Contacts of the helix formed by residues 479 - 487 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A PHE* 5.7 2.2 - + - -
350A TRP 6.4 0.7 - - - -
413B PHE* 3.8 21.0 - + - -
431B ASP* 2.8 30.4 + - - +
433B VAL* 3.7 30.2 - - + +
434B VAL* 3.8 9.6 - - + -
475B ILE* 3.7 22.4 - - + -
476B SER* 3.1 30.6 + - - -
477B GLU 3.0 1.0 - - - -
478B ASN* 1.3 92.6 + - + +
480B ASN* 1.3 64.9 + - - +
481B LYS* 3.2 3.5 + - - -
482B ALA 3.4 3.5 + - - -
483B MSE 2.9 23.6 + - - +
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Residues in contact with ASN 480 (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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318A VAL* 5.7 2.6 - - + +
319A ASN* 5.8 1.6 + - - -
476B SER 4.2 1.6 - - - +
477B GLU* 3.3 52.5 + - - +
478B ASN 3.6 1.2 + - - -
479B HIS* 1.3 77.7 - - - +
481B LYS* 1.3 54.3 + - - +
483B MSE 4.1 7.4 - - - +
484B ALA* 2.7 37.2 + - - +
492B ILE* 3.6 43.7 + - + +
497B ASN* 4.5 2.4 - - - +
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Residues in contact with LYS 481 (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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318A VAL* 5.9 5.6 - - + +
351A ASN* 3.2 29.1 + - - +
353A ASN* 5.7 0.6 + - - -
354A GLU* 3.3 23.5 + - - +
478B ASN 5.4 0.4 + - - -
479B HIS* 3.2 1.2 - - - -
480B ASN* 1.3 81.7 - - - +
482B ALA* 1.3 61.1 + - - +
484B ALA* 3.3 16.0 + - - +
485B LYS* 3.7 30.8 + - - +
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Residues in contact with ALA 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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429B PHE* 3.4 24.5 - - + +
430B GLY 4.8 0.4 - - - -
431B ASP* 3.4 34.0 + - + -
434B VAL* 3.8 17.0 - - + -
479B HIS 3.4 3.9 + - - +
481B LYS* 1.3 76.5 - - - +
483B MSE 1.3 60.1 + - - +
485B LYS* 3.1 7.1 + - - +
486B VAL* 3.0 29.6 + - - +
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Residues in contact with MSE 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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256B GLN* 5.3 1.1 - - - +
258B PHE* 3.7 33.2 - - + -
434B VAL* 4.7 7.0 - - + -
438B PHE* 6.0 0.2 - - - -
475B ILE* 3.7 31.9 - - + -
476B SER 5.4 0.7 - - - +
479B HIS 2.9 21.2 + - - +
480B ASN* 3.7 7.0 - - - +
482B ALA* 1.3 73.1 - - - +
484B ALA* 1.3 62.0 + - - +
485B LYS 3.0 6.5 + - - -
486B VAL* 4.0 20.4 - - - -
487B LEU* 3.1 50.9 + - + +
492B ILE* 3.9 13.9 - - + +
500B LEU* 3.7 21.1 - - + -
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Residues in contact with ALA 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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480B ASN 2.7 20.5 + - - +
481B LYS* 3.5 8.7 - - - +
482B ALA 3.3 0.4 - - - -
483B MSE 1.3 68.8 - - - +
485B LYS* 1.3 54.2 + - + +
487B LEU 2.3 23.7 - - - +
488B GLY* 4.1 0.2 - - - -
489B LYS* 2.6 30.6 + - - +
490B ASP 3.8 5.4 - - - +
491B GLU* 3.7 29.4 - - - -
492B ILE* 3.7 11.8 - - - +
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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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429B PHE* 3.7 42.5 + - + +
430B GLY* 5.9 1.4 - - - -
481B LYS* 3.7 36.3 + - - +
482B ALA 3.1 6.6 + - - +
483B MSE 3.0 0.8 - - - -
484B ALA* 1.3 78.8 - - + +
486B VAL* 1.3 66.6 + - - +
487B LEU 3.2 6.6 - - - +
488B GLY* 4.4 4.3 + - - -
489B LYS 4.9 0.9 - - - +
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Residues in contact with VAL 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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258B PHE* 4.0 23.8 - - + -
262B TYR* 2.6 50.0 + - + +
429B PHE* 3.7 20.9 - - + -
434B VAL* 3.5 26.9 - - + -
438B PHE* 3.9 4.9 - - + -
482B ALA 3.0 17.6 + - - +
483B MSE 3.6 15.3 - - - +
485B LYS* 1.3 78.6 - - - +
487B LEU* 1.3 66.1 + - + +
488B GLY 4.1 0.5 + - - -
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Residues in contact with LEU 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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258B PHE* 5.4 7.6 - - + -
262B TYR* 5.6 2.0 - - + -
483B MSE 3.1 43.2 + - + +
484B ALA 2.3 34.0 - - - +
485B LYS 3.2 2.7 - - - -
486B VAL* 1.3 82.9 - - + +
488B GLY* 1.3 53.4 + - - +
489B LYS* 3.1 31.0 - - + +
492B ILE* 4.5 2.9 - - + -
496B ASP* 6.1 0.9 - - + -
500B LEU* 4.2 25.8 - - + -
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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