Contacts of the helix formed by residues 226 - 237 (chain A) in PDB entry 6LU7
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 THR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A THR* 1.3 81.9 + - - +
227A LEU* 1.3 65.2 + - - +
228A ASN* 3.8 5.0 + - - +
229A ASP* 3.0 35.3 + - - +
230A PHE* 3.1 22.2 + - - +
262A LEU* 4.4 4.5 - - - -
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Residues in contact with LEU 227 (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 THR* 1.3 74.3 - - - +
228A ASN* 1.3 60.5 + - - +
230A PHE* 3.5 4.5 + - + +
231A ASN* 3.0 37.0 + - - +
242A LEU* 3.3 57.4 - - + +
243A THR* 4.0 1.6 - - - +
244A GLN* 4.0 35.2 - - + +
247A VAL* 4.8 4.5 - - + -
262A LEU* 4.0 23.9 - - + +
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Residues in contact with ASN 228 (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 THR* 3.2 5.6 + - - +
227A LEU* 1.3 79.8 - - - +
229A ASP* 1.3 63.7 + - - +
231A ASN* 3.2 13.5 + - - +
232A LEU* 3.0 33.9 + - + +
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Residues in contact with ASP 229 (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 THR* 3.6 12.6 - - - +
226A THR* 3.0 26.8 + - - +
228A ASN* 1.3 80.9 - - - +
230A PHE* 1.3 61.6 + - - +
232A LEU* 3.5 18.7 + - - +
233A VAL* 3.4 24.8 + - - +
269A LYS* 4.0 7.9 + - - +
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Residues in contact with PHE 230 (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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201A THR* 3.6 23.6 - - + -
205A LEU* 4.9 0.2 - - + -
225A THR* 3.9 9.8 + - + -
226A THR 3.1 16.5 + - - +
227A LEU* 3.8 6.7 - - + +
229A ASP* 1.3 75.4 - - - +
231A ASN* 1.3 69.2 + - - +
233A VAL* 3.1 6.9 + - + +
234A ALA* 2.8 36.3 + - + +
239A TYR* 5.5 0.2 - + - -
242A LEU* 3.9 23.1 - - + -
262A LEU* 5.8 0.2 - - + -
265A CYS* 3.4 45.8 - - + -
268A LEU* 3.6 33.9 - - + -
269A LYS* 4.2 19.1 - - + +
272A LEU* 5.2 5.2 - - + -
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Residues in contact with ASN 231 (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 LEU* 3.0 30.2 + - - +
228A ASN* 3.2 14.0 + - - +
230A PHE* 1.3 78.4 - - - +
232A LEU* 1.3 60.3 + - - +
234A ALA* 3.7 6.0 - - - +
235A MET* 3.2 36.0 + - + +
240A GLU 4.6 0.2 - - - +
241A PRO* 3.3 15.2 - - + +
242A LEU* 2.5 56.0 + - - +
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Residues in contact with LEU 232 (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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228A ASN* 3.0 18.5 + - + +
229A ASP* 3.6 23.8 - - - +
230A PHE 3.1 0.4 - - - -
231A ASN* 1.3 79.5 - - - +
233A VAL* 1.3 62.2 + - + +
235A MET* 3.7 14.9 + - + +
236A LYS* 3.7 16.3 + - - +
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Residues in contact with VAL 233 (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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229A ASP 3.4 15.0 + - - +
230A PHE* 3.1 7.6 + - + +
232A LEU* 1.3 76.5 - - + +
234A ALA* 1.3 66.0 + - - +
236A LYS* 3.2 10.1 + - + +
237A TYR* 3.2 49.6 - - + -
269A LYS* 4.0 29.4 - - + +
272A LEU* 4.8 8.1 - - + -
273A GLN* 4.0 25.4 - - + +
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Residues in contact with ALA 234 (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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230A PHE* 2.8 32.6 + - + +
231A ASN* 3.9 11.4 - - - +
232A LEU 3.4 0.2 - - - -
233A VAL* 1.3 78.5 - - - +
235A MET* 1.3 57.7 + - - +
237A TYR 3.4 1.4 + - - -
238A ASN 3.3 3.3 + - - -
239A TYR* 2.7 57.7 + - + +
240A GLU 4.1 9.4 - - - +
241A PRO* 5.2 0.7 - - + -
272A LEU* 4.9 6.0 - - + +
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Residues in contact with MET 235 (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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231A ASN* 3.2 29.5 + - + +
232A LEU* 3.9 15.3 - - + +
233A VAL 3.2 0.2 - - - -
234A ALA* 1.3 77.7 - - - +
236A LYS* 1.3 61.3 + - - +
238A ASN* 3.3 12.0 + - - +
239A TYR 4.3 8.3 - - - +
241A PRO* 5.4 15.7 - - + -
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Residues in contact with LYS 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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232A LEU 3.7 10.2 + - - +
233A VAL* 3.2 11.7 + - + +
235A MET* 1.3 79.5 - - - +
237A TYR* 1.3 97.9 + - + +
238A ASN* 3.4 1.3 + - - +
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Residues in contact with TYR 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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199A THR* 5.0 0.5 + - - -
233A VAL* 3.2 44.9 + - + +
234A ALA 4.2 0.4 - - - +
235A MET 3.2 0.8 - - - -
236A LYS* 1.3 112.2 + - + +
238A ASN* 1.3 69.9 + - - +
239A TYR* 3.2 25.2 - - + -
272A LEU* 3.2 45.0 + - + -
273A GLN* 3.4 25.6 + - + +
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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