Contacts of the helix formed by residues 477 - 488 (chain B) in PDB entry 3A8X
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 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B GLU* 2.7 32.8 + - - -
475B SER 3.8 1.4 + - - -
476B LEU* 1.3 77.2 - - - +
478B VAL* 1.3 60.3 + - - +
479B LYS* 3.6 6.0 + - - +
480B ALA* 3.2 16.1 + - - +
481B ALA* 3.0 27.2 + - - +
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Residues in contact with VAL 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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477B SER* 1.3 71.6 - - - +
479B LYS* 1.3 81.9 + - + +
481B ALA* 3.4 7.2 + - + +
482B SER* 3.0 26.1 + - - -
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Residues in contact with LYS 479 (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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343B GLU* 4.2 12.8 - - - +
347B ARG* 5.0 2.6 - - - +
477B SER* 3.8 8.3 - - - +
478B VAL* 1.3 89.6 - - + +
480B ALA* 1.3 57.6 + - - +
482B SER* 3.4 6.3 + - - -
483B VAL* 3.0 28.6 + - - +
510B HIS* 3.8 1.3 - - - -
511B PRO* 3.3 43.9 + - + +
512B PHE* 3.7 20.8 + - - +
514B ARG* 3.8 22.5 - - - +
515B ASN* 5.3 5.9 - - - +
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 3.8 11.0 - - - +
438B MET* 3.9 23.8 - - + -
476B LEU* 4.2 11.4 - - + -
477B SER* 3.2 23.7 + - - +
479B LYS* 1.3 76.1 - - - +
481B ALA* 1.3 67.0 + - - +
483B VAL* 3.3 1.6 - - - +
484B LEU* 3.0 31.5 + - - +
512B PHE* 3.7 11.6 - - + -
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Residues in contact with ALA 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 3.9 31.8 - - + +
476B LEU* 4.7 3.0 - - + +
477B SER 3.0 17.7 + - - +
478B VAL* 3.7 8.1 - - + +
480B ALA* 1.3 76.0 - - - +
482B SER* 1.3 58.2 + - - +
484B LEU* 3.5 2.6 + - - +
485B LYS* 3.0 34.0 + - + +
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B VAL* 3.0 21.8 + - - -
479B LYS* 3.6 7.0 - - - -
481B ALA* 1.3 76.4 - - - +
483B VAL* 1.3 56.8 + - - +
485B LYS* 3.3 5.1 + - - +
486B SER* 2.7 39.2 + - - -
510B HIS* 2.9 19.6 + - - -
511B PRO* 4.9 4.7 - - - +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B MET* 3.8 20.6 - - + -
438B MET* 4.5 1.1 - - + -
479B LYS 3.0 12.7 + - - +
480B ALA* 3.3 11.4 - - - +
482B SER* 1.3 76.0 - - - +
484B LEU* 1.3 72.8 + - + +
486B SER* 3.3 2.2 + - - -
487B PHE* 3.0 39.9 + - + -
496B LEU* 4.5 3.1 - - + -
510B HIS* 3.3 26.6 - - + +
512B PHE* 3.7 15.9 - - + -
513B PHE* 4.0 28.0 - - + -
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Residues in contact with LEU 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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431B GLY* 3.7 11.7 - - - +
434B MET* 3.8 13.9 - - + -
435B PHE* 3.3 49.8 - - + +
438B MET* 4.0 11.7 - - + -
472B ILE* 4.5 15.3 - - + -
476B LEU* 3.8 28.5 - - + -
480B ALA 3.0 18.5 + - - +
481B ALA 3.7 2.9 - - - +
483B VAL* 1.3 84.7 - - + +
485B LYS* 1.3 57.1 + - - +
487B PHE* 3.5 2.6 + - - -
488B LEU* 2.9 42.6 + - + +
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Residues in contact with LYS 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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469B GLN* 6.0 6.1 - - - -
470B ILE* 4.6 15.3 - - + +
472B ILE* 3.1 33.2 - - + -
481B ALA* 3.0 15.8 + - + +
482B SER* 3.8 5.8 - - - +
484B LEU* 1.3 77.1 - - - +
486B SER* 1.3 62.6 + - - +
488B LEU* 3.8 6.6 - - + +
489B ASN* 3.4 21.7 + - - +
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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 SER* 2.7 23.3 + - - -
483B VAL 3.6 5.4 - - - -
484B LEU 3.3 0.2 - - - -
485B LYS* 1.3 79.5 - - - +
487B PHE* 1.3 59.9 + - - +
489B ASN* 3.8 5.1 - - - +
495B ARG* 3.7 6.8 - - - +
496B LEU* 2.9 49.5 + - - +
510B HIS* 3.5 12.6 + - - -
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Residues in contact with PHE 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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427B TRP* 3.5 29.2 - + + +
428B TRP* 3.7 8.8 - - - -
430B LEU* 3.7 23.6 - - + -
431B GLY* 3.6 21.5 - - - -
434B MET* 3.9 23.3 - - - -
483B VAL* 3.0 34.1 + - + +
484B LEU* 4.1 1.6 - - - +
486B SER* 1.3 76.3 - - - +
488B LEU* 1.3 58.7 + - - +
489B ASN 3.2 3.7 + - - -
495B ARG* 3.2 26.5 + - + -
496B LEU* 3.5 31.9 - - + -
507B ILE* 3.7 33.4 - - + -
513B PHE* 4.4 5.6 - + - -
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Residues in contact with LEU 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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428B TRP* 3.1 38.3 - - + +
431B GLY* 3.7 16.6 - - - +
432B VAL* 3.6 34.5 - - + +
435B PHE* 4.3 16.4 - - + -
443B PRO* 4.7 2.5 - - + -
470B ILE* 3.6 42.8 - - + +
472B ILE* 6.2 0.7 - - + -
484B LEU* 2.9 25.5 + - + +
485B LYS* 3.8 9.2 - - + +
486B SER 3.4 0.2 - - - -
487B PHE* 1.3 77.0 - - - +
489B ASN* 1.3 59.8 + - - +
490B LYS* 3.4 6.8 + - - +
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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