Contacts of the helix formed by residues 484 - 496 (chain A) 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 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ILE* 4.4 2.4 - - - +
482A GLY* 3.8 1.3 - - - -
483A ASN* 1.3 82.5 + - - +
485A ALA* 1.3 66.3 + - - +
486A ALA* 3.2 13.6 + - - +
487A ALA* 2.9 32.2 + - - +
488A VAL* 3.1 19.2 + - - +
490A ARG* 4.7 2.3 + - - -
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Residues in contact with ALA 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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462A ASN* 5.5 3.4 - - - +
484A ASP* 1.3 75.7 - - - +
486A ALA* 1.3 61.7 + - - +
488A VAL* 3.5 9.4 + - - +
489A LYS* 3.1 22.2 + - - +
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Residues in contact with ALA 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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484A ASP* 3.1 15.7 + - - +
485A ALA* 1.3 78.5 - - - +
487A ALA* 1.3 63.6 + - - +
489A LYS* 3.2 6.8 + - - +
490A ARG* 3.0 46.7 + - + +
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Residues in contact with ALA 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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480A LEU* 3.7 18.0 - - + +
482A GLY* 3.7 31.0 - - - +
484A ASP* 2.9 17.8 + - - +
486A ALA* 1.3 73.0 - - - +
488A VAL* 1.3 61.1 + - + +
490A ARG* 3.1 26.9 + - - +
491A ALA* 2.8 31.4 + - - +
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Residues in contact with VAL 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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458A GLU* 4.4 11.9 - - + +
461A LEU* 4.0 27.0 - - + +
462A ASN* 3.8 20.0 - - - +
465A ILE* 3.2 35.9 - - + -
480A LEU* 4.4 7.0 - - + -
484A ASP 3.1 8.7 + - - +
485A ALA* 3.6 10.1 - - - +
487A ALA* 1.3 76.1 - - - +
489A LYS* 1.4 62.0 + - - +
491A ALA* 3.1 5.0 + - - +
492A LEU* 3.0 40.7 + - + +
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Residues in contact with LYS 489 (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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454A ARG* 4.4 8.1 - - - +
485A ALA 3.1 13.9 + - - +
486A ALA* 3.2 8.7 + - - +
488A VAL* 1.4 74.8 - - - +
490A ARG* 1.3 59.8 + - + +
492A LEU* 3.3 12.0 + - + +
493A ASP* 2.9 54.2 + - - +
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Residues in contact with ARG 490 (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 LEU 4.9 2.2 + - - +
481A GLY 3.7 15.0 + - - -
482A GLY* 4.9 1.0 - - - -
484A ASP* 4.7 1.8 + - - -
486A ALA* 3.0 45.4 + - - +
487A ALA* 3.1 31.4 + - - +
489A LYS* 1.3 78.0 - - + +
491A ALA* 1.3 57.0 + - - +
493A ASP* 3.4 8.7 + - - +
494A ARG* 3.0 38.0 + - - +
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Residues in contact with ALA 491 (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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461A LEU* 4.4 4.5 - - + -
479A TRP* 3.8 25.0 - - + -
480A LEU* 3.8 17.5 - - + +
487A ALA 2.8 16.5 + - - +
488A VAL 3.6 4.3 - - - +
490A ARG* 1.3 74.6 - - - +
492A LEU* 1.3 59.3 + - - +
494A ARG* 3.3 21.0 + - - +
495A LEU* 2.8 35.6 + - - +
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Residues in contact with LEU 492 (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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454A ARG* 3.5 41.1 + - + +
457A GLN* 3.5 40.5 - - + +
458A GLU* 3.6 42.6 - - + +
461A LEU* 3.9 12.8 - - + -
488A VAL* 3.0 24.4 + - + +
489A LYS* 3.7 5.8 - - - +
491A ALA* 1.3 75.6 - - - +
493A ASP* 1.3 58.1 + - - +
495A LEU* 3.4 6.5 + - + +
496A ALA* 3.0 28.4 + - - +
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Residues in contact with ASP 493 (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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454A ARG* 2.7 36.9 + - - +
489A LYS* 2.9 45.4 + - - +
490A ARG* 3.7 7.6 - - - +
492A LEU* 1.3 75.9 - - - +
494A ARG* 1.3 62.9 + - - +
496A ALA* 3.4 13.8 + - - +
497A GLY 3.8 3.1 + - - -
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Residues in contact with ARG 494 (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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479A TRP* 2.7 62.7 + - - +
480A LEU* 4.6 3.2 + - - +
490A ARG* 3.0 32.3 + - - +
491A ALA* 3.4 21.4 - - - +
492A LEU 3.2 0.2 - - - -
493A ASP* 1.3 76.2 - - - +
495A LEU* 1.3 65.2 + - + +
497A GLY* 3.0 12.8 + - - -
523A PRO* 3.2 29.0 - - + +
526A GLN* 5.5 4.7 - - - +
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Residues in contact with LEU 495 (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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399A PHE* 4.8 2.7 - - + -
405A LEU* 4.0 29.4 - - + -
457A GLN* 3.8 39.8 + - + +
461A LEU* 5.3 2.0 - - + -
479A TRP* 3.7 37.2 - - + +
491A ALA 2.8 23.1 + - - +
492A LEU* 3.9 4.7 - - - +
494A ARG* 1.3 74.2 - - + +
496A ALA* 1.3 62.7 + - - +
497A GLY 3.0 0.2 - - - -
498A THR* 2.9 27.9 + - + +
523A PRO* 3.8 28.7 - - + +
524A ALA* 4.2 3.4 - - + -
527A TYR* 4.5 1.6 - - + -
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Residues in contact with ALA 496 (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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454A ARG* 4.1 17.3 - - - +
457A GLN* 5.5 0.4 + - - -
492A LEU 3.0 16.8 + - - +
493A ASP* 3.6 9.2 - - - +
494A ARG 3.1 0.6 + - - -
495A LEU* 1.3 76.6 - - - +
497A GLY* 1.3 59.6 + - - +
498A THR* 3.2 8.7 + - - +
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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