Contacts of the helix formed by residues 238 - 245 (chain A) in PDB entry 6O0Z
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 PHE 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU* 5.4 11.9 - - + -
225A LEU* 4.8 9.0 - - + -
234A LYS* 3.0 14.7 + - + +
237A LEU* 1.3 78.1 - - + +
239A GLY* 1.3 60.9 + - - +
240A ASN 3.5 0.4 - - - -
241A LEU* 3.6 4.1 + - - +
242A ILE* 2.9 29.9 + - - +
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Residues in contact with GLY 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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234A LYS 2.6 18.4 + - - -
235A ASN* 3.2 14.1 - - - -
238A PHE* 1.3 70.9 - - - +
240A ASN* 1.3 59.9 + - - +
242A ILE* 3.4 6.8 - - - +
243A ALA* 2.9 29.1 + - - +
249A THR 5.0 10.5 + - - +
250A PRO* 5.1 6.6 - - - +
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Residues in contact with ASN 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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188A LEU* 6.2 0.7 - - - -
192A TYR* 5.0 13.9 - - + -
235A ASN 2.6 15.6 + - - +
236A GLY* 3.3 22.1 + - - +
238A PHE 3.5 0.4 - - - -
239A GLY* 1.3 71.2 - - - +
241A LEU* 1.3 61.7 + - - +
243A ALA* 3.4 6.7 + - - +
244A LEU* 2.9 30.1 + - - +
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU* 6.1 1.3 - - - -
225A LEU* 5.3 6.5 - - + -
236A GLY 4.4 0.4 + - - -
237A LEU 3.6 19.7 + - - +
238A PHE* 3.6 4.8 + - - +
239A GLY 3.4 0.2 - - - -
240A ASN* 1.3 76.2 - - - +
242A ILE* 1.3 61.4 + - - +
244A LEU* 3.9 5.3 - - - +
245A SER* 2.9 26.7 + - - -
246A LEU* 3.1 11.6 + - + +
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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 PHE 2.9 19.3 + - - +
239A GLY* 3.4 9.4 - - - +
241A LEU* 1.3 78.4 - - - +
243A ALA* 1.3 61.8 + - - +
244A LEU 3.2 1.0 + - - -
245A SER 3.7 0.7 + - - -
246A LEU* 2.8 33.8 + - + +
247A GLY 3.3 23.1 - - - +
248A LEU* 3.3 12.8 - - - +
249A THR* 4.0 6.1 - - - +
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Residues in contact with ALA 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 GLY 2.9 16.5 + - - +
240A ASN* 3.4 6.9 + - - +
242A ILE* 1.3 75.4 - - - +
244A LEU* 1.3 60.0 + - - +
248A LEU* 3.7 13.1 - - + +
250A PRO* 4.2 25.6 - - + -
264A LEU* 6.1 1.6 - - + -
265A GLN 5.1 5.7 - - - +
271A TYR* 5.4 5.0 + - - -
293A ALA* 4.3 7.3 - - - +
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Residues in contact with LEU 244 (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 LEU* 3.7 29.4 - - + -
240A ASN 2.9 17.3 + - - +
241A LEU* 3.9 5.6 - - - +
242A ILE 3.1 0.4 - - - -
243A ALA* 1.3 80.6 - - - +
245A SER* 1.3 63.5 + - - +
293A ALA* 2.9 38.0 - - + +
296A LEU* 4.7 3.1 - - + -
297A SER* 3.2 12.0 - - - -
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Residues in contact with SER 245 (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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241A LEU* 2.9 13.1 + - - -
244A LEU* 1.3 79.3 - - - +
246A LEU* 1.3 66.5 + - - +
296A LEU* 3.9 13.2 - - - -
297A SER* 4.0 12.2 - - - +
300A ILE* 3.9 28.1 - - - +
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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