Contacts of the helix formed by residues 477 - 494 (chain A) in PDB entry 4A9C
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 GLY 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A SER 3.7 3.4 + - - -
476A VAL* 1.3 77.9 - - - +
478A ASP* 1.3 55.8 + - - -
479A ARG 3.4 2.7 - - - -
480A GLU* 3.2 18.1 + - - +
481A TRP* 2.8 32.2 + - - +
509A LYS* 4.4 2.5 - - - -
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Residues in contact with ASP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL 3.8 0.2 + - - -
477A GLY* 1.3 68.3 - - - +
479A ARG* 1.3 60.4 + - - +
480A GLU* 4.4 0.2 + - - -
481A TRP* 4.0 1.8 - - - +
482A LEU* 3.4 17.8 + - - +
502A MET* 3.5 35.7 - - + +
504A SER* 2.7 33.3 + - - -
506A TRP 5.4 0.2 - - - +
509A LYS* 3.1 22.8 + - - +
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLY 3.4 0.4 - - - -
478A ASP* 1.3 75.4 - - - +
480A GLU* 1.3 102.3 + - - +
482A LEU* 3.5 7.6 + - - +
483A ASP* 3.2 50.9 + - - +
486A ARG* 5.5 0.8 + - - +
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Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 3.8 15.5 - - + -
477A GLY* 3.2 23.3 + - - +
479A ARG* 1.3 110.1 + - - +
481A TRP* 1.4 61.2 + - - +
483A ASP* 3.6 10.1 + - - +
484A LEU* 3.3 26.8 + - + +
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Residues in contact with TRP 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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433A MET* 4.5 8.1 - - + +
438A PRO* 5.5 3.6 - - + +
445A TRP* 5.5 2.0 - + - -
469A PHE* 3.4 30.5 - - + -
471A THR* 3.4 26.0 - - + +
474A ASN* 3.4 24.8 - - - +
476A VAL* 3.7 19.2 - - + +
477A GLY 2.8 20.2 + - - +
478A ASP* 4.0 2.5 - - - +
480A GLU* 1.4 71.2 - - - +
482A LEU* 1.4 62.7 + - - +
484A LEU* 3.2 15.5 + - + +
485A LEU* 3.1 51.7 + - + +
502A MET* 3.6 25.6 - - + -
509A LYS* 3.5 27.1 - - + -
510A VAL 4.0 0.9 - - - -
511A ALA* 3.6 22.7 - - + -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ASP 3.4 15.3 + - - +
479A ARG* 3.9 6.7 - - - +
481A TRP* 1.4 79.2 - - - +
483A ASP* 1.4 56.2 + - - +
485A LEU* 3.3 7.9 + - + +
486A ARG* 2.9 45.5 + - - +
499A PRO* 3.8 40.6 - - + -
501A ALA 5.5 0.4 - - - +
502A MET* 4.2 18.4 - - + -
511A ALA* 3.9 26.5 - - + -
513A LEU* 4.2 11.4 - - + -
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ARG* 3.2 49.4 + - - +
480A GLU* 3.6 8.9 - - - +
481A TRP 3.3 0.2 - - - -
482A LEU* 1.4 75.7 - - - +
484A LEU* 1.4 52.8 + - + +
486A ARG* 3.1 29.3 + - - +
487A GLY* 2.9 31.0 + - - -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PRO* 4.3 27.8 - - + -
446A PHE* 5.0 2.0 - - - -
476A VAL* 4.0 21.1 - - + -
480A GLU* 3.3 16.8 + - + +
481A TRP* 3.2 14.4 + - + +
483A ASP* 1.4 75.5 - - - +
485A LEU* 1.4 56.1 + - + +
487A GLY* 5.1 0.4 - - - -
488A GLY* 2.8 31.0 + - - -
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TRP* 4.8 6.3 - - + -
446A PHE* 4.5 13.0 - - + -
469A PHE* 3.6 50.3 - - + -
481A TRP* 3.1 61.6 + - + +
482A LEU* 3.7 9.0 - - - +
484A LEU* 1.4 73.9 - - + +
486A ARG* 1.4 58.3 + - - +
488A GLY* 3.3 1.5 + - - -
489A LEU* 2.9 37.8 + - - +
511A ALA* 3.9 13.7 - - + -
513A LEU* 4.4 7.6 - - + -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ARG* 5.5 0.8 + - - +
482A LEU* 2.9 33.4 + - - +
483A ASP* 3.1 28.5 + - - +
485A LEU* 1.4 74.0 - - - +
487A GLY* 1.3 57.2 + - - +
489A LEU* 3.6 4.5 + - - +
490A LYS* 3.1 28.1 + - - +
