Contacts of the helix formed by residues 236 - 245 (chain A) in PDB entry 4OTZ
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A PHE* 6.2 0.4 - + - -
229A PHE* 3.5 44.0 - + + -
233A ASP* 3.4 29.4 - - + -
234A THR 3.5 18.4 - - - -
235A ASP* 1.3 76.3 - - - +
237A GLN* 1.3 66.2 + - - +
238A SER 3.2 3.0 + - - -
239A GLN* 3.3 16.5 + - + +
240A ALA* 2.9 23.1 + - + +
259A ASP* 3.6 32.3 - - + -
262A ASN* 3.8 4.9 - - + -
263A LEU* 3.7 37.9 - - + -
266A GLN* 2.8 24.7 + - + +
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Residues in contact with GLN 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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235A ASP* 3.1 19.3 + - - +
236A PHE* 1.3 77.4 - - - +
238A SER* 1.3 58.9 + - - +
240A ALA* 4.0 0.3 - - - +
241A THR* 2.9 44.9 + - - +
266A GLN* 3.7 3.2 + - - +
270A LEU* 4.2 30.2 - - + +
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Residues in contact with SER 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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235A ASP* 5.4 0.8 + - - -
236A PHE 3.3 0.2 - - - -
237A GLN* 1.3 79.5 - - - +
239A GLN* 1.3 72.7 + - - +
241A THR* 3.9 3.5 - - - -
242A ASN* 2.9 39.8 + - - +
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Residues in contact with GLN 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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197A PHE* 3.7 19.4 - - + -
227A GLN* 3.4 28.3 - - + +
228A LYS 3.0 28.4 + - - +
229A PHE* 3.7 17.8 - - + +
233A ASP* 4.6 5.1 + - - -
235A ASP 4.4 3.3 + - - +
236A PHE* 3.5 26.9 - - + +
238A SER* 1.3 86.4 + - - +
240A ALA* 1.3 64.2 + - - +
242A ASN* 3.4 3.7 + - - +
243A ALA* 3.0 23.7 + - - +
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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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197A PHE* 4.0 11.4 - - - -
236A PHE* 2.9 18.4 + - + +
239A GLN* 1.3 78.6 - - - +
241A THR* 1.3 56.8 + - - +
243A ALA* 3.3 2.8 + - - +
244A ILE* 2.9 35.7 + - + +
263A LEU* 4.5 7.2 - - + -
266A GLN* 5.0 1.1 - - + -
267A LEU* 3.9 24.6 - - + +
270A LEU* 3.6 22.7 - - + -
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Residues in contact with THR 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 GLN* 2.9 24.8 + - - +
238A SER* 3.9 4.0 - - - -
240A ALA* 1.3 74.3 - - - +
242A ASN* 1.3 66.1 + - - +
244A ILE* 3.2 8.0 + - + -
245A ASN* 2.9 44.2 + - - +
270A LEU* 4.0 20.3 - - - +
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Residues in contact with ASN 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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227A GLN* 3.2 32.8 + - - +
238A SER* 2.9 29.5 + - - +
239A GLN* 3.4 8.0 - - - +
241A THR* 1.3 78.5 - - - +
243A ALA* 1.3 61.7 + - - +
245A ASN* 3.7 11.7 + - - +
246A LEU* 3.4 22.9 + - + +
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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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195A ALA* 3.9 20.0 - - + -
197A PHE* 3.5 32.3 - - + -
225A THR* 4.1 15.0 - - + -
227A GLN* 4.7 0.4 - - + -
239A GLN 3.0 5.0 + - - +
240A ALA 3.7 2.2 - - - +
242A ASN* 1.3 77.5 - - - +
244A ILE* 1.3 68.1 + - + +
246A LEU* 2.9 16.3 + - - +
248A PRO* 3.1 18.1 - - + +
251A VAL* 5.5 0.9 - - + -
267A LEU* 5.2 2.7 - - + -
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Residues in contact with ILE 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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240A ALA 2.9 23.8 + - - +
241A THR* 3.8 7.6 - - + +
243A ALA* 1.3 75.8 - - - +
245A ASN* 1.3 68.6 + - - +
247A LYS* 3.0 19.4 + - - +
248A PRO* 3.9 7.0 - - + +
267A LEU* 3.9 23.1 - - + +
270A LEU* 3.5 43.3 - - + +
271A GLY 5.5 1.3 - - - -
272A TYR* 3.9 26.9 - - + +
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Residues in contact with ASN 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 THR* 2.9 39.8 + - - +
242A ASN* 3.9 9.7 + - - +
243A ALA 3.2 0.2 - - - -
244A ILE* 1.3 81.8 - - - +
246A LEU* 1.3 64.7 + - + +
247A LYS* 3.3 11.0 + - - +
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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