Contacts of the helix formed by residues 235 - 243 (chain A) in PDB entry 3X0Y
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 ASN 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLY 4.6 1.4 - - - +
186A ALA* 3.6 19.0 - - + +
187A ILE* 2.8 35.2 + - - +
233A ALA 3.3 0.2 + - - -
234A PRO* 1.3 73.9 - - - +
236A ALA* 1.3 59.0 + - - +
237A PHE 3.3 3.1 - - - -
238A VAL* 3.1 43.0 + - - +
239A LEU* 2.9 42.3 + - + +
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Residues in contact with ALA 236 (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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107A ILE* 4.5 14.7 - - + +
187A ILE 4.2 1.8 + - - -
231A LEU 4.4 5.4 - - - +
232A GLY* 4.1 9.2 - - - -
233A ALA* 3.1 33.8 + - + +
234A PRO 3.2 1.7 - - - -
235A ASN* 1.3 77.6 - - - +
237A PHE* 1.3 56.8 + - - +
239A LEU* 3.6 9.4 + - - +
240A ALA* 2.9 30.2 + - - +
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Residues in contact with PHE 237 (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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103A MET* 3.8 29.6 - - + -
106A LEU* 5.3 2.9 - - + -
107A ILE* 3.3 43.5 - - + +
174A PHE* 3.5 37.9 - + - -
187A ILE* 5.3 8.8 + - + -
189A ALA* 3.8 10.1 - - + -
235A ASN 3.3 0.4 - - - -
236A ALA* 1.3 77.4 - - - +
238A VAL* 1.3 57.6 + - + +
240A ALA* 3.1 2.5 + - - +
241A PHE* 2.7 73.1 + + + -
247A GLY* 3.8 20.0 - - - -
250A PHE* 4.7 7.6 - + + -
415A PHE* 4.3 7.2 - + + -
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Residues in contact with VAL 238 (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 ILE* 3.8 30.1 - - + -
235A ASN* 3.1 39.1 + - - +
237A PHE* 1.3 77.3 - - + +
239A LEU* 1.3 62.1 + - + +
241A PHE* 3.6 12.7 + - + +
242A ILE* 3.2 39.4 + - + +
415A PHE* 6.5 0.2 - - + -
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Residues in contact with LEU 239 (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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233A ALA* 5.9 3.8 - - + -
234A PRO 4.4 8.7 - - - +
235A ASN* 2.9 37.0 + - + +
236A ALA* 3.8 7.9 - - - +
238A VAL* 1.3 76.6 - - + +
240A ALA* 1.3 62.4 + - - +
242A ILE* 3.2 13.2 + - + +
243A GLN* 3.0 34.2 + - + +
245A GLU* 5.5 0.4 - - - -
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Residues in contact with ALA 240 (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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107A ILE* 4.5 5.4 - - + -
236A ALA 2.9 20.5 + - - +
237A PHE* 3.1 7.6 + - - +
239A LEU* 1.3 75.7 - - - +
241A PHE* 1.3 57.8 + - - +
243A GLN 3.6 0.2 + - - -
244A SER* 3.0 22.5 + - - -
245A GLU* 3.0 28.2 + - + +
247A GLY* 4.1 27.6 - - - +
248A SER* 3.7 4.9 - - - +
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Residues in contact with PHE 241 (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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237A PHE* 2.7 40.7 + + + +
238A VAL* 3.8 11.2 - - + +
240A ALA* 1.3 70.8 - - - +
242A ILE* 1.3 66.6 + - + +
244A SER* 3.0 10.0 + - - -
247A GLY 4.0 8.1 - - - -
248A SER* 3.7 29.4 - - - -
250A PHE* 4.7 5.8 - - + -
413A PRO* 3.1 42.5 - - + +
414A GLY* 3.6 39.7 - - - -
415A PHE* 3.7 40.8 - + - -
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Residues in contact with ILE 242 (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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238A VAL* 3.2 33.6 + - + +
239A LEU* 3.2 13.7 + - + +
241A PHE* 1.3 77.9 - - + +
243A GLN* 1.3 73.1 + - - +
244A SER* 3.5 2.8 + - - -
413A PRO* 5.3 3.6 - - - +
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Residues in contact with GLN 243 (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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239A LEU* 3.0 22.4 + - + +
240A ALA 4.2 0.7 - - - +
242A ILE* 1.3 88.0 + - + +
244A SER* 1.3 69.2 + - - +
245A GLU* 3.1 36.9 + - + +
335A PRO* 4.3 10.3 - - - +
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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