Contacts of the helix formed by residues 513 - 520 (chain B) in PDB entry 3WOO
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 ASP 513 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415B SER* 4.0 4.5 - - - +
418B ARG* 6.4 0.9 - - - +
511B ALA 3.9 0.4 + - - -
512B ALA* 1.3 75.9 - - - +
514B ARG* 1.3 65.4 + - - +
515B LYS* 3.4 13.4 + - - +
516B ALA* 2.9 32.7 + - - +
517B PHE* 3.2 13.5 + - - -
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Residues in contact with ARG 514 (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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412B TYR* 4.2 12.5 + - + -
415B SER* 3.5 28.8 + - - +
416B ILE* 3.9 34.8 - - - +
419B GLU* 3.2 42.4 + - + +
513B ASP* 1.3 75.1 - - - +
515B LYS* 1.3 67.6 + - + +
517B PHE* 3.0 14.1 + - - +
518B GLU* 2.9 42.8 + - - +
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Residues in contact with LYS 515 (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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419B GLU* 5.0 12.1 + - - +
513B ASP* 3.2 12.9 - - - +
514B ARG* 1.3 80.9 - - + +
516B ALA* 1.3 57.2 + - - +
518B GLU* 3.3 20.1 + - + +
519B ALA* 2.9 29.9 + - - +
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Residues in contact with ALA 516 (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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509B TRP* 3.6 25.5 - - + -
512B ALA* 4.1 10.8 - - + -
513B ASP* 2.9 26.0 + - - +
515B LYS* 1.3 77.8 - - - +
517B PHE* 1.3 59.2 + - - +
519B ALA* 3.3 8.3 + - - +
520B SER* 3.3 15.1 + - - -
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Residues in contact with PHE 517 (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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408B ALA* 4.6 1.6 - - - -
411B LEU* 3.4 21.8 - - + -
412B TYR* 3.5 46.2 - + + -
415B SER* 3.6 24.2 - - - -
509B TRP* 3.2 57.0 - + + -
512B ALA* 3.8 7.6 - - + -
513B ASP 3.2 21.2 + - - -
514B ARG 3.0 5.9 + - - +
516B ALA* 1.3 75.1 - - - +
518B GLU* 1.3 59.3 + - - +
520B SER* 3.0 16.5 + - - +
525B ILE* 3.3 42.4 - - + +
529B VAL* 3.9 4.0 - - + +
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Residues in contact with GLU 518 (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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412B TYR* 2.7 31.9 + - + +
514B ARG* 2.9 49.2 + - - +
515B LYS* 3.8 23.1 - - + +
517B PHE* 1.3 75.4 - - - +
519B ALA* 1.3 60.2 + - - +
520B SER 3.5 3.1 + - - +
529B VAL* 4.3 17.6 - - + +
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Residues in contact with ALA 519 (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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515B LYS 2.9 16.4 + - - +
516B ALA* 3.8 7.4 - - - +
517B PHE 3.2 0.4 - - - -
518B GLU* 1.3 77.9 - - - +
520B SER* 1.3 62.7 + - - +
521B ASN* 3.5 7.8 + - - +
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Residues in contact with SER 520 (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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509B TRP* 3.5 27.1 - - - -
516B ALA 3.3 2.7 + - - -
517B PHE 3.0 18.1 + - - +
518B GLU 4.5 2.6 - - - +
519B ALA* 1.3 79.2 - - - +
521B ASN* 1.3 59.5 + - - +
522B ASP* 2.9 30.4 + - - +
525B ILE* 3.7 15.5 - - - -
526B GLN* 3.3 22.9 + - - +
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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