Contacts of the helix formed by residues 502 - 512 (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 SER 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A LYS 3.5 4.2 + - - -
500A LEU 3.1 1.3 - - - +
501A GLY* 1.3 77.5 - - - +
503A THR* 1.3 66.3 + - - +
504A GLU* 3.5 23.3 + - - +
505A GLU* 3.2 24.3 + - - +
506A ARG* 3.1 23.9 + - - +
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Residues in contact with THR 503 (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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441A LEU 4.1 2.5 - - - +
442A LYS* 4.0 34.8 - - + -
445A GLU* 2.9 34.5 + - - +
501A GLY 4.2 0.2 + - - -
502A SER* 1.3 72.0 - - - +
504A GLU* 1.3 69.6 + - - +
506A ARG* 3.1 27.1 + - - +
507A LEU* 3.0 27.0 + - + +
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Residues in contact with GLU 504 (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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502A SER* 3.5 19.6 + - - +
503A THR* 1.3 83.6 + - - +
505A GLU* 1.3 65.6 + - - +
507A LEU* 3.4 6.2 + - - +
508A LYS* 3.1 22.7 + - - +
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Residues in contact with GLU 505 (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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499A LYS* 3.2 50.8 - - - +
500A LEU* 4.0 3.6 - - + -
502A SER* 3.2 15.4 + - - +
504A GLU* 1.3 81.6 - - + +
506A ARG* 1.3 63.0 + - - +
508A LYS* 3.1 23.5 + - - +
509A TRP* 3.2 48.9 + - + -
522A ASP* 4.8 2.4 - - - +
810A ZN 2.5 27.5 - - - -
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Residues in contact with ARG 506 (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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404A MET* 4.2 2.2 - - - +
407A SER* 3.6 25.6 - - - +
411A LEU* 3.8 7.1 - - + +
441A LEU* 2.9 49.4 + - + -
444A LEU* 3.8 18.6 - - - +
445A GLU* 3.4 22.2 - - - +
448A TYR* 5.0 2.6 - - - -
500A LEU* 2.8 58.8 + - + +
501A GLY* 3.2 21.4 + - - -
502A SER 3.1 3.4 + - - +
503A THR* 3.1 32.4 + - - +
505A GLU* 1.3 77.3 - - - +
507A LEU* 1.3 58.1 + - - +
509A TRP* 3.2 4.9 + - - +
510A PHE* 2.9 26.0 + - - +
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Residues in contact with LEU 507 (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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438A GLU* 3.5 20.6 - - + +
441A LEU* 3.9 25.6 - - + -
442A LYS* 3.4 40.8 - - + +
503A THR* 3.0 26.1 + - + +
504A GLU* 4.0 6.7 - - - +
505A GLU 3.3 0.2 - - - -
506A ARG* 1.3 72.5 - - - +
508A LYS* 1.3 68.3 + - - +
510A PHE* 3.2 25.0 + - + +
511A ALA* 3.3 8.7 + - - +
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Residues in contact with LYS 508 (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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504A GLU 3.1 14.6 + - - +
505A GLU* 3.1 26.2 + - - +
507A LEU* 1.3 79.3 - - - +
509A TRP* 1.3 82.9 + - + +
511A ALA* 3.1 12.6 + - - +
512A ALA* 3.2 15.2 + - + +
810A ZN 2.1 38.0 - - - -
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Residues in contact with TRP 509 (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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411A LEU* 3.9 15.2 - - + +
500A LEU* 3.4 19.4 - - + +
505A GLU* 3.2 42.0 + - + +
506A ARG 3.7 6.5 - - - +
508A LYS* 1.3 95.8 - - - +
510A PHE* 1.3 61.5 + - - +
512A ALA* 3.3 17.0 + - + +
516A ALA* 3.3 48.2 - - + -
517A PHE* 3.0 58.1 - + + -
520A SER* 3.7 18.2 - - - -
522A ASP* 5.1 3.3 + - + +
525A ILE* 3.1 22.5 - - + +
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Residues in contact with PHE 510 (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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411A LEU* 3.3 13.0 - - + +
414A LEU* 3.7 17.1 - - + +
418A ARG* 2.7 51.5 + - - -
434A LEU* 3.9 21.1 - - + -
437A ILE* 3.6 31.0 - - + -
438A GLU* 3.7 42.2 - - + -
441A LEU* 3.9 9.6 - - + -
506A ARG 2.9 14.0 + - - +
507A LEU* 3.2 19.3 - - + +
509A TRP* 1.3 77.5 - - - +
511A ALA* 1.3 58.4 + - + +
512A ALA 4.8 0.7 - - - +
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Residues in contact with ALA 511 (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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418A ARG* 4.3 12.3 + - - +
507A LEU 3.3 5.4 + - - +
508A LYS* 3.1 9.5 + - - +
510A PHE* 1.3 83.4 - - + +
512A ALA* 1.3 61.9 + - - +
513A ASP* 4.1 0.3 + - - +
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Residues in contact with ALA 512 (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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415A SER* 3.8 7.6 - - - -
418A ARG* 5.1 5.5 + - - -
508A LYS* 3.2 15.9 + - + +
509A TRP* 3.3 39.4 + - + +
510A PHE 4.8 1.2 - - - +
511A ALA* 1.3 79.3 - - - +
513A ASP* 1.3 63.8 + - - +
516A ALA* 4.1 9.0 - - + -
517A PHE* 3.6 11.7 - - + -
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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