Contacts of the helix formed by residues 486 - 504 (chain B) in PDB entry 2JDQ
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 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B GLU 3.5 6.8 + - - -
483B PHE 3.7 2.5 - - - +
484B LEU 3.3 4.9 - - - +
485B GLN* 1.3 76.9 - - - +
487B HIS* 1.3 58.3 + - - +
488B GLU* 3.3 15.7 + - - +
489B ASN* 2.9 44.8 + - - +
490B GLN* 3.2 20.6 + - - +
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Residues in contact with HIS 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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485B GLN 3.4 6.5 + - - +
486B SER* 1.3 69.7 + - - +
488B GLU* 1.3 60.1 + - - +
490B GLN* 3.1 40.1 + - + +
491B GLU* 2.9 56.8 + - + +
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Residues in contact with GLU 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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486B SER* 3.5 8.8 + - - +
487B HIS* 1.3 75.0 - - - +
489B ASN* 1.3 66.6 + - - +
491B GLU* 3.2 17.5 + - - +
492B ILE* 3.0 31.9 + - + +
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Residues in contact with ASN 489 (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 PHE* 3.0 61.6 + - + +
486B SER* 2.9 26.9 + - - +
488B GLU* 1.3 77.0 - - - +
490B GLN* 1.3 63.0 + - - +
492B ILE* 3.3 13.3 + - - +
493B TYR* 3.1 33.3 + - + -
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Residues in contact with GLN 490 (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 LEU 5.9 2.7 + - - +
486B SER 3.2 10.7 + - - +
487B HIS* 3.1 37.7 + - + +
489B ASN* 1.3 79.5 - - - +
491B GLU* 1.3 62.3 + - + +
493B TYR* 3.5 4.3 + - - +
494B GLN* 3.1 28.9 + - + +
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Residues in contact with GLU 491 (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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487B HIS* 2.9 47.2 + - + +
488B GLU* 3.2 19.3 + - - +
490B GLN* 1.3 78.8 - - + +
492B ILE* 1.3 61.8 + - + +
494B GLN* 3.8 5.4 - - - +
495B LYS* 3.1 24.3 + - - +
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Residues in contact with ILE 492 (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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488B GLU* 3.0 22.0 + - + +
489B ASN* 3.3 16.1 + - - +
491B GLU* 1.3 77.4 - - + +
493B TYR* 1.3 72.5 + - + +
495B LYS* 3.3 6.3 + - - +
496B ALA* 2.9 30.4 + - + +
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Residues in contact with TYR 493 (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 PHE* 3.5 37.4 - + - -
489B ASN* 3.1 28.3 + - + +
490B GLN* 4.0 4.9 - - - +
492B ILE* 1.3 87.4 - - + +
494B GLN* 1.3 67.3 + - - +
496B ALA* 3.1 9.0 + - + +
497B PHE* 2.9 56.4 + + + -
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Residues in contact with GLN 494 (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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490B GLN* 3.1 22.8 + - + +
491B GLU* 3.8 6.3 - - - +
493B TYR* 1.3 76.1 - - - +
495B LYS* 1.3 62.6 + - - +
497B PHE* 3.6 8.5 + - - +
498B ASP* 3.0 39.8 + - - +
699D LYS* 4.8 16.7 + - - +
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Residues in contact with LYS 495 (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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491B GLU 3.1 19.0 + - - +
492B ILE* 3.5 7.0 - - - +
493B TYR 3.2 0.2 - - - -
494B GLN* 1.3 76.9 - - - +
496B ALA* 1.3 58.3 + - - +
498B ASP* 3.4 5.8 + - + +
499B LEU* 2.9 52.1 + - + +
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Residues in contact with ALA 496 (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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492B ILE* 2.9 20.6 + - + +
493B TYR* 3.1 10.5 + - + +
495B LYS* 1.3 76.7 - - - +
497B PHE* 1.3 62.2 + - + +
499B LEU* 3.3 4.7 + - - -
500B ILE* 3.1 35.7 + - + +
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Residues in contact with PHE 497 (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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493B TYR* 2.9 55.6 + + + +
494B GLN* 3.8 6.7 - - - +
496B ALA* 1.3 78.7 - - + +
498B ASP* 1.3 60.5 + - - +
500B ILE* 4.1 2.1 - - - +
501B GLU* 3.0 55.0 + - + +
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Residues in contact with ASP 498 (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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494B GLN* 3.0 40.4 + - - +
495B LYS* 3.9 5.9 - - + +
497B PHE* 1.3 77.0 - - - +
499B LEU* 1.3 65.5 + - - +
501B GLU* 4.4 6.9 - - - +
502B HIS* 3.1 25.8 + - - +
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Residues in contact with LEU 499 (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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495B LYS* 2.9 41.0 + - + +
496B ALA* 3.7 5.6 - - - +
498B ASP* 1.3 79.8 - - - +
500B ILE* 1.3 73.2 + - + +
502B HIS* 4.8 0.4 - - - -
503B TYR* 3.2 60.1 + - + +
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Residues in contact with ILE 500 (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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496B ALA* 3.1 22.4 + - + +
497B PHE* 4.3 2.2 - - - +
499B LEU* 1.3 90.2 - - + +
501B GLU* 1.3 64.2 + - + +
504B PHE* 2.7 66.5 + - + +
505B GLY 5.2 3.1 - - - +
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Residues in contact with GLU 501 (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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497B PHE* 3.0 45.6 + - + +
498B ASP* 4.4 7.1 - - - +
500B ILE* 1.3 79.6 - - + +
502B HIS* 1.3 60.6 + - - +
505B GLY* 3.3 26.2 + - - +
506B THR* 3.8 37.4 + - + +
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Residues in contact with HIS 502 (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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498B ASP 3.1 19.8 + - - +
499B LEU* 3.6 3.8 - - - +
500B ILE 3.2 0.2 - - - -
501B GLU* 1.3 78.9 - - - +
503B TYR* 1.3 97.9 + + + +
505B GLY* 4.6 1.2 + - - -
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Residues in contact with TYR 503 (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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499B LEU* 3.2 49.7 + - + +
502B HIS* 1.3 106.5 + + + +
504B PHE* 1.3 77.3 + - + +
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Residues in contact with PHE 504 (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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499B LEU 5.9 0.2 - - - -
500B ILE* 2.7 58.6 + - + +
503B TYR* 1.3 86.6 - - + +
505B GLY* 1.3 59.8 + - - +
507B GLU* 4.9 5.4 - - - +
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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