Contacts of the helix formed by residues 484 - 496 (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 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B ILE* 4.2 8.4 - - - +
482B GLY* 3.7 5.9 + - - -
483B ASN* 1.3 87.9 + - - +
485B ALA* 1.3 67.7 + - + +
486B ALA* 2.9 25.6 + - - +
487B ALA* 2.9 19.1 + - - +
488B VAL* 3.2 17.2 + - - +
490B ARG* 5.2 1.0 + - - -
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Residues in contact with ALA 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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462B ASN* 5.7 2.0 - - - -
465B ILE* 4.9 1.8 - - - +
484B ASP* 1.3 73.4 - - - +
486B ALA* 1.3 51.7 + - - +
488B VAL* 3.5 9.6 - - - +
489B LYS* 2.8 36.3 + - - +
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Residues in contact with ALA 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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484B ASP* 3.0 19.2 + - - +
485B ALA* 1.3 78.8 - - - +
487B ALA* 1.3 57.2 + - - +
489B LYS* 3.3 10.5 - - - +
490B ARG* 3.0 46.1 + - + +
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Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.7 16.7 - - + +
482B GLY 3.3 33.0 - - - +
484B ASP* 2.9 10.0 + - - +
486B ALA* 1.3 74.7 - - - +
488B VAL* 1.3 58.1 + - + +
490B ARG* 2.9 30.2 + - - +
491B ALA* 2.7 36.6 + - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 4.7 9.0 - - + +
461B LEU* 4.3 25.6 - - + -
462B ASN* 3.9 19.7 - - - +
465B ILE* 3.9 30.1 - - + -
480B LEU* 4.6 3.8 - - + +
484B ASP 3.6 10.5 - - - +
485B ALA* 3.5 11.0 - - - +
487B ALA* 1.3 77.6 - - + +
489B LYS* 1.3 58.6 + - - +
491B ALA* 3.4 7.3 + - - +
492B LEU* 2.9 49.9 + - + +
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Residues in contact with LYS 489 (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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454B ARG* 4.9 5.5 - - - +
485B ALA 2.8 19.4 + - - +
486B ALA* 3.3 11.2 - - - +
487B ALA 3.2 0.2 - - - -
488B VAL* 1.3 78.3 - - - +
490B ARG* 1.3 58.3 + - + +
492B LEU* 3.6 8.0 + - - +
493B ASP* 3.1 59.0 + - - +
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Residues in contact with ARG 490 (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 LEU 3.7 4.8 + - - +
481B GLY* 2.4 33.3 + - - -
482B GLY* 4.5 0.2 - - - -
484B ASP* 5.2 1.2 + - - -
486B ALA* 3.0 50.6 + - - +
487B ALA* 2.9 23.2 + - - +
489B LYS* 1.3 75.5 - - + +
491B ALA* 1.3 58.4 + - - +
493B ASP* 3.3 7.1 + - - +
494B ARG* 2.8 50.7 + - - +
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Residues in contact with ALA 491 (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* 4.0 9.0 - - + -
479B TRP* 3.8 16.6 - - + -
480B LEU* 3.6 24.5 - - + -
487B ALA 2.7 19.1 + - - +
488B VAL 3.4 4.7 - - - +
490B ARG* 1.3 70.5 - - - +
492B LEU* 1.3 61.2 + - - +
494B ARG* 3.2 16.9 + - - +
495B LEU* 2.9 37.2 + - - +
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Residues in contact with LEU 492 (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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454B ARG* 3.3 47.0 + - + +
457B GLN* 3.9 17.4 - - + +
458B GLU* 3.7 42.2 - - + +
461B LEU* 3.5 29.6 - - + -
488B VAL* 2.9 39.0 + - + +
489B LYS* 3.8 4.0 - - - +
491B ALA* 1.3 75.0 - - - +
493B ASP* 1.4 61.8 + - - +
495B LEU* 3.5 5.4 + - + +
496B ALA* 3.1 18.9 + - - +
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Residues in contact with ASP 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 2.9 26.7 + - - +
489B LYS* 3.1 47.7 + - - +
490B ARG* 3.6 7.8 - - - +
491B ALA 3.2 0.2 - - - -
492B LEU* 1.4 71.2 - - - +
494B ARG* 1.3 67.6 + - - +
496B ALA* 3.4 13.1 + - - +
497B GLY* 3.9 2.4 + - - -
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Residues in contact with ARG 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TRP* 2.8 56.9 + - - +
480B LEU* 4.2 7.9 + - - +
490B ARG* 2.8 49.3 + - - +
491B ALA* 3.2 24.5 + - - +
493B ASP* 1.3 73.7 - - - +
495B LEU* 1.3 59.5 + - + +
497B GLY* 2.8 20.4 + - - -
523B PRO* 3.3 28.4 - - + +
526B GLN* 5.8 2.0 - - - +
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Residues in contact with LEU 495 (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* 5.1 2.2 - - + -
404B MET* 6.5 0.7 - - + -
405B LEU* 4.1 28.5 - - + -
457B GLN* 3.9 37.9 + - + +
461B LEU* 5.2 0.7 - - + -
479B TRP* 3.7 35.4 - - + -
491B ALA 2.9 24.6 + - - +
492B LEU* 3.9 8.1 - - + +
494B ARG* 1.3 67.9 - - + +
496B ALA* 1.3 61.7 + - - +
497B GLY 2.9 6.3 - - - -
498B THR* 2.9 29.0 + - - +
523B PRO* 3.8 30.5 - - + +
524B ALA* 4.1 3.6 - - + -
527B TYR* 4.8 0.2 - - + -
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 3.9 16.4 - - + +
492B LEU 3.1 16.9 + - - +
493B ASP* 3.6 9.0 - - - +
494B ARG 3.0 1.2 + - - -
495B LEU* 1.3 76.8 - - - +
497B GLY* 1.3 59.4 + - - +
498B THR* 3.3 7.1 + - - +
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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