Contacts of the helix formed by residues 463 - 484 (chain A) in PDB entry 3ODX
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 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A PHE 3.4 0.2 - - - -
462A PRO* 1.3 77.1 + - - +
464A LEU* 1.3 68.6 + - - +
465A ASP 3.1 2.2 - - - -
466A GLU* 2.8 21.9 + - - +
467A LEU* 2.9 10.0 + - - -
511A ILE* 4.1 34.5 - - - +
514A ARG* 2.7 24.1 + - - -
515A PHE* 4.0 7.7 - - - +
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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
----------------------------------------------------------
435A LEU* 4.2 17.0 - - + +
438A LEU* 4.1 20.9 - - + -
439A HIS* 3.6 39.3 - - + +
443A PHE* 4.2 21.9 - - + -
461A PHE* 3.4 25.0 + - + +
463A SER* 1.3 74.8 - - - +
465A ASP* 1.3 64.2 + - - +
467A LEU* 3.0 7.7 + - + +
468A ILE* 2.8 39.1 + - + +
515A PHE* 3.8 22.4 - - + -
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Residues in contact with ASP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A HIS* 3.0 35.2 + - - -
443A PHE* 4.4 13.5 - - - -
463A SER 2.8 4.8 + - - -
464A LEU* 1.3 78.1 - - - +
466A GLU* 1.3 59.1 + - + +
468A ILE* 3.5 8.2 + - - +
469A GLU* 3.4 23.0 + - - +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A SER* 2.8 16.5 + - - +
465A ASP* 1.3 73.1 - - - +
467A LEU* 1.3 60.6 + - - +
468A ILE 3.2 0.4 - - - -
469A GLU* 3.3 20.1 + - - +
470A VAL* 3.0 30.3 + - - +
507A TRP* 3.0 45.5 + - + +
511A ILE* 4.0 11.2 - - + -
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.8 20.9 - - + -
463A SER 2.9 12.4 + - - +
464A LEU* 3.4 11.9 - - + +
466A GLU* 1.3 74.0 - - - +
468A ILE* 1.3 66.3 + - - +
470A VAL* 3.4 14.8 + - + +
471A HIS* 3.5 19.2 + - + +
511A ILE* 3.7 11.4 - - + +
512A SER* 3.9 25.4 - - - +
515A PHE* 3.8 31.4 - - + -
561A GLU* 3.2 41.1 - - - +
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Residues in contact with ILE 468 (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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432A VAL* 4.7 4.1 - - + +
435A LEU* 3.8 35.7 - - + +
436A ARG* 4.1 25.1 - - + -
439A HIS* 3.7 37.2 - - + -
464A LEU* 2.8 25.0 + - + +
465A ASP* 3.6 9.2 - - - +
466A GLU 3.2 0.2 - - - -
467A LEU* 1.3 78.7 - - - +
469A GLU* 1.3 63.1 + - - +
471A HIS* 3.4 2.4 + - - +
472A SER* 2.4 44.7 + - - +
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Residues in contact with GLU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ASP 3.4 14.0 - - - +
466A GLU* 3.3 28.0 + - - +
468A ILE* 1.3 83.8 - - - +
470A VAL* 1.3 52.3 + - - +
472A SER* 3.2 13.6 + - - -
473A LEU* 2.6 38.0 + - - +
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 3.0 20.2 + - - +
467A LEU* 3.5 20.6 - - + +
468A ILE 3.3 0.4 + - - -
469A GLU* 1.3 76.9 - - - +
471A HIS* 1.3 68.9 + - + +
473A LEU* 3.1 12.2 + - - +
474A PHE* 3.3 12.5 + - - +
499A ARG* 4.4 6.2 - - + +
507A TRP* 3.5 35.0 - - + +
508A PHE* 3.3 40.6 - - + +
511A ILE* 4.5 7.9 - - + -
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Residues in contact with HIS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 2.8 25.2 + - - +
431A HIS* 3.3 26.0 + + + -
432A VAL* 3.6 15.9 - - + +
435A LEU* 3.8 5.2 - - + -
467A LEU* 3.5 20.1 + - + -
468A ILE 3.4 4.8 + - - +
470A VAL* 1.3 80.0 - - + +
472A SER* 1.3 60.7 + - - +
474A PHE* 3.3 6.2 + - - +
475A LEU* 2.8 29.3 + - - +
499A ARG* 5.1 0.6 + - - -
508A PHE* 3.5 25.6 - + - -
561A GLU* 2.8 31.1 + - - -
564A ARG* 4.2 2.2 - - + -
565A LEU* 4.9 0.2 - - + -
568A TYR* 3.0 23.4 + + - -
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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
----------------------------------------------------------
432A VAL* 3.6 18.3 - - - +
436A ARG* 5.6 0.3 - - - -
468A ILE* 2.4 38.1 + - - +
469A GLU* 3.2 18.4 + - - -
471A HIS* 1.3 76.7 - - - +
473A LEU* 1.3 56.7 + - - +
475A LEU* 3.3 5.6 + - - +
476A ASP* 2.9 39.0 + - - -
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLU 2.6 19.9 + - - +
470A VAL* 3.1 6.0 + - - +
472A SER* 1.3 73.3 - - - +
474A PHE* 1.3 57.3 + - - +
476A ASP* 3.2 15.6 + - + +
477A ARG* 3.0 54.3 + - + +
499A ARG* 6.3 2.0 - - + -
504A GLU* 3.9 21.8 - - - +
