Contacts of the helix formed by residues 476 - 488 (chain B) in PDB entry 2DB3
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 ALA 476 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472B VAL* 3.5 15.3 - - + +
473B ASN* 2.8 19.1 + - + +
475B TYR* 1.3 96.9 - - + +
477B LYS* 1.3 64.9 + - - +
478B ARG 3.3 1.3 - - - -
479B SER* 2.9 26.3 + - - -
480B LYS* 3.3 6.5 + - + +
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B VAL* 3.6 16.4 - - + +
473B ASN 3.3 6.9 + - - +
474B LYS* 3.7 24.8 - - + +
475B TYR 3.4 1.2 - - - -
476B ALA* 1.3 76.9 - - - +
478B ARG* 1.3 63.4 + - - +
479B SER 3.1 1.2 + - - -
480B LYS 3.3 0.9 + - - +
481B LEU* 3.1 23.7 + - - +
564B TYR* 3.1 44.9 + - + +
565B ASP* 2.7 33.9 + - - +
566B MET 4.6 0.8 - - - +
592B PHE* 3.7 27.6 + - + -
594B ASP* 4.4 25.2 + - - +
597B LYS* 4.1 12.3 - - - +
598B ASP* 4.8 0.2 + - - -
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Residues in contact with ARG 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B LYS 4.7 4.7 - - - -
475B TYR* 3.0 39.7 + - - +
476B ALA 3.3 1.2 + - - -
477B LYS* 1.3 76.3 - - - +
479B SER* 1.3 57.9 + - - +
481B LEU* 4.2 2.8 - - - +
482B ILE* 3.2 28.2 + - - +
504B PHE* 5.1 15.4 - - + -
505B LEU* 5.6 0.2 - - - -
508B PHE* 3.9 29.5 - - + -
564B TYR* 3.0 24.0 - - - +
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B TYR 5.2 1.6 + - - -
476B ALA* 2.9 16.5 + - - -
478B ARG* 1.3 77.3 - - - +
480B LYS* 1.3 67.5 + - - +
482B ILE* 3.0 17.1 + - - +
483B GLU* 3.2 18.3 + - - +
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Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B TYR* 4.0 37.9 - - + +
471B GLU 5.0 2.7 - - - -
472B VAL* 3.9 34.1 - - + -
476B ALA* 3.3 4.7 + - + +
477B LYS* 3.3 5.4 + - - +
479B SER* 1.3 78.9 - - - +
481B LEU* 1.3 63.9 + - - +
483B GLU* 3.0 47.5 + - - +
484B ILE* 3.1 18.5 + - + +
592B PHE* 3.5 21.1 - - + -
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Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LYS 3.1 14.8 + - - +
478B ARG 4.2 4.3 - - - +
480B LYS* 1.3 78.0 - - - +
482B ILE* 1.3 63.3 + - + +
484B ILE* 3.6 3.4 + - - +
485B LEU* 3.0 48.3 + - + +
494B VAL* 4.2 14.6 - - + -
505B LEU* 3.4 25.1 - - + -
508B PHE* 6.1 0.9 - - + -
509B LEU* 4.6 9.4 - - + -
562B ILE* 4.6 15.5 - - + -
564B TYR* 3.3 33.7 - - + -
592B PHE* 3.8 10.9 - - + -
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ARG 3.2 17.7 + - - +
479B SER* 3.0 9.7 + - - +
481B LEU* 1.3 75.4 - - + +
483B GLU* 1.3 71.4 + - - +
485B LEU* 4.0 2.7 - - + +
486B SER* 2.8 33.5 + - - +
508B PHE* 4.6 4.3 - - + -
509B LEU* 3.9 23.6 - - + -
512B LYS* 3.4 44.9 - - + +
514B PHE* 4.3 10.3 - - + -
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Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B SER* 3.4 12.7 - - - +
480B LYS* 3.0 50.0 + - - +
482B ILE* 1.3 84.2 - - - +
484B ILE* 1.3 67.9 - - + +
486B SER* 2.8 18.2 + - - -
487B GLU* 3.5 6.2 + - - +
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Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B TYR* 4.6 9.9 - - + -
480B LYS* 3.3 17.5 - - + +
481B LEU* 3.7 8.1 - - - +
483B GLU* 1.3 83.4 - - + +
485B LEU* 1.3 61.2 + - + +
487B GLU* 3.5 9.6 + - - +
488B GLN* 3.1 24.5 + - - +
560B HIS* 3.8 28.9 - - + +
562B ILE* 4.0 14.8 - - + -
588B ARG* 4.8 4.9 - - - +
590B THR* 4.0 16.6 - - + +
592B PHE* 3.6 33.0 - - + -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 3.0 40.8 + - + +
482B ILE* 4.1 2.9 - - - +
483B GLU 3.0 0.2 + - - -
484B ILE* 1.3 75.3 - - + +
486B SER* 1.3 64.6 + - - +
487B GLU 3.2 2.6 + - - -
488B GLN 3.5 7.4 - - - +
489B ALA* 3.5 35.4 + - - +
492B THR* 3.6 33.9 - - + +
509B LEU* 3.7 32.3 - - + -
514B PHE* 3.6 23.6 - - + -
542B VAL* 3.8 13.0 - - + -
560B HIS* 6.4 0.2 - - - +
562B ILE* 5.0 4.9 - - + -
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ILE* 2.8 24.2 + - - +
483B GLU* 2.8 16.1 + - - -
485B LEU* 1.3 73.8 - - - +
487B GLU* 1.3 62.9 + - - +
514B PHE* 4.0 16.1 - - - -
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B GLU 3.5 5.3 + - - +
484B ILE* 3.6 12.2 - - - +
485B LEU 3.2 0.6 - - - -
486B SER* 1.3 82.4 - - - +
488B GLN* 1.3 92.7 + - + +
588B ARG* 4.0 13.7 + - - -
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Residues in contact with GLN 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B ILE* 3.1 17.7 + - - +
485B LEU* 3.5 10.5 - - - +
487B GLU* 1.3 105.0 + - + +
489B ALA* 1.3 61.1 + - - +
490B ASP* 5.2 2.9 - - + +
492B THR* 5.4 1.0 - - - +
559B LYS* 5.6 5.5 - - - -
560B HIS* 5.1 4.9 + - - -
588B ARG* 2.9 33.8 + - - +
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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