Contacts of the helix formed by residues 479 - 487 (chain A) in PDB entry 2W8D
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 HIS 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PHE* 3.8 21.8 - + - -
431A ASP* 3.0 30.8 + - - +
433A VAL* 3.7 29.1 - - + +
434A VAL* 3.7 8.3 - - + -
475A ILE* 3.7 22.4 - - + -
476A SER* 3.3 32.8 + - - -
477A GLU 3.1 0.8 - - - -
478A ASN* 1.3 91.8 + - + +
480A ASN* 1.3 61.9 + - - +
481A LYS* 3.2 3.6 - - - -
482A ALA* 3.2 4.6 + - - -
483A MSE 3.0 22.7 + - - +
349B PHE* 5.8 2.2 - + - -
350B TRP 6.3 0.4 - - - -
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Residues in contact with ASN 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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476A SER 4.4 1.4 - - - +
477A GLU* 3.3 53.8 + - - +
478A ASN 3.5 1.4 + - - -
479A HIS* 1.3 77.4 - - - +
481A LYS* 1.3 64.2 + - - +
483A MSE 4.3 5.9 - - - +
484A ALA* 3.1 22.2 + - - +
492A ILE* 3.3 47.5 + - + +
497A ASN* 4.7 1.9 - - - +
318B VAL* 5.7 2.6 - - + +
319B ASN* 5.9 0.6 + - - -
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Residues in contact with LYS 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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430A GLY 6.0 2.2 - - - +
478A ASN 5.4 0.4 + - - -
479A HIS 3.2 1.4 - - - -
480A ASN* 1.3 78.8 - - - +
482A ALA* 1.3 62.0 + - - +
484A ALA* 3.7 10.1 + - - +
485A LYS* 3.8 29.3 + - - +
318B VAL* 6.0 4.1 - - + +
351B ASN* 5.6 2.7 - - - +
354B GLU* 3.8 23.3 + - - +
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Residues in contact with ALA 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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429A PHE* 3.4 30.9 - - + +
430A GLY 4.9 0.2 - - - -
431A ASP* 3.5 28.9 + - + +
434A VAL* 3.9 15.7 - - + -
479A HIS 3.2 4.2 + - - +
481A LYS* 1.3 77.4 - - - +
483A MSE 1.3 61.5 + - - +
485A LYS* 3.0 8.3 + - - +
486A VAL* 2.9 28.9 + - - +
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Residues in contact with MSE 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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256A GLN* 5.2 1.6 - - - +
258A PHE* 3.8 39.0 - - + -
434A VAL* 4.5 7.6 - - + -
475A ILE* 3.6 32.5 - - + +
476A SER 5.2 1.6 - - - +
479A HIS 3.0 20.4 + - - +
480A ASN* 4.0 6.5 - - - +
482A ALA* 1.3 76.8 - - - +
484A ALA* 1.3 57.5 + - - +
486A VAL* 3.3 23.5 + - + +
487A LEU* 3.0 34.6 + - + +
492A ILE* 4.0 13.9 - - + -
500A LEU* 3.9 30.1 - - + -
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Residues in contact with ALA 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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480A ASN 3.1 17.8 + - - +
481A LYS* 3.9 6.5 - - - +
482A ALA 3.2 0.2 - - - -
483A MSE 1.3 74.6 - - - +
485A LYS* 1.3 59.9 + - + +
487A LEU 3.5 0.5 + - - -
488A GLY 3.0 6.1 + - - -
489A LYS* 2.6 48.1 + - - +
490A ASP 3.9 4.0 - - - +
491A GLU* 3.9 27.4 - - - -
492A ILE* 3.6 10.0 - - - +
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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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428A ASP 5.2 1.8 - - - +
429A PHE* 3.6 47.7 - - + +
430A GLY* 5.3 1.8 - - - -
481A LYS* 4.1 28.7 + - - +
482A ALA* 3.0 9.6 + - - +
484A ALA* 1.3 75.0 - - + +
486A VAL* 1.3 67.3 + - - +
488A GLY* 3.0 13.6 + - - +
489A LYS 4.9 1.6 - - - +
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Residues in contact with VAL 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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258A PHE* 3.9 25.4 - - + -
262A TYR* 2.4 48.4 + - + +
429A PHE* 3.8 19.7 - - + -
434A VAL* 3.6 31.0 - - + -
438A PHE* 3.8 8.1 - - + -
482A ALA 2.9 13.1 + - - +
483A MSE 3.3 18.4 + - - +
485A LYS* 1.3 78.0 - - - +
487A LEU* 1.3 68.5 + - + +
488A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 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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258A PHE* 4.7 20.0 - - + -
262A TYR* 4.8 5.8 - - + -
483A MSE 3.0 14.9 + - + +
484A ALA* 4.1 3.8 - - - +
486A VAL* 1.3 92.0 - - + +
488A GLY* 1.3 63.7 + - - +
489A LYS* 4.1 33.2 + - + +
492A ILE* 4.1 12.1 - - + -
496A ASP* 5.6 1.3 - - + -
500A LEU* 3.9 35.0 - - + -
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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