Contacts of the helix formed by residues 525 - 534 (chain C) in PDB entry 1C2O
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 ARG 525 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C VAL* 6.0 1.6 - - - +
331C VAL 5.9 0.4 + - - -
332C LYS 4.1 17.8 + - - -
400C ALA* 5.1 9.9 - - - +
404C ASP* 3.3 30.5 + - - +
408C VAL* 4.2 23.5 - - + +
409C CYS* 5.0 0.2 - - - -
429C ILE* 5.8 6.1 - - - +
510C TYR* 5.5 1.0 + - - -
523C GLY 3.3 5.1 + - - -
524C LEU* 1.3 77.0 - - + +
526C ALA* 1.3 53.6 + - - +
527C GLN 3.1 3.5 + - - -
528C THR* 3.1 17.0 + - + -
529C CYS* 2.7 48.2 + - - -
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Residues in contact with ALA 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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385B TRP* 3.4 32.3 - - - +
386B LEU* 4.0 9.0 - - + +
508C GLN* 4.3 4.7 - - - +
523C GLY* 4.2 20.3 + - - -
524C LEU 2.7 10.1 + - - +
525C ARG* 1.3 69.7 - - - +
527C GLN* 1.3 67.8 + - - +
529C CYS* 3.9 2.0 - - - +
530C ALA* 3.0 22.2 + - - +
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Residues in contact with GLN 527 (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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380B LEU* 4.7 5.9 - - + +
381B HIS 6.1 0.9 - - - +
383B THR 3.8 3.4 + - - +
384B ASP* 2.9 35.7 + - - +
385B TRP* 3.1 31.8 + - + +
386B LEU* 5.7 0.5 - - - +
381C HIS* 4.8 8.5 - - + -
525C ARG 3.4 0.4 - - - -
526C ALA* 1.3 76.1 + - - +
528C THR* 1.3 62.7 + - - +
530C ALA* 2.5 26.5 + - - +
531C PHE* 2.8 11.5 + - - +
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Residues in contact with THR 528 (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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381C HIS* 3.2 27.9 + - + +
382C TYR* 3.2 29.5 - - + +
404C ASP* 3.4 16.6 - - + +
409C CYS* 4.4 1.8 - - - -
525C ARG* 3.1 20.8 + - - -
527C GLN* 1.3 82.4 - - - +
529C CYS* 1.3 57.1 + - - +
531C PHE* 2.9 24.1 + - - +
532C TRP* 3.1 20.0 - - + +
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Residues in contact with CYS 529 (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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408C VAL* 4.3 4.7 - - - -
409C CYS* 2.1 58.1 - - + -
412C ALA* 4.6 5.4 - - + -
524C LEU 4.0 9.4 - - - +
525C ARG* 2.7 37.5 + - - +
526C ALA* 3.9 2.7 - - - +
528C THR* 1.3 69.9 - - - +
530C ALA* 1.3 58.3 + - - +
532C TRP 4.4 0.4 - - - +
533C ASN* 2.7 48.9 + - - +
534C ARG* 5.3 0.4 + - - -
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Residues in contact with ALA 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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380B LEU* 4.6 2.9 - - + -
385B TRP* 3.5 38.4 - - + +
526C ALA 3.0 14.9 + - - +
527C GLN 2.5 19.2 + - - +
529C CYS* 1.3 69.5 - - - +
531C PHE* 1.3 56.8 + - - +
534C ARG* 2.7 56.2 + - + +
535C PHE* 3.3 2.1 + - - +
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Residues in contact with PHE 531 (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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380B LEU* 4.2 17.6 - - + +
377C ALA* 3.8 17.7 - - + -
378C VAL* 3.7 33.2 - - + -
381C HIS* 4.0 34.8 - + + -
382C TYR* 4.4 0.9 - + - -
527C GLN 2.8 6.8 + - - +
528C THR* 2.9 16.4 - - - +
530C ALA* 1.3 80.9 - - - +
532C TRP* 1.3 83.2 + + - +
535C PHE* 3.2 31.6 + + - +
536C LEU* 2.7 49.4 + - + +
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Residues in contact with TRP 532 (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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367C VAL* 4.2 7.2 - - + -
378C VAL* 4.0 15.7 - - + -
382C TYR* 2.6 41.7 + + - -
401C VAL* 4.0 20.2 - - + -
404C ASP* 3.7 3.6 - - + +
405C HIS* 3.3 53.6 - + + +
409C CYS* 3.5 23.8 - - + -
528C THR* 3.1 26.0 + - + +
529C CYS 4.1 0.2 - - - +
531C PHE* 1.3 87.2 - + - +
533C ASN* 1.3 70.0 + - - +
536C LEU* 3.5 37.1 - - + +
537C PRO* 2.9 28.2 - - - +
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Residues in contact with ASN 533 (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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409C CYS* 3.1 40.0 + - - +
410C PRO* 4.3 1.0 - - - +
412C ALA* 4.6 1.8 - - - +
413C GLN* 3.7 38.7 + - + +
529C CYS* 2.7 37.1 + - - +
530C ALA* 5.2 0.2 - - - -
532C TRP* 1.3 76.6 - - - +
534C ARG* 1.3 62.9 + - + +
537C PRO* 3.8 10.2 - - - +
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Residues in contact with ARG 534 (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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385B TRP* 4.2 32.6 - - + +
526C ALA 5.6 0.2 + - - -
529C CYS 5.3 0.6 + - - -
530C ALA* 2.7 40.0 + - + +
533C ASN* 1.3 80.2 - - + +
535C PHE* 1.3 60.5 + - + +
536C LEU 3.8 0.2 - - - -
537C PRO* 3.8 5.8 - - - +
538C LYS* 3.0 25.7 + - - +
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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