Contacts of the helix formed by residues 487 - 501 (chain A) in PDB entry 1DQA
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 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A GLU* 5.4 2.6 - - - +
485A ILE* 3.7 12.6 - - + +
486A GLU* 1.3 78.5 - - + +
488A HIS* 1.3 64.7 + - - +
489A GLU* 3.3 15.6 + - - +
490A ARG* 3.7 27.5 + - + -
491A GLY* 3.4 15.2 + - - -
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Residues in contact with HIS 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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482A GLU* 3.8 26.6 + - + +
486A GLU 3.8 5.4 + - - -
487A THR* 1.3 69.9 + - - +
489A GLU* 1.3 66.1 + - - +
491A GLY* 3.1 12.0 + - - -
492A VAL* 3.1 17.2 + - - +
519A TYR* 3.6 22.9 - - + -
520A SER* 3.7 30.5 + - - +
523A MET* 3.3 35.0 - - + +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A THR* 3.3 8.1 + - - +
488A HIS* 1.3 80.0 - - - +
490A ARG* 1.3 57.2 + - - +
492A VAL* 3.2 5.6 + - - +
493A SER* 2.9 25.5 + - - -
514A TYR* 3.9 22.8 + - + +
515A ARG* 3.6 27.2 + - - +
516A ASP* 3.2 26.0 + - - +
517A TYR 4.6 4.1 + - - +
519A TYR* 4.3 14.0 - - + -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU 2.8 30.5 + - - +
463A SER* 3.2 15.0 - - - +
464A ASP* 3.0 29.5 + - - +
467A ILE* 3.3 21.7 - - - +
485A ILE* 4.1 20.3 - - + +
487A THR* 3.6 27.2 + - + +
488A HIS 3.3 0.8 - - - -
489A GLU* 1.3 75.0 - - - +
491A GLY* 1.3 61.6 + - - +
493A SER* 3.2 8.7 + - - -
494A ILE* 2.9 36.0 + - + +
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Residues in contact with GLY 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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481A LEU* 3.7 14.4 - - - +
482A GLU* 4.3 8.1 - - - -
485A ILE* 3.9 18.7 - - - +
487A THR 3.4 7.6 + - - -
488A HIS 3.1 7.3 + - - -
490A ARG* 1.3 79.7 - - - +
492A VAL* 1.3 56.5 + - - +
494A ILE* 3.4 3.4 + - - +
495A ARG* 2.8 35.2 + - - +
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Residues in contact with VAL 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLU* 3.9 11.4 - - - +
488A HIS 3.1 12.9 + - - +
489A GLU* 3.4 9.0 - - - +
491A GLY* 1.3 77.4 - - - +
493A SER* 1.3 58.6 + - - +
495A ARG* 3.2 3.7 + - - +
496A ARG* 2.9 34.5 + - - +
514A TYR* 3.9 21.1 - - + -
519A TYR* 4.3 28.3 - - + +
523A MET* 5.7 0.9 - - - -
530A VAL* 3.5 30.5 - - + +
531A ILE 3.8 20.9 - - - -
532A GLY 4.0 2.0 - - - +
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Residues in contact with SER 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP* 4.3 4.0 + - - -
489A GLU 2.9 13.5 + - - -
490A ARG* 3.4 15.5 - - - -
492A VAL* 1.3 77.6 - - - +
494A ILE* 1.3 61.5 + - - +
496A ARG* 3.3 8.8 + - - +
497A GLN* 3.0 42.5 + - - +
514A TYR* 3.7 28.8 + - - -
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Residues in contact with ILE 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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464A ASP* 3.4 50.3 - - + +
467A ILE* 4.2 14.8 - - + -
468A ILE* 4.3 3.8 - - + -
471A VAL* 5.2 0.4 - - + -
481A LEU* 4.0 22.9 - - + -
485A ILE* 3.7 18.4 - - + -
490A ARG* 2.9 24.0 + - + +
491A GLY 3.7 5.2 - - - +
493A SER* 1.3 71.2 - - - +
495A ARG* 1.3 67.0 + - - +
497A GLN* 3.0 12.2 + - - +
