Contacts of the strand formed by residues 455 - 464 (chain A) in PDB entry 2ADU
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ASN 2.8 20.1 + - - +
227A ASN* 3.7 20.4 - - - +
228A CYS 3.5 4.9 + - - -
229A ALA* 3.6 13.0 - - + -
247A ILE* 3.4 16.2 - - - +
249A LYS* 3.1 28.9 + - - -
276A LEU* 4.6 0.9 - - - -
325A ILE* 4.0 13.2 - - + -
367A GLY 3.0 8.1 - - - -
368A SER* 3.6 20.2 - - - +
449A ASP* 4.2 7.2 - - + -
454A TYR* 1.3 79.4 - - - +
456A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 456 (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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247A ILE* 4.2 0.9 - - + -
249A LYS* 4.0 4.7 - - - -
266A THR* 3.8 10.1 - - - +
276A LEU* 3.9 17.5 - - + -
277A LEU* 4.0 17.0 - - + -
280A VAL* 3.6 25.8 - - + +
366A PHE* 3.2 9.0 - - - +
367A GLY 2.8 29.1 + - - -
455A THR* 1.3 75.0 - - - +
457A GLN* 1.3 60.2 + - - +
458A PHE* 5.5 0.4 - - + -
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Residues in contact with GLN 457 (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 ALA 4.4 1.4 - - - +
230A ALA* 5.5 0.8 - - - +
249A LYS* 3.7 25.6 - - + +
251A ASP* 3.2 23.5 + - - +
264A ALA* 3.8 17.1 - - - +
265A PHE 3.6 3.7 - - - +
266A THR* 2.7 36.0 + - - -
280A VAL* 4.0 0.9 - - - -
364A GLU* 2.8 29.0 + - + +
365A THR 3.4 10.1 - - - +
366A PHE* 3.1 35.1 - - + -
456A ALA* 1.3 74.3 - - - +
458A PHE* 1.3 79.8 + - - +
459A GLU* 3.8 6.9 + - - +
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Residues in contact with PHE 458 (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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264A ALA 3.5 5.8 - - - -
265A PHE* 3.8 15.9 - - + -
266A THR* 3.8 32.5 - - - -
277A LEU* 3.5 35.4 - - + -
280A VAL* 4.0 6.5 - - + +
281A LYS* 3.5 52.0 - - + -
284A THR* 3.0 38.5 + - + +
364A GLU* 3.3 2.3 - - - +
365A THR 3.3 18.5 + - - -
457A GLN* 1.3 86.9 - - - +
459A GLU* 1.3 60.2 + - - +
460A HIS* 6.5 0.2 - - + -
478A TYR* 4.0 18.4 - + + -
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Residues in contact with GLU 459 (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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251A ASP* 3.1 8.0 - - - +
262A ASP* 2.4 22.5 - - - +
263A CYS* 3.2 11.3 - - - -
264A ALA* 3.0 36.9 + - + +
284A THR* 4.5 0.9 - - - +
331A HIS* 3.4 1.7 + - - -
362A ALA* 3.6 4.5 - - + +
363A ILE 3.2 7.9 - - - +
364A GLU* 2.4 29.4 - - + +
457A GLN* 4.3 1.8 - - - +
458A PHE* 1.3 73.9 - - - +
460A HIS* 1.3 71.6 + - - +
478A TYR* 4.1 1.7 - - - -
501A CO 1.8 30.6 + - - -
502A CO 1.8 29.3 + - - -
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Residues in contact with HIS 460 (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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180A ARG* 4.2 0.4 - - - -
262A ASP 3.5 6.9 - - - +
263A CYS* 3.6 4.7 - - - -
284A THR* 4.9 4.2 - - + +
285A ASN* 4.5 1.6 - - - -
288A ILE* 3.7 26.9 - - + -
362A ALA* 3.5 2.1 - - - -
363A ILE* 2.8 32.7 + - - +
458A PHE* 6.5 0.7 - - + -
459A GLU* 1.3 74.9 - - - +
461A THR* 1.3 60.4 + - - +
462A ILE* 4.9 0.7 - - - -
471A VAL* 3.9 9.9 - - + -
473A SER* 2.7 41.6 + - - +
474A ARG* 3.5 26.2 + - - -
478A TYR* 2.8 55.9 + + - -
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Residues in contact with THR 461 (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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169A PHE* 4.9 0.7 - - + -
260A ILE 4.1 10.8 - - - +
261A ILE* 4.3 7.6 - - + -
262A ASP* 2.7 38.3 + - - +
333A ILE* 3.7 8.4 - - + +
360A VAL* 3.7 27.6 - - + -
361A TYR 3.3 6.3 - - - +
362A ALA* 4.6 0.3 - - - -
460A HIS* 1.3 72.1 + - - +
462A ILE* 1.3 66.2 + - - +
463A LEU* 4.7 1.3 - - + -
471A VAL* 3.9 1.7 - - - +
472A VAL* 3.3 38.8 + - + +
473A SER* 3.0 12.5 + - - -
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Residues in contact with ILE 462 (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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288A ILE* 4.4 10.1 - - + +
291A ALA* 3.7 24.7 - - + -
355A MET* 5.0 0.2 - - + -
360A VAL* 3.5 6.1 - - - +
361A TYR* 2.8 52.1 + - + +
363A ILE* 3.7 31.0 - - + -
460A HIS 4.8 1.8 - - - +
461A THR* 1.3 79.7 - - - +
463A LEU* 1.3 63.5 + - - +
464A LEU* 4.1 17.4 + - + -
469A LYS* 4.6 11.0 - - + -
470A GLU 3.2 9.2 - - - +
471A VAL* 4.1 26.5 - - + -
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Residues in contact with LEU 463 (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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166A TRP* 3.8 31.2 - - + +
169A PHE* 3.8 36.3 - - + -
170A ARG* 5.3 0.4 - - - +
359A GLU 4.0 2.2 - - - -
360A VAL* 3.5 34.1 - - + -
462A ILE* 1.3 74.1 - - - +
464A LEU* 1.3 62.7 + - - +
465A ARG* 3.0 18.6 + - + +
469A LYS* 3.6 4.0 - - - +
470A GLU* 2.8 47.9 + - + +
472A VAL* 4.0 24.5 - - + -
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Residues in contact with LEU 464 (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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137A TYR* 3.2 29.1 + - + +
166A TRP* 5.2 1.9 - - - -
292A GLY* 4.1 15.9 - - - +
293A ILE* 4.6 2.9 - - + +
355A MET* 3.7 26.0 - - + -
356A GLU 3.2 27.4 - - - +
357A GLU* 4.2 1.0 - - - -
358A GLY* 2.6 34.9 + - - +
359A GLU 2.8 21.4 + - - +
361A TYR* 3.9 20.9 - - + -
462A ILE* 4.3 19.7 - - + -
463A LEU* 1.3 73.5 - - - +
465A ARG* 1.3 60.7 + - - +
469A LYS* 4.6 5.2 - - + -
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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