Contacts of the helix formed by residues 477 - 488 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLU* 2.6 35.8 + - - -
347A ARG* 5.8 0.2 + - - -
475A SER 3.8 1.2 + - - -
476A LEU* 1.3 77.9 - - - +
478A VAL* 1.3 63.5 + - - +
479A LYS* 3.3 9.9 + - - +
480A ALA 2.9 17.3 + - - -
481A ALA* 3.0 20.4 + - - +
512A PHE* 5.2 0.2 - - - -
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A SER* 1.3 75.0 - - - +
479A LYS* 1.3 62.7 + - + +
481A ALA* 3.4 8.4 + - + +
482A SER* 3.0 28.3 + - - -
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Residues in contact with LYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ARG* 5.7 3.8 - - - +
477A SER* 3.3 8.8 + - - +
478A VAL* 1.3 80.0 - - + +
480A ALA* 1.3 58.0 + - - +
482A SER* 3.4 6.5 + - - -
483A VAL 3.0 22.0 + - - -
510A HIS* 3.7 1.7 - - - -
511A PRO* 3.9 28.7 - - + +
512A PHE* 3.7 26.9 - - + +
514A ARG* 4.4 28.1 - - - +
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Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLU* 3.8 20.2 - - - +
438A MET* 4.0 20.0 - - + -
476A LEU* 4.2 7.9 - - + -
477A SER* 2.9 21.7 + - - +
479A LYS* 1.3 75.7 - - - +
481A ALA* 1.3 65.9 + - - +
483A VAL* 3.3 2.8 + - - +
484A LEU* 3.0 32.0 + - - +
512A PHE* 3.8 12.0 - - + -
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ILE* 3.9 34.2 - - + +
476A LEU* 4.9 1.1 - - - +
477A SER 3.0 13.5 + - - +
478A VAL* 3.4 12.5 + - + +
480A ALA* 1.3 75.2 - - - +
482A SER* 1.3 58.5 + - - +
484A LEU* 3.9 1.3 - - - +
485A LYS* 2.9 36.6 + - + +
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A VAL* 3.0 19.7 + - - -
479A LYS* 3.6 8.3 - - - -
480A ALA 3.1 0.2 - - - -
481A ALA* 1.3 77.4 - - - +
483A VAL* 1.3 51.2 + - - +
485A LYS* 3.3 5.8 + - - +
486A SER* 2.4 38.6 + - - -
510A HIS* 3.1 17.5 + - - -
511A PRO* 5.6 1.9 - - - +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A MET* 3.9 17.0 - - + -
438A MET* 4.9 0.7 - - + -
479A LYS 3.0 8.4 + - - +
480A ALA* 3.4 11.2 - - - +
482A SER* 1.3 75.2 - - - +
484A LEU* 1.3 65.4 + - + +
486A SER* 3.3 4.3 + - - -
487A PHE* 2.9 44.4 + - + +
496A LEU* 3.8 18.6 - - + -
510A HIS* 3.5 26.6 - - + +
512A PHE* 3.8 22.4 - - + -
513A PHE* 4.1 16.8 - - + -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLY* 3.6 13.9 - - - +
434A MET* 3.6 15.5 - - + -
435A PHE* 3.4 46.7 - - + +
438A MET* 3.9 13.0 - - + -
472A ILE* 4.1 17.3 - - + -
476A LEU* 3.7 29.6 - - + -
480A ALA 3.0 16.9 + - - +
481A ALA 3.9 2.5 - - - +
483A VAL* 1.3 85.3 - - + +
485A LYS* 1.3 61.8 + - - +
487A PHE* 3.4 2.8 + - - -
488A LEU* 2.9 35.4 + - + +
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A GLN* 4.8 13.5 - - - +
470A ILE* 2.8 43.5 + - - +
472A ILE* 4.0 21.0 - - + +
481A ALA* 2.9 23.4 + - + +
482A SER* 3.7 5.4 - - - +
484A LEU* 1.3 77.2 - - - +
486A SER* 1.3 59.8 + - - +
488A LEU* 3.4 7.0 + - - +
489A ASN* 3.2 20.6 + - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A SER* 2.4 33.5 + - - -
483A VAL* 3.6 5.5 + - - -
485A LYS* 1.3 74.4 - - - +
487A PHE* 1.3 64.8 + - - +
488A LEU 3.4 0.2 + - - -
489A ASN* 3.6 12.6 + - - +
494A GLU 4.9 1.3 - - - +
495A ARG* 3.4 5.4 - - - +
496A LEU* 3.1 42.4 + - - -
510A HIS* 3.9 9.0 + - - -
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A TRP* 3.6 31.6 - + + +
428A TRP* 3.7 9.4 - - - -
430A LEU* 3.8 16.6 - - + -
431A GLY* 3.6 20.9 - - - -
434A MET* 3.6 32.8 - - - -
483A VAL* 2.9 35.8 + - + +
484A LEU* 4.0 1.8 - - - +
486A SER* 1.3 77.4 - - - +
488A LEU* 1.3 57.6 + - - +
489A ASN 3.3 0.4 - - - -
495A ARG* 3.1 26.9 + - - -
496A LEU* 3.5 41.5 - - + -
507A ILE* 4.0 20.0 - - + -
513A PHE* 4.5 4.7 - + - -
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A TRP* 3.2 35.2 - - + +
431A GLY 3.7 18.6 - - - +
432A VAL* 3.6 37.9 - - + +
435A PHE* 4.6 13.5 - - + -
443A PRO* 5.3 1.3 - - + -
444A PHE* 5.0 0.4 - - + -
470A ILE* 4.0 29.9 - - + +
472A ILE* 5.5 0.9 - - + -
484A LEU* 2.9 35.0 + - + +
485A LYS* 3.5 9.4 - - - +
486A SER 3.2 0.4 - - - -
487A PHE* 1.3 76.3 - - - +
489A ASN* 1.3 63.6 + - - +
490A LYS* 3.4 7.6 + - - +
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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