Contacts of the helix formed by residues 466 - 481 (chain A) in PDB entry 3AEF
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 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A ILE 3.8 0.6 + - - -
465A ARG* 1.3 76.8 - - - +
467A SER* 1.3 62.8 + - - +
469A LEU* 3.3 3.8 + - - +
470A ARG* 3.1 32.3 + - - +
507A LEU* 3.7 11.4 - - - +
508A LYS 3.7 14.2 + - - -
519A ASP* 4.1 10.3 + - - +
522A GLU* 3.9 12.6 - - + +
523A THR* 2.7 50.1 + - - +
526A LEU* 4.0 13.6 - - + +
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ARG* 3.4 8.4 - - - +
466A THR* 1.3 80.5 - - - +
468A GLU* 1.3 62.1 + - - +
470A ARG* 3.5 21.3 + - - +
471A LEU* 3.1 27.7 + - - +
53B ASN* 2.7 60.0 + - - +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR 5.3 0.7 - - - +
464A ILE* 4.2 13.3 - - + +
465A ARG* 3.2 31.1 + - + +
467A SER* 1.3 86.3 + - - +
469A LEU* 1.3 60.6 + - - +
471A LEU* 3.6 5.9 + - - +
472A SER* 2.9 29.7 + - - -
53B ASN 5.2 1.1 - - - +
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Residues in contact with LEU 469 (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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464A ILE* 4.0 18.5 - - + +
465A ARG 3.4 3.1 + - - +
466A THR 3.3 8.3 + - - +
468A GLU* 1.3 75.5 - - - +
470A ARG* 1.3 65.3 + - - +
472A SER* 3.5 4.6 - - - +
473A MET* 3.1 22.9 + - - +
500A LEU* 3.6 42.8 - - + +
503A ASP* 3.8 22.2 - - + +
504A LEU* 3.9 32.1 - - + +
507A LEU* 4.2 8.5 - - + -
526A LEU* 3.8 24.6 - - + +
530A MET* 5.6 2.7 - - + -
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Residues in contact with ARG 470 (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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219A ARG* 6.3 0.9 - - - +
466A THR* 3.1 22.4 + - + +
467A SER* 3.5 29.5 + - - +
468A GLU 3.3 0.2 - - - -
469A LEU* 1.3 76.7 - - - +
471A LEU* 1.3 58.1 + - - +
473A MET* 3.1 13.2 + - + +
474A GLN* 2.8 58.2 + - - +
522A GLU* 2.7 43.1 + - - +
526A LEU* 3.6 21.3 - - + +
529A LEU* 4.5 11.2 - - + +
53B ASN* 3.4 30.3 + - - +
63B ARG* 6.0 0.9 - - - -
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 3.8 35.9 - - + -
467A SER 3.1 13.9 + - - +
468A GLU* 4.0 7.0 - - - +
470A ARG* 1.3 75.4 - - - +
472A SER* 1.3 66.0 + - - +
474A GLN* 3.8 13.8 - - - +
475A LYS* 3.0 33.3 + - + +
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Residues in contact with SER 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU 2.9 19.4 + - - -
469A LEU* 3.5 12.8 - - - +
470A ARG 3.2 0.2 - - - -
471A LEU* 1.3 76.5 - - - +
473A MET* 1.3 57.5 + - - +
475A LYS* 4.0 2.2 - - - +
476A SER* 2.6 34.6 + - - -
500A LEU* 3.7 24.9 - - - +
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Residues in contact with MET 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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219A ARG 3.6 23.6 - - - +
220A THR* 3.8 9.6 - - - +
469A LEU 3.1 11.1 + - - +
470A ARG* 3.5 12.8 - - + +
472A SER* 1.3 76.6 - - - +
474A GLN* 1.3 70.3 + - + +
476A SER* 3.3 2.9 + - - -
477A MET* 2.9 31.5 + - + +
497A ILE* 4.3 5.2 - - + -
500A LEU* 3.6 12.2 - - + +
526A LEU* 4.7 3.1 - - + -
529A LEU* 3.8 44.2 - - + +
530A MET* 3.5 34.3 - - - +
533A ALA* 4.1 14.1 - - + -
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Residues in contact with GLN 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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219A ARG* 3.1 35.3 + - - +
220A THR 3.3 8.3 - - - +
