Contacts of the helix formed by residues 522 - 535 (chain C) in PDB entry 3HB0
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 CYS 522 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294C TYR* 3.8 12.3 - - + +
424C TRP* 3.5 20.6 - - - -
520C ILE* 4.3 2.9 - - - +
521C SER* 1.3 82.4 - - - +
523C HIS* 1.3 69.2 + - - +
524C ALA* 3.9 18.6 - - - +
525C ASP* 3.0 33.5 + - - +
526C LEU* 3.6 4.0 + - - +
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Residues in contact with HIS 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C PHE* 4.5 3.6 - + - -
294C TYR* 4.3 24.8 + + - -
421C THR 3.2 24.7 + - - -
422C ASP* 3.3 26.8 + - + -
424C TRP* 3.5 38.6 - + - -
427C HIS* 3.8 29.3 - + + +
522C CYS* 1.3 73.7 - - - +
524C ALA* 1.3 64.9 + - - +
526C LEU* 2.9 22.2 + - - +
527C GLU* 3.0 11.7 + - - +
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Residues in contact with ALA 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C CYS* 3.2 15.3 - - - +
523C HIS* 1.3 78.3 - - - +
525C ASP* 1.3 58.6 + - - +
527C GLU* 3.2 10.3 + - - +
528C ALA* 2.9 28.8 + - - +
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Residues in contact with ASP 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C TRP* 3.5 13.6 + - - +
519C ARG* 3.7 22.1 - - - +
520C ILE* 3.7 10.7 - - + +
521C SER* 2.8 32.6 + - - -
522C CYS* 3.0 21.3 + - - +
524C ALA* 1.3 77.0 - - - +
526C LEU* 1.3 65.3 + - - +
528C ALA* 3.4 6.5 + - - +
529C LEU* 3.2 18.4 + - - +
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Residues in contact with LEU 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C TRP* 4.1 22.0 - - + -
278C THR 3.8 13.7 - - - +
424C TRP* 3.6 34.8 - - + +
427C HIS* 3.8 23.9 - - + +
428C SER* 3.7 27.1 - - - +
431C ALA* 4.7 4.8 - - + +
520C ILE* 3.7 28.0 - - + -
522C CYS 3.6 1.7 + - - +
523C HIS* 2.9 11.3 + - - +
525C ASP* 1.3 77.7 - - - +
527C GLU* 1.3 56.7 + - - +
529C LEU* 3.3 6.6 + - + +
530C ARG* 3.1 26.3 + - - +
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Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C HIS* 5.0 11.9 - - + -
523C HIS 3.0 11.2 + - - +
524C ALA* 3.2 13.9 + - - +
526C LEU* 1.3 76.2 - - - +
528C ALA* 1.3 67.1 + - - +
530C ARG* 3.0 44.5 + - - +
531C HIS* 2.9 28.4 + - + +
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Residues in contact with ALA 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ALA* 5.5 2.3 - - - +
531B HIS* 4.7 12.7 + - + +
518C TRP* 3.6 15.6 - - + +
524C ALA 2.9 16.3 + - - +
525C ASP* 3.7 9.4 - - - +
526C LEU 3.4 0.2 - - - -
527C GLU* 1.3 77.4 - - - +
529C LEU* 1.3 62.0 + - - +
531C HIS* 3.5 7.7 + - - +
532C ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B TYR* 4.8 3.6 - - + -
271C PHE* 4.5 14.8 - - + -
273C TRP* 3.4 36.3 - - + -
431C ALA* 4.1 4.3 - - + -
435C ILE* 5.2 0.4 - - + -
498C VAL* 5.8 0.4 - - + -
500C ILE* 3.7 22.7 - - + -
518C TRP* 3.5 37.4 - - + +
520C ILE* 4.9 5.4 - - + -
525C ASP 3.2 12.8 + - - +
526C LEU* 3.4 9.9 - - + +
527C GLU 3.1 0.4 - - - -
528C ALA* 1.3 75.6 - - - +
530C ARG* 1.3 64.5 + - - +
532C ALA* 3.2 5.1 + - + +
533C LEU* 2.9 42.7 + - + +
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Residues in contact with ARG 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C HIS 5.6 0.9 - - - +
430C LYS* 4.0 44.0 - - + +
431C ALA* 4.7 7.6 - - - +
434C LEU* 3.9 10.1 - - + +
526C LEU 3.1 13.1 + - - +
527C GLU* 3.0 44.7 + - - +
529C LEU* 1.3 76.1 - - - +
531C HIS* 1.3 77.9 + - - +
533C LEU* 3.0 14.7 + - - +
534C GLU* 2.4 59.5 + - - +
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Residues in contact with HIS 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ALA* 3.6 35.0 - - + -
525B ASP* 2.9 24.7 + - - -
528B ALA* 4.1 9.7 - - + +
527C GLU* 2.9 23.5 + - + +
528C ALA* 3.6 9.8 - - - +
530C ARG* 1.3 92.6 + - - +
532C ALA* 1.3 63.7 + - - +
534C GLU* 3.1 23.6 + - - +
535C LEU* 3.3 28.1 + - + +
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TRP* 4.0 25.9 - - + -
528B ALA* 5.1 7.1 - - + +
532B ALA* 5.2 2.0 - - + -
537B TYR* 4.3 20.8 + - + -
438C ARG* 4.5 0.3 + - - -
518C TRP* 3.8 19.7 - - + -
528C ALA 3.1 13.9 + - - +
529C LEU* 3.2 8.9 + - + +
531C HIS* 1.3 74.9 - - - +
533C LEU* 1.3 62.2 + - - +
534C GLU 3.2 0.9 + - - -
535C LEU* 3.4 10.1 + - - +
536C GLU* 3.8 10.9 + - - +
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Residues in contact with LEU 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B TYR* 3.6 9.6 - - - +
271C PHE* 3.4 34.3 - - + -
431C ALA* 3.6 40.4 - - + +
434C LEU* 3.7 16.9 - - + +
435C ILE* 3.5 22.2 - - + -
438C ARG* 2.8 41.8 + - - +
441C CYS* 5.3 0.2 - - - -
529C LEU* 2.9 26.0 + - + +
530C ARG* 3.0 10.3 + - - +
532C ALA* 1.3 75.8 - - - +
534C GLU* 1.3 59.9 + - - +
535C LEU 3.5 0.6 + - - -
536C GLU 4.2 1.7 - - - +
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Residues in contact with GLU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ASP* 5.0 0.9 - - - +
434C LEU* 4.1 9.6 - - + -
530C ARG* 2.4 52.9 + - - +
531C HIS* 3.6 21.8 + - - +
532C ALA 3.1 0.8 - - - -
533C LEU* 1.3 78.6 - - - +
535C LEU* 1.3 66.2 + - + +
536C GLU 3.6 1.1 - - - -
537C TYR* 4.1 16.1 + - - -
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Residues in contact with LEU 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PHE 3.4 1.6 - - - +
518B TRP* 3.3 29.2 - - + -
519B ARG* 2.9 48.9 + - + +
520B ILE* 5.9 0.7 - - + -
521B SER* 5.6 0.2 - - - +
525B ASP* 3.4 46.0 - - + +
528B ALA* 4.0 8.5 - - + -
531C HIS* 3.3 35.9 - - + +
532C ALA 3.4 3.6 + - - +
534C GLU* 1.3 88.4 - - + +
536C GLU* 1.3 59.4 + - - +
537C TYR* 3.6 10.1 - - - -
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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