495A LEU 5.0 1.0 - - - +
496A ASP* 5.6 2.9 - - - +
497A TYR* 3.6 30.8 + - - +
499A PRO* 3.5 32.3 - - - +
513A LEU* 4.2 9.8 - - + +
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Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP 2.9 17.7 + - - -
484A LEU* 3.9 1.1 - - - -
486A ARG* 1.3 73.8 - - - +
488A GLY* 1.3 59.0 + - - +
490A LYS* 3.3 7.9 + - - +
491A GLU* 3.1 29.6 + - - +
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Residues in contact with GLY 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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442A VAL* 6.1 0.7 - - - -
446A PHE* 3.8 24.6 - - - -
484A LEU 2.8 22.4 + - - -
485A LEU 3.7 0.9 - - - -
487A GLY* 1.3 73.4 - - - +
489A LEU* 1.3 59.1 + - - +
491A GLU* 3.6 6.0 + - - +
492A LEU* 3.3 22.9 + - - +
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Residues in contact with LEU 489 (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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446A PHE* 4.4 12.3 - - + -
467A TYR* 3.7 48.7 - - + +
469A PHE* 4.1 26.7 - - + -
485A LEU 2.9 20.8 + - - +
486A ARG 3.9 3.6 - - - +
488A GLY* 1.3 72.6 - - - +
490A LYS* 1.4 55.2 + - - +
492A LEU* 4.5 6.3 - - + -
493A THR* 2.7 45.0 + - + +
495A LEU 4.3 0.7 - - - -
497A TYR* 3.9 36.3 - - + -
513A LEU* 4.2 11.2 - - + -
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Residues in contact with LYS 490 (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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486A ARG 3.1 18.0 + - - +
487A GLY* 3.3 9.4 + - - +
489A LEU* 1.4 75.3 - - - +
491A GLU* 1.3 58.3 + - - +
494A ASP* 2.9 64.3 + - - +
495A LEU 3.5 18.5 + - - +
496A ASP* 3.2 38.9 + - - +
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Residues in contact with GLU 491 (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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487A GLY 3.1 15.9 + - - +
488A GLY* 4.0 6.7 - - - +
489A LEU 3.4 0.2 - - - -
490A LYS* 1.3 76.1 - - - +
492A LEU* 1.3 61.4 + - - +
494A ASP* 4.8 1.2 + - - +
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Residues in contact with LEU 492 (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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443A THR* 3.8 19.3 - - + +
446A PHE* 3.8 35.0 - - + -
447A THR* 3.7 27.4 - - + -
460A VAL 6.0 2.0 - - - +
467A TYR* 4.6 8.7 - - - +
488A GLY 3.3 16.3 + - - +
489A LEU* 3.8 6.3 - - + +
490A LYS 3.3 0.6 - - - -
491A GLU* 1.3 78.8 - - - +
493A THR* 1.3 72.1 + - + +
494A ASP 3.7 0.2 - - - -
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Residues in contact with THR 493 (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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463A PRO* 3.7 37.9 - - + +
467A TYR* 4.2 11.7 - - + +
489A LEU* 2.7 27.1 + - + +
492A LEU* 1.3 87.4 - - + +
494A ASP* 1.4 67.1 + - - +
495A LEU* 3.1 24.9 + - - +
497A TYR* 3.3 23.5 - - + +
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Residues in contact with ASP 494 (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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490A LYS* 2.9 46.5 + - - +
491A GLU 4.6 1.3 - - - +
492A LEU 3.7 0.6 - - - -
493A THR* 1.4 78.4 - - - +
495A LEU* 1.3 63.5 + - + +
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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