Contacts of the helix formed by residues 256 - 263 (chain A) in PDB entry 2Y05
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 PRO 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ASN* 4.4 19.3 - - + +
227A ILE* 4.6 4.9 - - + -
254A GLY 4.0 0.9 - - - +
255A PRO* 1.3 82.5 - - + +
257A PRO* 1.3 72.4 - - + +
258A GLU* 3.3 13.9 - - - +
259A ILE* 3.0 40.1 + - + +
260A VAL* 3.2 11.7 + - - +
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Residues in contact with PRO 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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255A PRO 3.1 10.3 - - - +
256A PRO* 1.3 83.3 - - + +
258A GLU* 1.3 59.8 + - + +
260A VAL* 3.3 7.6 + - + +
261A ILE* 2.8 46.4 + - + +
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Residues in contact with GLU 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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256A PRO* 4.4 12.7 - - + +
257A PRO* 1.3 81.4 - - - +
259A ILE* 1.3 72.8 + - + +
261A ILE* 4.1 5.9 - - - +
262A TYR* 3.0 32.1 + - - +
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Residues in contact with ILE 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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227A ILE* 3.6 31.4 - - + +
228A GLY* 4.0 19.5 - - - +
256A PRO* 3.0 33.4 + - + +
258A GLU* 1.3 89.9 - - + +
260A VAL* 1.3 60.5 + - - +
262A TYR* 4.7 2.7 - - - -
263A GLN* 2.9 42.4 + - + +
265A LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 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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227A ILE* 3.9 17.5 - - + -
255A PRO* 4.1 17.5 - - + +
256A PRO 3.2 12.8 + - - +
257A PRO* 3.7 9.6 - - + +
259A ILE* 1.3 76.3 - - - +
261A ILE* 1.3 65.4 + - + +
264A GLU* 3.2 15.6 + - - -
265A LEU* 3.2 22.8 + - + +
267A MET* 3.3 34.5 - - + -
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Residues in contact with ILE 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 PRO* 2.8 32.9 + - + +
258A GLU* 4.1 5.4 - - - +
260A VAL* 1.3 79.3 - - + +
262A TYR* 1.3 62.8 + - - +
264A GLU* 2.9 28.2 + - - +
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Residues in contact with TYR 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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232A LYS* 4.5 10.5 - - + +
258A GLU 3.0 20.0 + - - +
259A ILE* 4.3 2.9 - - - +
261A ILE* 1.3 78.2 - - + +
263A GLN* 1.3 85.3 + - + +
264A GLU* 3.2 9.6 + - - +
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Residues in contact with GLN 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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227A ILE 5.2 1.6 - - - +
228A GLY 6.1 0.7 - - - +
230A MET 3.1 24.9 + - - +
231A LYS 4.4 0.7 - - - +
232A LYS* 3.3 15.1 - - - +
233A PHE 2.7 31.1 + - - -
259A ILE* 2.9 33.3 + - + +
262A TYR* 1.3 103.3 - - + +
264A GLU* 1.3 60.3 + - - +
265A LEU* 3.2 22.3 + - + +
1331A EDO 2.7 29.1 + - - -
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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