Contacts of the helix formed by residues 502 - 512 (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 SER 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B LYS 3.4 3.0 + - - -
500B LEU 3.1 0.9 - - - +
501B GLY* 1.3 79.3 - - - +
503B THR* 1.3 65.0 + - - +
504B GLU* 3.6 22.8 - - - +
505B GLU* 3.1 37.1 + - - +
506B ARG* 3.2 17.6 + - - +
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Residues in contact with THR 503 (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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441B LEU 4.0 2.9 - - - +
442B LYS* 3.8 37.5 - - + -
445B GLU* 2.7 34.6 + - - +
501B GLY 4.2 0.2 + - - -
502B SER* 1.3 70.5 - - - +
504B GLU* 1.3 63.9 + - - +
506B ARG* 3.2 26.8 + - - +
507B LEU* 2.9 33.2 + - + +
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Residues in contact with GLU 504 (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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502B SER* 3.6 22.2 + - - +
503B THR* 1.3 84.1 + - - +
505B GLU* 1.3 71.2 + - + +
507B LEU* 3.4 5.1 + - - +
508B LYS* 3.0 22.5 + - - +
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Residues in contact with GLU 505 (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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499B LYS* 3.1 54.3 - - + +
500B LEU* 4.2 4.5 - - + -
502B SER* 3.1 15.1 + - - +
504B GLU* 1.3 80.5 - - + +
506B ARG* 1.3 64.5 + - - +
508B LYS* 3.2 15.2 + - - +
509B TRP* 3.1 39.7 + - - -
522B ASP* 5.3 0.2 - - - +
806B ZN 2.2 35.9 - - - -
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Residues in contact with ARG 506 (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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404B MET* 4.2 2.2 - - - +
407B SER* 3.7 26.0 - - - +
411B LEU* 3.8 13.0 - - + +
441B LEU* 2.9 50.8 + - + +
444B LEU* 3.8 20.0 - - - +
445B GLU* 3.5 20.6 - - - +
448B TYR* 5.1 1.8 - - - -
500B LEU* 2.7 53.9 + - + +
501B GLY* 3.2 22.0 + - - -
502B SER 3.2 1.6 + - - -
503B THR* 3.2 34.7 + - - +
505B GLU* 1.3 78.5 - - - +
507B LEU* 1.3 63.1 + - - +
509B TRP 3.4 0.7 + - - -
510B PHE* 3.0 20.4 + - - +
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Residues in contact with LEU 507 (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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438B GLU* 3.4 22.0 - - + +
441B LEU* 3.8 30.7 - - + -
442B LYS* 3.4 39.9 - - + +
503B THR* 2.9 24.4 + - + +
504B GLU* 4.2 4.9 - - - +
506B ARG* 1.3 72.3 - - - +
508B LYS* 1.4 67.7 + - - +
510B PHE* 3.3 22.0 + - + +
511B ALA* 3.4 8.5 + - - +
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Residues in contact with LYS 508 (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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504B GLU 3.0 12.2 + - - +
505B GLU* 3.2 21.0 + - - +
507B LEU* 1.4 76.2 - - - +
509B TRP* 1.3 84.5 + - + +
511B ALA* 3.0 20.8 + - - +
512B ALA* 3.2 13.0 + - + +
806B ZN 2.4 36.4 - - - -
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Residues in contact with TRP 509 (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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411B LEU* 4.1 12.1 - - + +
500B LEU* 3.4 21.8 - - + +
505B GLU* 3.1 41.0 + - - +
506B ARG 3.4 3.6 + - - +
508B LYS* 1.3 93.7 - - + +
510B PHE* 1.3 65.4 + - - +
512B ALA* 3.1 23.2 + - + +
516B ALA* 3.6 41.3 - - + -
517B PHE* 3.2 43.5 - + + -
520B SER* 3.5 21.3 - - - -
522B ASP* 5.1 4.3 + - + -
525B ILE* 3.2 24.2 - - + +
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Residues in contact with PHE 510 (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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411B LEU* 3.7 8.8 - - + +
414B LEU* 3.7 27.4 - - + +
418B ARG* 2.7 45.4 + - - -
434B LEU* 3.8 24.9 - - + -
437B ILE* 3.8 24.9 - - + -
438B GLU* 3.7 39.5 - - + -
441B LEU* 3.8 15.0 - - + -
506B ARG 3.0 14.0 + - - +
507B LEU* 3.3 16.2 - - + +
508B LYS 3.2 0.2 - - - -
509B TRP* 1.3 76.2 - - - +
511B ALA* 1.4 58.4 + - + +
512B ALA 4.8 0.7 - - - +
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Residues in contact with ALA 511 (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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418B ARG* 4.5 9.2 + - - +
507B LEU 3.4 6.0 + - - +
508B LYS* 3.0 10.8 + - - +
510B PHE* 1.4 83.7 - - + +
512B ALA* 1.3 62.7 + - - +
513B ASP 3.9 0.5 + - - -
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Residues in contact with ALA 512 (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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415B SER* 3.9 7.8 - - - -
418B ARG* 5.0 5.9 + - - -
508B LYS* 3.2 12.6 + - + +
509B TRP* 3.1 37.1 + - + +
510B PHE 4.8 1.7 - - - +
511B ALA* 1.3 80.4 - - - +
513B ASP* 1.3 62.7 + - - +
516B ALA* 4.1 12.6 - - + -
517B PHE* 3.8 13.0 - - + -
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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