 + - + +
254A ILE* 3.1 26.3 + - + +
255A GLU* 3.4 10.8 - - - +
257A VAL* 1.3 79.0 - - + +
259A ALA* 1.3 54.5 + - - +
261A SER* 3.1 2.8 + - - -
262A MET* 2.8 62.3 + - + +
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Residues in contact with ALA 259 (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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205A VAL* 5.8 0.2 - - + -
223A PHE* 4.3 7.6 - - + -
226A ALA* 3.2 22.5 - - + +
250A PHE* 3.3 25.6 - - + -
255A GLU 3.2 3.2 + - - -
256A ALA 3.5 5.6 - - - +
258A GLN* 1.3 78.3 - - - +
260A ILE* 1.3 56.6 + - - +
261A SER 2.9 0.5 + - - -
262A MET* 4.5 0.4 - - - -
263A PHE* 2.6 58.1 + - + +
275A VAL* 4.8 0.4 - - + -
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Residues in contact with ILE 260 (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 SER 5.2 0.2 - - - +
205A VAL* 3.5 27.4 - - + -
256A ALA* 3.2 16.6 - - + +
257A VAL* 3.0 10.5 + - + +
259A ALA* 1.3 75.0 - - - +
261A SER* 1.3 51.5 + - - +
263A PHE 3.6 0.5 - - - -
264A ASN* 2.6 39.8 + - + +
275A VAL* 3.0 40.0 - - + +
276A LYS* 4.5 4.5 - - + -
277A MET* 3.4 45.5 - - + +
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Residues in contact with SER 261 (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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257A VAL* 3.1 12.1 + - - -
258A GLN* 3.1 8.4 + - - -
259A ALA 2.9 1.4 + - - -
260A ILE* 1.3 74.0 - - - +
262A MET* 1.3 65.3 + - - +
263A PHE 2.6 6.8 + - - -
264A ASN* 2.6 40.2 + - - +
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Residues in contact with MET 262 (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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225A MET* 5.0 11.2 - - + +
226A ALA* 6.2 0.7 - - + -
258A GLN* 2.8 58.2 + - + +
259A ALA* 4.5 0.2 - - - -
261A SER* 1.3 81.3 - - - +
263A PHE* 1.3 73.9 + - + +
264A ASN 5.2 0.2 - - - +
266A GLN* 3.7 17.2 - - - +
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Residues in contact with PHE 263 (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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222A VAL* 3.3 43.7 - - + -
223A PHE* 2.9 50.7 - + - -
225A MET* 4.1 22.4 - - + -
226A ALA 5.1 1.1 - - - -
259A ALA* 2.6 46.7 + - + +
261A SER 2.6 2.0 + - - -
262A MET* 1.3 80.9 - - + +
264A ASN* 1.3 58.2 + - - +
265A GLY 3.0 1.4 + - - -
266A GLN* 2.9 29.6 + - + +
273A MET* 3.7 21.3 - - + +
275A VAL* 3.3 23.7 - - + +
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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