Contacts of the helix formed by residues 487 - 501 (chain D) in PDB entry 1DQ8
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482D GLU* 5.5 1.7 - - - +
485D ILE* 3.8 7.4 - - - +
486D GLU* 1.3 93.3 + - - +
488D HIS* 1.3 69.5 + - - +
489D GLU* 3.4 21.3 - - + +
490D ARG* 3.4 15.8 + - + +
491D GLY* 3.3 15.4 + - - -
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Residues in contact with HIS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D GLU* 3.9 24.9 - - + +
486D GLU 4.0 2.6 + - - -
487D THR* 1.3 75.3 - - + +
489D GLU* 1.3 65.4 + - - +
491D GLY* 3.1 12.1 + - - -
492D VAL* 3.2 16.9 + - - +
519D TYR* 3.8 16.6 - - + +
520D SER* 3.6 39.2 + - - -
523D MET* 3.6 29.7 - - + +
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Residues in contact with GLU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D THR* 3.3 12.3 - - + +
488D HIS* 1.3 79.8 - - - +
490D ARG* 1.3 56.5 + - - +
492D VAL* 3.1 6.2 + - - +
493D SER* 2.9 25.9 + - - -
514D TYR* 4.0 19.4 + - + +
515D ARG* 3.7 29.0 + - - +
516D ASP* 3.6 19.4 + - - +
517D TYR 4.9 3.6 + - - +
519D TYR* 4.5 15.5 - - + -
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Residues in contact with ARG 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ALA* 2.9 29.5 + - - +
460D LYS* 3.8 10.3 - - - +
462D LEU 2.9 23.4 + - - -
463D SER* 3.4 6.9 - - - +
464D ASP* 2.9 30.6 + - - +
467D ILE* 3.3 23.1 - - - +
485D ILE* 3.6 26.6 - - + +
486D GLU* 5.2 3.9 - - - +
487D THR* 3.4 14.8 + - - +
488D HIS 3.2 0.8 - - - -
489D GLU* 1.3 75.2 - - - +
491D GLY* 1.3 66.1 + - - +
493D SER* 3.1 8.8 + - - -
494D ILE* 2.9 27.7 + - + +
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Residues in contact with GLY 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D LEU* 3.7 17.4 - - - +
482D GLU* 4.3 7.0 - - - -
485D ILE* 3.5 21.6 - - - +
487D THR 3.3 8.4 + - - -
488D HIS 3.1 8.0 + - - -
490D ARG* 1.3 77.7 - - - +
492D VAL* 1.3 57.4 + - - +
494D ILE 3.6 0.2 + - - -
495D ARG* 3.0 35.7 + - - +
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Residues in contact with VAL 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D GLU* 4.3 3.8 - - - +
488D HIS 3.2 11.8 + - - +
489D GLU* 3.1 8.9 + - - +
490D ARG 3.1 0.6 - - - -
491D GLY* 1.3 76.5 - - - +
493D SER* 1.3 64.3 + - - +
495D ARG* 3.3 13.5 + - - +
496D ARG* 3.0 23.9 + - - +
514D TYR* 3.8 22.2 - - + -
519D TYR* 4.1 31.0 - - + +
523D MET* 4.9 1.1 - - + -
530D VAL* 3.9 13.0 - - + +
531D ILE* 3.7 31.6 - - - +
532D GLY 4.0 2.2 - - - +
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Residues in contact with SER 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ASP* 4.3 3.3 + - - -
489D GLU* 2.9 14.0 + - - -
490D ARG* 3.1 15.9 + - - -
492D VAL* 1.3 76.8 - - - +
494D ILE* 1.3 56.9 + - - +
496D ARG* 3.1 9.4 + - - +
497D GLN* 3.0 48.3 + - - +
514D TYR* 3.7 26.4 + - - -
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Residues in contact with ILE 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ASP* 3.7 34.8 - - + +
467D ILE* 3.5 35.0 - - + -
468D ILE* 4.3 7.0 - - + -
481D LEU* 3.9 23.6 - - + -
485D ILE* 3.4 25.4 - - + -
490D ARG* 2.9 17.5 + - + +
