Contacts of the helix formed by residues 473 - 481 (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 VAL 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392B ARG* 4.1 23.6 - - + -
396B LEU* 4.5 21.3 - - + -
464B TYR* 2.8 25.1 + - + +
472B ARG* 1.3 77.9 - - - +
474B ALA* 1.3 68.4 + - - +
475B ALA* 3.9 4.7 - - + +
476B VAL* 2.9 27.4 + - + +
477B ASP* 2.9 25.3 + - - -
531B VAL* 5.8 0.7 - - + -
534B THR* 3.6 31.4 - - + +
538B LEU* 5.6 0.7 - - + -
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Residues in contact with ALA 474 (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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472B ARG 4.1 1.4 + - - -
473B VAL* 1.3 72.7 - - - +
475B ALA* 1.3 63.9 + - - +
476B VAL 3.1 0.3 + - - -
477B ASP* 3.3 10.1 + - - +
478B ALA* 2.9 25.7 + - - +
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Residues in contact with ALA 475 (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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473B VAL* 3.3 5.4 - - + +
474B ALA* 1.3 80.0 - - - +
476B VAL* 1.3 59.0 + - - +
478B ALA* 4.0 5.0 - - - +
479B TRP* 3.0 27.9 + - - +
530B ALA* 3.9 23.4 - - + +
531B VAL* 4.5 9.8 - - + +
534B THR* 3.5 23.5 + - - +
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Residues in contact with VAL 476 (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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396B LEU* 4.2 13.2 - - + -
399B PHE* 5.0 11.7 - - + -
461B LEU* 5.5 1.6 - - + -
464B TYR* 3.5 39.9 - - + +
473B VAL* 2.9 23.0 + - + +
475B ALA* 1.3 74.7 - - - +
477B ASP* 1.3 64.6 - - - +
479B TRP* 3.3 19.5 + - + +
480B LEU* 2.9 29.0 + - + +
527B TYR* 4.1 11.0 - - + +
531B VAL* 4.0 20.2 - - + -
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Residues in contact with ASP 477 (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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464B TYR* 2.8 19.5 + - - -
472B ARG* 2.9 48.0 + - - +
473B VAL 2.9 16.2 + - - +
474B ALA* 3.5 10.8 - - - +
476B VAL* 1.3 73.3 - - - +
478B ALA* 1.3 56.1 + - - +
480B LEU* 3.0 8.6 + - - +
481B GLY* 2.8 28.2 + - - -
482B GLY 4.3 2.8 + - - -
483B ASN* 5.5 1.8 - - - +
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Residues in contact with ALA 478 (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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474B ALA 2.9 19.9 + - - +
475B ALA* 4.0 5.8 - - - +
477B ASP* 1.3 66.6 - - - +
479B TRP* 1.3 68.1 + - - +
480B LEU 2.9 2.8 + - - -
481B GLY* 3.2 12.8 + - - +
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Residues in contact with TRP 479 (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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399B PHE* 4.2 11.9 - + - -
461B LEU* 4.2 14.1 - - + -
475B ALA 3.0 19.9 + - - +
476B VAL* 3.6 13.5 - - + +
478B ALA* 1.3 77.0 - - - +
480B LEU* 1.3 75.4 + - + +
491B ALA* 3.8 13.5 - - + -
494B ARG* 2.8 54.1 + - - +
495B LEU* 3.7 42.6 - - + -
523B PRO 4.6 4.6 + - - -
526B GLN* 5.4 2.2 - - + +
527B TYR* 3.6 47.1 - + + +
530B ALA* 4.9 12.6 - - + -
531B VAL* 5.6 0.4 - - + -
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Residues in contact with LEU 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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461B LEU* 4.3 14.8 - - + -
464B TYR* 4.4 17.7 - - + -
465B ILE* 3.9 23.8 - - + -
472B ARG* 5.3 2.5 - - - +
476B VAL* 2.9 17.5 + - + +
477B ASP* 3.3 6.1 - - - +
478B ALA 3.0 0.4 - - - -
479B TRP* 1.3 94.9 - - + +
481B GLY* 1.3 65.1 + - - +
482B GLY 3.5 20.4 - - - +
487B ALA* 3.7 22.2 - - + +
488B VAL* 4.6 1.8 - - + +
490B ARG* 3.7 6.4 + - - -
491B ALA* 3.6 29.6 - - + -
494B ARG* 4.2 6.4 + - - +
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Residues in contact with GLY 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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477B ASP 2.8 16.2 + - - -
478B ALA* 3.2 9.3 + - - -
480B LEU* 1.3 71.4 - - - +
482B GLY* 1.3 52.9 + - - -
490B ARG* 2.4 28.6 + - - -
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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