Contacts of the helix formed by residues 481 - 495 (chain D) in PDB entry 4QY2
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 ASP 481 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479D THR 3.2 6.1 + - - +
480D TYR* 1.3 73.2 - - - +
482D HIS* 1.3 68.4 + - - +
483D SER* 2.8 28.5 + - - -
484D GLN* 3.3 33.9 + - + +
485D TYR* 3.6 12.4 - - + -
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Residues in contact with HIS 482 (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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464B TYR* 5.5 0.2 + - - -
448D GLN 3.9 18.7 + - - +
449D LEU 4.5 0.2 - - - +
450D ARG* 3.1 60.4 + - + +
452D ASN* 2.9 34.7 + - - +
480D TYR* 3.6 8.6 + - + -
481D ASP* 1.3 78.2 + - - +
483D SER* 1.3 80.1 + - - +
484D GLN 3.3 0.3 + - - -
485D TYR 3.3 0.3 + - - -
486D ARG* 3.1 33.5 + - + +
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Residues in contact with SER 483 (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 ASP* 2.8 25.9 + - - -
482D HIS* 1.3 97.8 - - - +
484D GLN* 1.3 62.4 + - - +
486D ARG* 3.8 7.3 + - - +
487D GLU* 3.3 18.4 - - - +
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Residues in contact with GLN 484 (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 ASP* 3.3 27.9 + - - +
482D HIS 3.2 0.2 - - - -
483D SER* 1.3 81.8 + - - +
485D TYR* 1.3 93.6 + - + +
486D ARG 3.6 0.2 - - - -
487D GLU* 3.6 11.8 - - - +
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Residues in contact with TYR 485 (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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452D ASN* 3.8 5.8 - - - +
465D HIS* 3.2 45.9 - + + +
466D ALA 4.1 7.0 - - - -
468D ASP* 5.4 0.7 + - - -
471D CYS* 4.0 19.1 - - + +
474D SER* 5.6 0.6 + - - -
480D TYR* 3.6 29.2 - + - -
481D ASP 3.6 19.7 - - - -
482D HIS 3.3 1.8 + - - -
484D GLN* 1.3 109.1 + - + +
486D ARG* 1.3 59.6 + - - +
487D GLU* 3.3 2.9 + - - -
488D GLU* 3.5 15.8 + - - +
489D ALA* 2.9 27.4 + - - +
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Residues in contact with ARG 486 (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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454B GLU* 2.7 43.0 + - - -
464B TYR* 3.6 12.8 + - - -
493B ARG* 3.1 25.8 + - - +
495B ASN* 6.2 1.6 - - - +
450D ARG* 4.0 2.0 - - - +
451D GLN* 3.8 15.1 - - - +
452D ASN* 3.4 16.8 - - - +
482D HIS* 3.1 37.4 + - + +
483D SER* 4.1 7.6 - - - +
485D TYR* 1.3 77.9 - - - +
487D GLU* 1.3 63.0 + - - +
489D ALA 3.1 0.2 + - - -
490D LEU* 2.7 58.6 + - + +
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Residues in contact with GLU 487 (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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495B ASN* 6.1 3.4 - - - +
483D SER 3.3 23.4 - - - +
484D GLN 3.6 10.6 - - - +
485D TYR 3.8 0.2 - - - -
486D ARG* 1.3 79.1 + - + +
488D GLU* 1.3 64.6 + - - +
490D LEU* 3.4 6.1 + - - +
491D LEU* 3.0 23.1 + - - +
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Residues in contact with GLU 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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465D HIS* 3.7 14.5 - - + +
466D ALA* 3.4 25.4 + - - +
485D TYR* 3.5 16.1 + - - +
487D GLU* 1.3 78.0 + - - +
489D ALA* 1.3 57.5 + - - +
491D LEU* 3.2 10.7 - - + +
492D ASN* 3.0 41.5 + - - +
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Residues in contact with ALA 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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451D GLN 4.5 0.4 - - - +
452D ASN* 3.6 42.0 - - + +
464D TYR* 3.4 18.1 - - - +
465D HIS* 4.3 2.9 - - + -
485D TYR 2.9 19.1 + - - +
486D ARG 3.5 3.1 - - - +
488D GLU* 1.3 75.5 - - - +
490D LEU* 1.3 66.6 + - - +
492D ASN 3.2 1.2 + - - -
493D ARG* 3.0 28.7 + - - +
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Residues in contact with LEU 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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493B ARG 3.5 24.9 - - - +
494B LEU* 4.4 18.8 - - + +
495B ASN* 6.3 0.2 - - + -
451D GLN* 3.9 32.1 - - + +
486D ARG* 2.7 43.8 + - + +
487D GLU* 3.9 5.6 - - - +
489D ALA* 1.3 71.6 - - - +
491D LEU* 1.3 57.8 + - - +
493D ARG* 4.2 12.1 - - - +
494D LEU* 2.9 52.5 + - + +
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Residues in contact with LEU 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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487D GLU 3.0 15.2 + - - +
488D GLU* 3.2 14.1 - - + +
490D LEU* 1.3 76.7 - - - +
492D ASN* 1.3 71.2 + - - +
494D LEU* 5.4 0.2 - - - -
495D ASN* 3.0 28.1 + - - -
496D ILE 3.2 27.4 - - - +
497D ASN* 4.7 12.1 - - + +
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Residues in contact with ASN 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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464D TYR* 2.5 48.5 + - + +
465D HIS* 4.2 2.4 - - - +
488D GLU* 3.0 31.1 + - - +
489D ALA 3.2 0.4 + - - +
491D LEU* 1.3 91.6 - - - +
493D ARG* 1.3 61.9 + - - +
495D ASN* 3.9 10.8 + - - +
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Residues in contact with ARG 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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450D ARG 5.2 0.2 + - - -
451D GLN* 2.9 56.2 + - - +
453D ALA 4.6 4.7 + - - +
454D GLU* 2.5 42.8 + - - +
464D TYR* 3.2 40.7 - - + -
489D ALA 3.0 16.1 + - - +
490D LEU* 3.9 11.8 - - + +
492D ASN* 1.3 77.7 - - - +
494D LEU* 1.3 76.4 + - + +
495D ASN* 4.5 2.4 - - - +
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Residues in contact with LEU 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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494B LEU* 3.5 40.4 - - + -
490D LEU* 2.9 32.2 + - + +
491D LEU* 4.8 0.4 - - - +
493D ARG* 1.3 89.0 - - + +
495D ASN* 1.3 71.1 + - - +
496D ILE* 3.1 30.8 + - + +
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Residues in contact with ASN 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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491D LEU* 3.0 17.7 + - - -
492D ASN 4.4 9.1 + - - +
493D ARG 3.4 3.3 - - - +
494D LEU* 1.3 79.2 - - - +
496D ILE* 1.3 63.1 + - - +
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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