Contacts of the helix formed by residues 472 - 488 (chain A) in PDB entry 1ORZ
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 SER 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A SER 4.1 0.4 + - - -
471A ARG* 1.4 75.3 + - - +
473A THR* 1.3 65.0 + - - +
474A ALA* 3.5 17.9 + - - +
475A GLU* 3.7 16.8 + - - +
476A ILE* 3.8 13.9 + - - +
514A VAL* 4.3 0.7 - - - -
515A LYS* 4.3 16.8 - - - +
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Residues in contact with THR 473 (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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471A ARG 3.5 3.0 + - - -
472A SER* 1.3 71.6 + - - +
474A ALA* 1.3 58.7 + - - +
475A GLU 3.2 0.7 - - - -
476A ILE* 3.0 6.9 + - - +
477A ARG* 2.7 78.2 + - - +
511A PHE* 4.8 1.2 - - - -
514A VAL* 3.6 22.8 - - - +
515A LYS 5.0 3.2 + - - +
526A ASP* 4.9 4.3 - - - +
530A THR* 4.7 10.6 - - + -
533A LEU* 3.7 14.7 - - - +
55B ASP* 4.5 7.0 - - - +
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Residues in contact with ALA 474 (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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472A SER* 3.3 10.3 + - - +
473A THR* 1.3 83.6 - - - +
475A GLU* 1.3 58.7 + - - +
477A ARG* 3.2 8.1 + - - +
478A MET* 2.8 37.0 + - + +
481A LYS* 5.4 0.3 + - - -
55B ASP* 3.8 28.3 - - - +
56B GLU* 5.0 14.1 - - + +
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 5.7 6.5 - - - +
472A SER* 3.7 14.9 + - - +
473A THR 3.2 0.6 - - - -
474A ALA* 1.3 78.1 - - - +
476A ILE* 1.3 67.8 + - + +
478A MET* 3.2 9.1 + - - +
479A ASN* 2.9 33.9 + - + +
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Residues in contact with ILE 476 (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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471A ARG* 3.3 8.1 - - + +
472A SER 3.9 8.3 - - - +
473A THR* 3.0 9.3 + - - +
475A GLU* 1.3 78.8 - - + +
477A ARG* 1.3 65.1 + - - +
479A ASN* 3.3 3.8 + - - +
480A MET* 2.9 42.6 + - - +
507A VAL* 3.1 26.9 - - + -
510A THR* 3.3 34.1 - - + -
511A PHE* 3.4 9.6 - - + -
514A VAL* 2.9 36.3 - - + -
533A LEU* 4.5 9.6 - - + -
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A THR* 2.7 47.8 + - - +
474A ALA* 3.5 8.7 - - - +
476A ILE* 1.3 73.0 - - - +
478A MET* 1.3 62.7 + - - +
480A MET* 3.1 6.0 + - - +
481A LYS* 3.0 40.7 + - - +
526A ASP* 4.7 1.0 + - - -
529A GLU* 2.9 58.8 + - - +
530A THR* 2.9 20.6 - - - +
533A LEU* 3.0 34.7 - - + +
536A LEU* 4.5 11.2 - - + +
55B ASP* 3.9 16.8 + - - -
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Residues in contact with MET 478 (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 PHE* 3.2 36.5 - - + -
474A ALA* 2.8 21.3 + - + +
475A GLU* 3.8 11.9 - - - +
477A ARG* 1.3 78.3 - - - +
479A ASN* 1.3 63.7 + - - +
481A LYS* 3.2 17.9 + - - +
482A GLN* 2.9 24.4 + - - +
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Residues in contact with ASN 479 (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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475A GLU* 2.9 27.7 + - + +
476A ILE* 3.9 5.8 - - - +
478A MET* 1.3 76.0 - - - +
480A MET* 1.3 66.8 + - - +
482A GLN* 3.0 19.6 + - - +
483A THR* 2.9 25.9 + - - +
503A ASN* 3.3 35.4 + - - +
507A VAL* 4.8 11.9 - - + +
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Residues in contact with MET 480 (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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222A TYR* 4.8 0.7 - - - +
225A ALA* 4.2 2.2 - - - -
476A ILE* 2.9 39.8 + - + +
477A ARG* 3.4 5.6 - - - +
479A ASN* 1.3 77.2 - - - +
481A LYS* 1.3 60.8 + - + +
483A THR* 2.9 28.5 - - - +
484A MET* 3.2 12.0 + - - +
504A ILE* 5.2 4.7 - - + -
507A VAL* 4.1 15.7 - - + -
