Contacts of the helix formed by residues 482 - 495 (chain D) in PDB entry 3UK3
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 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A T 6.2 0.9 - - - -
3A T 4.0 21.7 - - - +
471D ARG* 3.8 9.5 - - - +
480D PHE* 3.2 5.9 - - - +
481D ARG* 1.3 89.3 + - - +
483D ASN* 1.3 63.0 + - - +
484D TYR* 3.5 9.8 + - - +
485D TYR* 2.8 33.8 + - - +
486D LEU* 3.1 19.8 + - - +
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Residues in contact with ASN 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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3A T 4.9 5.6 + - - +
470D SER 3.0 41.3 + - - +
471D ARG* 3.7 7.5 - - + +
482D SER* 1.3 70.7 - - - +
484D TYR* 1.3 65.2 + - - +
486D LEU* 3.3 4.5 + - - +
487D ASN* 3.0 56.2 + - - +
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Residues in contact with TYR 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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2A T 4.8 0.7 - - + -
3A T 3.4 72.5 + + + +
4A G 3.7 51.0 + + - +
5A C 5.8 1.2 - - - -
482D SER* 3.1 9.6 - - - +
483D ASN* 1.3 83.6 - - - +
485D TYR* 1.3 68.1 + + + +
487D ASN* 3.6 6.4 + - - +
488D ILE* 3.5 48.0 + - + +
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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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15B T 3.2 18.4 - - - +
16B C 2.6 43.1 + + + -
17B T 3.8 31.0 - - + -
480D PHE* 3.6 32.3 - + + -
481D ARG* 5.1 8.1 - - + +
482D SER* 2.8 22.6 + - - +
484D TYR* 1.3 78.7 - + + +
486D LEU* 1.3 54.9 + - - +
488D ILE* 3.1 31.9 + - + -
489D HIS* 2.7 36.9 + - + -
510D GLN* 3.2 15.6 + - - -
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Residues in contact with LEU 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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470D SER* 3.2 41.7 - - - +
471D ARG* 3.5 12.3 - - - -
472D GLU 3.7 5.6 - - - +
473D CYS* 3.8 30.5 - - + +
480D PHE* 4.0 20.1 - - + +
482D SER 3.1 14.4 + - - +
483D ASN* 3.3 10.5 + - - +
485D TYR* 1.3 76.7 - - - +
487D ASN* 1.3 59.7 + - - +
489D HIS* 3.0 10.7 + - + +
490D LEU* 2.8 44.3 + - + +
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Residues in contact with ASN 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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483D ASN* 3.0 49.2 + - - +
484D TYR* 3.8 6.7 - - - +
486D LEU* 1.3 77.1 - - - +
488D ILE* 1.3 62.9 + - + +
490D LEU* 3.6 28.1 + - - +
491D ARG* 3.8 15.2 + - - +
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Residues in contact with ILE 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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484D TYR* 3.5 49.3 + - + +
485D TYR* 3.1 20.1 + - + +
487D ASN* 1.3 74.1 - - + +
489D HIS* 1.3 68.3 + - - +
491D ARG* 3.0 54.0 + - - +
492D THR 4.2 0.5 + - - -
499D TYR* 6.0 1.3 - - - +
509D ALA* 4.5 1.1 - - - +
510D GLN* 3.4 41.7 + - + +
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Residues in contact with HIS 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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15B T 4.7 1.3 - - - -
16B C 2.8 33.4 + - - -
473D CYS* 3.6 11.0 - - + -
476D CYS* 3.5 7.7 - - - -
478D LYS* 4.8 1.8 - - + -
480D PHE* 3.2 35.6 - + + -
485D TYR* 2.7 26.6 + - + +
486D LEU* 3.2 12.1 - - + +
488D ILE* 1.3 73.3 - - - +
490D LEU* 1.3 63.5 + - - +
492D THR* 3.0 38.5 + - + +
493D HIS* 3.2 5.3 + + - -
510D GLN* 5.0 3.1 - - - +
968D ZN 2.0 37.7 - - - -
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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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473D CYS* 3.9 16.2 - - - -
474D SER* 4.5 9.6 - - - +
475D TYR* 3.9 31.9 - - + -
486D LEU* 2.8 35.8 + - + +
487D ASN* 3.8 27.8 - - - +
488D ILE 3.2 0.4 - - - -
489D HIS* 1.3 74.1 - - - +
491D ARG* 1.3 62.4 + - - +
493D HIS* 2.9 16.5 + - - +
494D THR* 3.0 22.9 + - + +
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Residues in contact with ARG 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 ASN* 3.8 12.0 + - - +
488D ILE* 3.0 45.1 + - - +
490D LEU* 1.3 77.1 - - - +
492D THR* 1.3 56.1 + - - +
494D THR* 3.5 9.0 - - - -
495D GLY* 2.9 29.8 + - - -
496D GLU* 3.4 38.2 + - - +
497D LYS* 5.8 0.3 - - - +
498D PRO* 3.9 24.1 - - - +
499D TYR* 3.7 21.0 + - - -
509D ALA* 2.9 39.1 + - + +
510D GLN* 5.0 0.2 - - - +
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Residues in contact with THR 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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15B T 2.5 44.1 + - - -
488D ILE 4.2 0.6 + - - -
489D HIS* 3.0 33.3 + - + +
491D ARG* 1.3 78.3 - - - +
493D HIS* 1.3 85.8 + - + +
495D GLY* 4.5 2.3 + - - -
509D ALA* 4.8 0.8 - - - +
510D GLN* 6.1 1.1 - - - -
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Residues in contact with HIS 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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473D CYS* 3.3 13.6 - - - -
475D TYR* 3.4 41.8 - + + +
476D CYS* 3.9 15.5 - - + -
489D HIS* 3.2 6.9 + + - -
490D LEU* 2.9 10.1 + - - +
492D THR* 1.3 95.9 + - + +
494D THR* 1.3 62.8 + - - +
495D GLY* 3.4 1.0 + - - -
968D ZN 2.0 36.2 - - - -
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Residues in contact with THR 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D TYR* 3.7 26.7 - - + +
490D LEU* 3.0 24.2 + - + +
491D ARG* 3.5 8.3 - - - -
493D HIS* 1.3 76.9 - - - +
495D GLY* 1.3 60.5 + - - +
496D GLU* 3.3 19.3 + - - +
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Residues in contact with GLY 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 ARG 2.9 10.0 + - - -
492D THR 4.5 1.8 - - - -
493D HIS 3.4 3.0 - - - -
494D THR* 1.3 77.9 - - - +
496D GLU* 1.3 66.5 + - - +
497D LYS* 3.4 23.7 + - - +
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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