491D GLY 4.1 0.7 - - - +
493D SER* 1.3 73.1 - - - +
495D ARG* 1.3 60.5 + - - +
497D GLN* 3.0 9.9 + - - +
498D LEU* 2.8 42.9 + - + +
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Residues in contact with ARG 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C VAL* 4.8 3.1 - - + -
478D ALA* 2.9 31.7 + - + -
479D TYR* 4.0 3.6 - - - +
481D LEU* 3.6 18.7 - - + +
482D GLU* 2.5 40.9 + - - -
491D GLY 3.0 21.6 + - - +
492D VAL* 3.8 8.4 - - - +
493D SER 3.3 0.2 - - - -
494D ILE* 1.3 74.5 - - - +
496D ARG* 1.3 58.7 + - - +
498D LEU* 3.2 4.6 + - + +
499D LEU* 2.9 34.3 + - + +
529D ASN* 3.2 39.3 + - - +
530D VAL* 2.6 39.4 + - - +
531D ILE* 3.8 13.2 - - + -
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Residues in contact with ARG 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D VAL* 3.0 20.8 + - - +
493D SER* 3.1 9.4 + - - +
495D ARG* 1.3 76.5 - - - +
497D GLN* 1.3 53.2 + - + +
499D LEU* 3.5 3.6 + - - +
500D SER* 2.7 39.6 + - - +
509D LEU* 3.0 45.5 + - + +
510D GLN* 4.7 4.9 + - - +
512D LEU* 2.8 32.9 + - - +
514D TYR* 3.3 45.8 - - - +
531D ILE* 2.8 44.1 + - + +
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Residues in contact with GLN 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ASP* 2.9 40.7 + - - +
468D ILE* 3.9 17.2 - - + +
493D SER* 3.0 34.6 + - - +
494D ILE* 3.0 8.4 + - - +
496D ARG* 1.3 74.0 - - + +
498D LEU* 1.3 67.7 + - - +
500D SER* 3.3 14.7 + - - -
501D LYS* 3.4 26.0 + - - +
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Residues in contact with LEU 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ILE* 3.4 42.8 - - + +
471D VAL* 3.8 28.0 - - + -
472D ASN* 5.1 7.2 - - - +
478D ALA* 3.9 24.2 - - + -
481D LEU* 4.4 11.0 - - + -
494D ILE* 2.8 24.4 + - + +
495D ARG* 3.5 9.2 - - + +
497D GLN* 1.3 74.7 - - - +
499D LEU* 1.3 63.5 + - - +
501D LYS* 3.3 21.6 + - - +
502D LYS* 4.0 11.0 + - - +
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Residues in contact with LEU 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C VAL* 4.5 10.8 - - + -
552C GLN* 3.5 42.8 - - + +
820C MET* 4.1 9.2 - - - -
495D ARG* 2.9 18.9 + - + +
496D ARG 3.7 2.0 - - - +
498D LEU* 1.3 75.3 - - - +
500D SER* 1.3 65.0 + - - +
502D LYS* 2.9 21.7 + - + +
503D LEU* 3.3 22.8 - - + +
509D LEU* 3.6 27.4 - - + -
531D ILE* 3.9 29.6 - - + -
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Residues in contact with SER 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D ARG 2.7 23.8 + - - -
497D GLN* 3.3 10.5 + - - -
499D LEU* 1.3 75.1 - - - +
501D LYS* 1.3 62.9 + - - +
502D LYS 3.1 1.4 + - - -
503D LEU* 3.3 21.4 + - - +
506D PRO* 3.4 41.7 + - - +
509D LEU* 4.3 13.0 - - - +
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Residues in contact with LYS 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ILE* 4.0 37.4 - - + +
472D ASN* 5.7 2.7 - - - +
497D GLN* 3.4 23.3 + - - +
498D LEU* 3.3 9.2 + - - +
499D LEU 3.2 0.8 - - - -
500D SER* 1.3 76.7 - - - +
502D LYS* 1.3 60.4 + - + +
503D LEU 3.4 2.9 + - - +
506D PRO* 5.9 1.6 - - - -
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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