Contacts of the helix formed by residues 458 - 468 (chain B) in PDB entry 2AX1
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 ASP 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B GLU* 2.8 30.0 + - - +
457B LEU* 1.3 82.3 - - - +
459B LEU* 1.3 64.1 + - - +
460B PRO 3.3 0.2 - - - -
461B GLN* 3.0 33.9 + - - +
462B ILE* 3.1 33.2 + - + +
517B ARG* 5.1 10.7 + - - -
545B LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B TRP* 5.4 1.3 - - + -
409B LEU* 4.2 22.0 - - + -
412B ILE* 4.2 24.2 - - + -
413B ILE* 3.8 32.3 - - + -
430B PHE* 3.7 24.0 - - + -
454B ILE* 5.4 1.1 - - + -
455B GLU 4.0 1.0 + - - +
456B PRO* 3.2 25.8 + - + +
458B ASP* 1.3 76.4 - - - +
460B PRO* 1.3 63.5 - - + +
462B ILE* 3.1 9.2 + - + -
463B ILE* 2.8 44.8 + - + +
525B LEU* 4.4 9.0 - - + -
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Residues in contact with PRO 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B LEU 3.8 2.2 - - - +
458B ASP 3.5 3.6 - - - -
459B LEU* 1.3 94.1 - - + +
461B GLN* 1.3 62.3 + - - +
464B GLU* 3.0 24.9 + - - +
472B PHE* 3.2 22.1 - - + -
520B ILE* 4.1 12.6 - - + +
521B CYS* 3.7 42.2 - - - -
524B TYR* 4.7 5.6 - - + -
525B LEU* 4.3 8.5 - - + -
539B ILE* 3.6 22.7 - - + -
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Residues in contact with GLN 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B LEU 3.5 6.9 + - - +
458B ASP* 3.0 48.4 + - - +
460B PRO* 1.3 78.3 - - - +
462B ILE* 1.3 59.9 + - - +
464B GLU 3.4 0.5 + - - -
465B ARG* 2.9 30.7 + - - +
520B ILE* 5.4 2.0 - - - +
539B ILE* 3.7 17.5 - - + -
541B ALA* 3.5 28.5 - - + +
542B ALA* 3.9 20.3 - - - +
545B LEU* 3.5 18.1 - - + +
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ILE* 4.2 14.6 - - + -
454B ILE* 3.8 29.4 - - + -
458B ASP* 3.1 30.6 + - + +
459B LEU* 3.6 11.9 - - + +
461B GLN* 1.3 76.7 - - - +
463B ILE* 1.3 61.8 + - + +
465B ARG* 3.4 1.6 + - - +
466B LEU* 2.9 40.4 + - + +
545B LEU* 3.9 17.5 - - + -
547B LEU* 4.2 6.1 - - + -
550B TRP* 3.9 34.1 - - + -
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Residues in contact with ILE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ILE* 4.4 11.4 - - + +
413B ILE* 5.3 4.0 - - - -
416B ALA* 3.7 33.7 - - + -
426B MET* 3.8 20.4 - - + -
459B LEU* 2.8 31.6 + - + +
460B PRO 3.9 3.4 - - - +
462B ILE* 1.3 76.9 - - + +
464B GLU* 1.3 58.6 + - - +
466B LEU* 5.7 0.2 - - - -
467B HIS* 2.8 34.8 + - + +
468B GLY 3.5 0.7 + - - +
471B ALA* 3.8 15.5 - - + -
472B PHE* 3.6 18.8 - - + -
525B LEU* 3.9 16.8 - - + -
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Residues in contact with GLU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B PRO 3.0 16.5 + - - +
461B GLN* 3.4 4.2 + - - +
463B ILE* 1.3 77.8 - - - +
465B ARG* 1.3 60.0 + - - +
468B GLY* 2.9 33.2 + - - -
469B LEU* 3.6 32.1 - - + +
472B PHE* 3.9 8.4 - - + -
538B PRO* 3.3 23.9 - - - +
539B ILE* 3.0 35.3 + - - +
542B ALA* 3.8 16.3 - - + +
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Residues in contact with ARG 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B GLN 2.9 18.1 + - - +
462B ILE 3.6 4.3 - - - +
464B GLU* 1.3 81.2 - - - +
466B LEU* 1.3 62.5 + - + +
468B GLY 4.7 0.5 + - - -
542B ALA* 3.6 18.2 + - + +
543B GLY* 5.0 9.0 + - - -
545B LEU* 2.8 33.9 + - + +
546B ASP* 5.0 8.3 + - - +
547B LEU* 3.7 26.6 - - + +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B SER* 4.4 12.9 + - - -
197B PRO* 5.0 5.6 - - + -
198B GLY* 4.4 15.2 + - - -
413B ILE* 3.7 32.8 - - + +
414B MET* 5.3 0.4 - - - -
462B ILE* 2.9 26.9 + - + +
463B ILE* 5.7 0.2 - - - -
465B ARG* 1.3 81.0 - - + +
467B HIS* 1.3 77.3 + - + +
547B LEU* 3.7 20.4 - - + -
550B TRP* 4.4 3.8 - - + -
551B PHE* 3.3 43.5 - - + -
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Residues in contact with HIS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PRO* 3.8 21.7 - - + +
198B GLY* 4.7 6.7 + - - -
381B VAL* 6.1 0.2 - - - +
413B ILE 2.8 24.2 + - - -
414B MET 3.5 21.5 + - - -
416B ALA* 3.7 22.1 - - + +
417B PRO* 3.5 23.0 - - + +
463B ILE* 2.8 24.1 + - + +
466B LEU* 1.3 87.3 + - + +
468B GLY* 1.3 60.6 + - - +
470B SER* 3.8 12.1 + - - -
471B ALA* 3.8 15.8 + - + -
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ILE 3.5 3.7 + - - +
464B GLU* 2.9 26.4 + - - -
465B ARG 4.6 0.6 + - - -
466B LEU 3.7 1.0 - - - -
467B HIS* 1.3 78.1 - - - +
469B LEU* 1.3 62.0 + - - -
470B SER* 3.1 8.6 + - - -
471B ALA* 3.1 17.5 + - - +
472B PHE* 4.6 0.9 - - - -
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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