533A LEU* 3.4 30.5 - - - -
536A LEU* 3.3 15.0 - - + +
537A LEU* 3.0 50.9 - - + +
540A ALA* 4.7 8.7 - - + -
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Residues in contact with LYS 481 (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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224A ARG* 3.3 31.4 - - + +
225A ALA* 2.9 18.0 - - - +
226A TYR* 3.7 17.0 - - - +
227A PHE* 3.7 17.6 - - + -
474A ALA 5.4 0.2 + - - -
477A ARG* 3.0 42.0 + - - +
478A MET* 3.4 25.7 - - - +
480A MET* 1.3 78.9 - - + +
482A GLN* 1.3 53.8 + - - +
484A MET 3.2 1.4 + - - -
485A GLN* 2.8 34.7 + - - +
536A LEU* 6.1 4.3 - - + -
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Residues in contact with GLN 482 (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 PHE* 2.9 32.9 - - + -
478A MET* 2.9 14.7 + - - +
479A ASN* 3.4 20.8 + - - +
481A LYS* 1.3 74.3 - - - +
483A THR* 1.3 65.4 + - - +
485A GLN* 2.9 12.4 + - + +
486A LYS* 3.0 16.3 + - + +
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Residues in contact with THR 483 (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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479A ASN* 2.9 17.8 + - - +
480A MET* 2.9 21.1 - - - +
482A GLN* 1.3 77.8 - - - +
484A MET* 1.3 78.4 + - + +
486A LYS* 4.6 4.3 - - - -
487A ASP* 2.8 54.0 + - - +
500A GLY* 3.8 13.0 + - - -
503A ASN* 4.1 20.2 + - - +
504A ILE* 3.8 25.8 - - + -
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Residues in contact with MET 484 (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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222A TYR* 4.8 0.4 - - + -
225A ALA* 3.5 28.5 - - + +
226A TYR* 3.7 19.2 - - + +
480A MET 3.2 14.4 + - - +
481A LYS 3.5 0.2 - - - +
483A THR* 1.3 87.5 - - + +
485A GLN* 1.3 66.1 + - - +
488A VAL* 2.7 67.7 + - + +
504A ILE* 5.1 4.9 - - - -
540A ALA* 3.5 38.8 - - + +
543A THR* 3.9 21.5 - - + +
544A ALA* 5.1 4.9 - - - -
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Residues in contact with GLN 485 (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 TYR* 3.4 20.9 - - - +
227A PHE* 3.2 32.4 + - + +
228A SER* 3.7 11.3 + - - +
258A PHE* 5.3 5.7 - - - -
369A VAL* 5.8 0.4 - - - +
481A LYS 2.8 14.0 + - - +
482A GLN* 2.9 13.9 + - + +
484A MET* 1.3 80.8 - - - +
486A LYS* 1.3 61.4 + - + +
489A SER* 3.2 32.3 + - - +
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Residues in contact with LYS 486 (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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482A GLN* 3.0 12.9 + - + +
483A THR* 3.7 9.0 - - - +
485A GLN* 1.3 85.4 - - + +
487A ASP* 1.3 106.4 + - - +
489A SER* 3.5 14.6 + - - -
491A PHE 4.8 1.2 - - - +
496A SER* 4.8 11.2 - - - +
499A GLU* 5.6 6.9 - - - +
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Residues in contact with ASP 487 (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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483A THR* 2.8 38.9 + - - +
486A LYS* 1.3 105.7 + - - +
488A VAL* 1.3 64.8 + - + +
489A SER 3.8 0.2 + - - -
492A ARG* 3.6 12.6 - - - +
496A SER* 2.9 43.3 + - - +
497A LEU* 3.3 22.6 - - + +
499A GLU* 4.7 1.7 - - - +
500A GLY* 3.4 15.2 + - - -
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Residues in contact with VAL 488 (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 TYR* 3.0 27.4 - - + +
258A PHE* 4.1 3.6 - - - -
484A MET* 2.7 56.6 + - + +
487A ASP* 1.3 80.1 - - + +
489A SER* 1.3 67.1 + - - +
492A ARG* 2.9 27.8 + - - +
497A LEU* 4.7 7.9 - - + -
543A THR* 4.2 11.9 - - + -
544A ALA* 5.3 8.1 - - + -
547A ALA* 5.6 2.0 - - + -
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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