498A LEU* 2.9 44.4 + - + +
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Residues in contact with ARG 495 (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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478A ALA* 2.7 30.8 + - + -
479A TYR* 3.7 9.9 + - - +
481A LEU* 3.7 16.9 - - + +
482A GLU* 2.7 44.0 + - - -
491A GLY 2.8 22.1 + - - +
492A VAL* 3.2 6.5 + - - +
494A ILE* 1.3 77.1 - - - +
496A ARG* 1.3 57.0 + - - +
498A LEU* 3.2 6.8 + - + +
499A LEU* 2.9 30.1 + - + +
529A ASN* 2.9 44.5 + - - +
530A VAL 2.9 29.5 + - - +
531A ILE* 3.8 12.1 - - + -
540B VAL* 4.6 4.0 - - + -
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Residues in contact with ARG 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A VAL* 2.9 22.4 + - - +
493A SER* 3.5 7.9 - - - +
494A ILE 3.2 0.2 - - - -
495A ARG* 1.3 76.7 - - - +
497A GLN* 1.3 53.9 + - + +
499A LEU* 3.4 2.6 + - - -
500A SER* 2.8 38.5 + - - +
509A LEU* 3.0 48.0 + - + +
510A GLN* 4.8 3.4 + - - +
512A LEU* 2.8 35.5 + - - +
514A TYR* 3.4 42.8 - - - +
531A ILE* 2.9 44.1 + - + +
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Residues in contact with GLN 497 (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 ASP* 3.0 35.4 + - - +
468A ILE* 3.8 22.8 - - + +
493A SER* 3.0 31.5 + - - +
494A ILE* 3.0 17.6 + - - +
496A ARG* 1.3 76.0 - - + +
498A LEU* 1.3 63.6 + - - +
499A LEU 3.4 0.3 + - - -
500A SER* 3.4 14.3 + - - -
501A LYS* 3.6 20.9 + - - +
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Residues in contact with LEU 498 (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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468A ILE* 3.3 42.2 - - + -
471A VAL* 4.0 26.7 - - + -
472A ASN* 5.2 6.1 - - - +
478A ALA* 4.5 13.2 - - + -
481A LEU* 3.9 28.0 - - + -
494A ILE* 2.9 23.3 + - + +
495A ARG* 3.2 7.6 + - - +
497A GLN* 1.3 75.8 - - - +
499A LEU* 1.3 62.1 + - - +
501A LYS* 3.7 16.6 + - - +
502A LYS* 3.7 27.1 - - - +
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Residues in contact with LEU 499 (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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495A ARG* 2.9 18.4 + - + +
496A ARG 3.7 3.8 - - - +
498A LEU* 1.3 74.4 - - - +
500A SER* 1.3 56.3 + - - +
501A LYS 3.1 2.2 - - - -
502A LYS* 2.8 33.8 + - + +
503A LEU* 3.4 15.9 - - + +
509A LEU* 4.0 11.7 - - + -
531A ILE* 4.0 38.1 - - + -
540B VAL* 4.4 12.3 - - + -
552B GLN* 3.6 41.7 - - + +
820B MET* 4.2 12.8 - - - -
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ARG* 2.8 23.0 + - - +
497A GLN* 3.4 8.8 + - - -
499A LEU* 1.3 75.9 - - - +
501A LYS* 1.3 62.3 + - - +
503A LEU* 3.3 20.4 + - - +
506A PRO* 3.6 42.6 + - - +
509A LEU* 3.8 13.4 - - - +
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Residues in contact with LYS 501 (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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468A ILE* 3.4 37.1 - - - +
472A ASN* 4.2 8.6 - - - +
497A GLN* 3.6 17.0 + - - +
498A LEU* 3.8 11.2 - - - +
499A LEU 3.1 0.8 - - - -
500A SER* 1.3 76.7 - - - +
502A LYS* 1.3 60.7 + - + +
503A LEU 3.3 4.4 + - - +
506A PRO* 5.8 1.3 - - - -
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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