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Residues in contact with PHE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 4.2 17.5 - - + -
428A GLU* 3.5 36.3 - - + -
470A VAL 3.3 5.4 + - - +
471A HIS* 3.5 7.2 - - - +
473A LEU* 1.3 73.7 - - - +
475A LEU* 1.3 66.7 + - - +
476A ASP 2.9 2.2 + - - -
477A ARG* 3.0 8.7 + - - +
478A LEU* 3.0 55.2 + - + +
495A VAL* 4.6 10.3 - - + -
496A LEU* 4.6 14.8 - - + -
499A ARG* 2.9 68.8 - - + +
500A PHE* 4.2 3.8 - + - -
568A TYR* 3.9 7.2 - + - -
572A LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 4.1 14.8 - - + +
428A GLU* 4.2 8.2 - - + +
429A ALA* 3.6 46.0 - - + +
432A VAL* 4.3 21.8 - - + -
471A HIS 2.8 17.4 + - - +
472A SER* 3.4 10.3 - - - +
474A PHE* 1.3 72.4 - - - +
476A ASP* 1.3 64.1 + - - +
478A LEU* 3.6 4.0 + - - +
479A MET* 3.1 53.8 + - - +
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Residues in contact with ASP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A SER* 2.9 21.5 + - - +
473A LEU* 3.3 20.7 - - + +
474A PHE 2.9 0.8 - - - -
475A LEU* 1.3 86.1 - - - +
477A ARG* 1.3 59.1 + - - +
479A MET* 3.4 9.2 + - - +
480A LYS* 3.0 29.6 + - - +
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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 LEU* 3.0 44.4 + - + +
474A PHE* 3.0 14.3 + - - +
476A ASP* 1.3 74.6 - - - +
478A LEU* 1.3 54.8 + - - +
480A LYS* 3.1 7.9 + - - +
481A ARG* 2.9 34.7 + - - +
495A VAL* 3.5 31.0 - - + +
498A ALA* 3.5 42.0 + - - +
499A ARG* 5.1 3.7 - - - +
504A GLU* 4.8 8.1 - - - +
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Residues in contact with LEU 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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421A ILE* 6.0 1.8 - - + +
424A LEU* 4.0 30.7 - - + +
425A LEU* 3.4 42.6 - - + +
428A GLU* 4.4 5.8 - - + -
474A PHE* 3.0 39.9 + - + +
475A LEU* 3.8 1.8 - - - +
477A ARG* 1.3 75.9 - - - +
479A MET* 1.3 61.4 + - - +
481A ARG* 3.9 5.5 - - + +
482A ARG* 3.0 27.2 + - - +
492A ILE* 4.4 19.1 - - + -
495A VAL* 4.2 16.8 - - + -
496A LEU* 4.7 1.3 - - + -
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Residues in contact with MET 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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425A LEU* 3.7 19.3 - - + -
475A LEU* 3.1 40.9 + - - +
476A ASP* 3.9 10.8 - - - +
477A ARG 3.2 0.2 - - - -
478A LEU* 1.3 74.6 - - - +
480A LYS* 1.3 68.1 + - - +
482A ARG* 3.2 4.5 + - - +
483A GLN* 2.8 28.5 + - + +
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Residues in contact with LYS 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 ASP 3.0 17.0 + - - +
477A ARG* 3.1 6.9 + - - +
479A MET* 1.3 76.3 - - - +
481A ARG* 1.3 64.0 + - - +
483A GLN* 3.4 5.4 + - - +
484A GLU* 3.0 43.5 + - + +
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Residues in contact with ARG 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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477A ARG 2.9 15.9 + - - +
478A LEU* 3.9 6.1 - - + +
480A LYS* 1.3 73.8 - - - +
482A ARG* 1.3 70.6 + - - +
484A GLU* 2.7 46.7 + - - +
485A SER* 3.2 16.7 + - - -
489A ILE* 4.2 13.7 - - + -
490A GLU 4.8 3.4 - - - -
491A GLU* 2.7 47.4 + - - +
492A ILE* 5.1 5.2 - - + -
494A ASP* 2.6 41.2 + - - -
495A VAL* 3.7 19.5 - - + +
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Residues in contact with ARG 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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418A GLN* 5.7 0.6 + - - -
422A SER* 5.8 3.8 + - - -
425A LEU* 4.9 18.6 - - + -
478A LEU 3.0 18.1 + - - +
479A MET* 3.7 5.6 - - - +
481A ARG* 1.3 75.6 - - - +
483A GLN* 1.3 64.5 + - - +
485A SER* 2.8 41.3 + - - -
489A ILE* 3.7 43.9 - - + +
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Residues in contact with GLN 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 MET* 2.8 22.2 + - + +
480A LYS* 3.7 7.0 - - - +
482A ARG* 1.3 78.5 - - - +
484A GLU* 1.3 57.2 + - - +
485A SER 3.1 7.8 + - - -
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS* 3.0 38.7 + - + +
481A ARG* 2.7 47.3 + - - +
482A ARG 3.0 0.6 + - - -
483A GLN* 1.3 74.8 - - - +
485A SER* 1.3 57.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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