221A TYR 3.3 18.3 - - - +
222A PHE* 3.4 32.1 + - + +
470A ARG* 2.8 41.0 + - - +
471A LEU* 3.8 31.1 - - - +
472A SER 3.4 0.2 - - - -
473A MET* 1.3 77.6 - - + +
475A LYS* 1.3 56.9 + - - +
477A MET* 3.4 2.1 + - - +
478A GLN* 2.9 23.4 + - - +
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Residues in contact with LYS 475 (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 PHE* 3.6 42.3 - - + -
471A LEU* 3.0 26.9 + - + +
472A SER* 4.4 2.0 - - - +
474A GLN* 1.3 74.0 - - - +
476A SER* 1.3 53.8 + - - +
478A GLN* 3.9 8.7 - - + +
479A SER* 2.6 40.4 + - - -
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Residues in contact with SER 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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472A SER 2.6 24.0 + - - -
473A MET* 3.6 4.0 - - - -
475A LYS* 1.3 75.8 - - - +
477A MET* 1.3 63.2 + - - +
479A SER* 4.0 3.4 - - - -
480A HIS* 3.0 35.6 + - - +
493A GLY* 5.2 1.4 - - - -
496A LYS* 4.0 26.6 - - - +
497A ILE* 3.9 20.4 - - - -
500A LEU* 4.0 6.9 - - - +
537A ILE* 5.5 0.2 - - - +
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Residues in contact with MET 477 (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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220A THR* 3.4 27.4 - - - +
221A TYR* 3.1 45.2 - - + +
473A MET 2.9 16.3 + - - +
474A GLN 3.8 0.4 - - - +
476A SER* 1.3 74.4 - - - +
478A GLN* 1.3 59.4 + - - +
480A HIS* 5.2 0.4 - - - -
481A ALA* 3.0 31.2 + - + +
497A ILE* 4.0 20.9 - - + -
533A ALA* 4.1 21.3 - - + +
536A THR* 3.8 29.6 - - + -
537A ILE* 4.1 23.3 - - + -
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Residues in contact with GLN 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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221A TYR* 3.8 13.1 - - - -
222A PHE* 4.2 16.4 - - + +
223A SER* 3.4 38.4 + - - +
253A PHE* 4.5 13.7 - - - -
364A VAL* 4.8 0.5 - - - +
474A GLN 2.9 18.3 + - - +
475A LYS* 3.9 13.7 - - + +
476A SER 3.3 0.2 - - - -
477A MET* 1.3 78.8 - - - +
479A SER* 1.3 58.9 + - - +
482A ALA* 3.7 28.2 - - - +
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Residues in contact with SER 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 LYS* 2.6 27.7 + - - -
476A SER* 4.0 0.2 - - - -
478A GLN* 1.3 76.2 - - - +
480A HIS* 1.3 80.0 + - - +
482A ALA* 5.1 2.8 - - - +
489A VAL* 3.7 12.0 - - - +
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Residues in contact with HIS 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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476A SER* 3.0 26.5 + - - +
479A SER* 1.3 94.7 + - - +
481A ALA* 1.3 60.0 + - - +
482A ALA 3.9 1.6 - - - -
484A PHE 5.8 0.7 - - - -
485A ARG* 4.3 4.2 - - - +
489A VAL* 2.9 43.5 - - + +
490A LEU* 3.4 22.9 - - - +
492A GLU* 3.3 30.7 + - + +
493A GLY* 3.4 26.7 + - - -
496A LYS* 4.1 20.9 - - + -
537A ILE* 4.0 4.6 - - + +
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Residues in contact with ALA 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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221A TYR* 3.0 28.7 + - + +
253A PHE* 3.8 2.6 - - - -
477A MET* 3.0 19.4 + - + +
480A HIS* 1.3 80.5 - - - +
482A ALA* 1.3 61.8 + - - +
485A ARG* 2.8 32.4 + - - +
490A LEU* 4.8 0.7 - - + -
536A THR* 5.6 1.8 - - + -
537A ILE* 3.5 21.8 - - + -
540A ALA* 5.6 1.8 - - + -
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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