Contacts of the helix formed by residues 432 - 439 (chain C) in PDB entry 3B60
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 THR 432 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ASP* 1.3 83.7 - - - +
433C VAL* 1.3 65.7 + - - +
434C ALA* 4.1 2.3 - - - +
435C ASN* 2.9 30.1 + - - +
436C ASN* 2.9 22.6 + - - -
470C LEU 3.1 16.9 + - - -
471C ASP* 3.1 32.3 + - + +
472C THR 2.9 8.1 - - - +
473C ILE* 4.4 2.5 - - + +
474C ILE* 4.6 0.7 - - - -
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C THR* 1.3 75.4 - - - +
434C ALA* 1.3 69.2 + - - +
436C ASN* 3.0 14.6 + - - +
437C ILE* 3.1 31.1 + - + +
460C MET* 5.9 0.2 - - + -
463C ILE* 3.3 38.6 - - + -
466C MET* 4.4 15.7 - - + -
469C GLY 3.7 17.5 - - - +
470C LEU* 3.2 11.6 + - + -
472C THR* 3.1 9.5 + - - +
474C ILE* 4.9 10.2 - - + +
489C ILE* 4.5 16.2 - - + -
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Residues in contact with ALA 434 (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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432C THR* 4.1 4.5 - - - +
433C VAL* 1.3 74.6 - - - +
435C ASN* 1.3 54.7 + - - +
437C ILE* 3.1 12.0 + - - +
438C ALA* 2.6 36.6 + - + +
447C ARG* 4.1 17.7 - - - +
450C ILE* 4.1 15.8 - - + +
470C LEU* 2.8 38.7 + - + +
471C ASP* 4.8 0.9 - - - +
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Residues in contact with ASN 435 (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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431C ASP* 2.9 32.8 - - + +
432C THR* 2.9 25.4 + - - +
434C ALA* 1.3 78.9 - - - +
436C ASN* 1.3 55.2 + - - +
437C ILE 2.8 5.6 - - - -
438C ALA* 2.6 18.7 + - - +
439C TYR* 2.5 47.5 + - + +
443C GLU 4.8 4.4 + - - -
444C GLU* 5.6 2.8 + - - -
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Residues in contact with ASN 436 (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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428C LEU* 3.6 21.3 - - + +
429C PHE* 2.7 41.9 + - - +
431C ASP* 3.9 7.4 - - - +
432C THR 2.9 18.6 + - - -
433C VAL* 3.7 7.8 - - - +
435C ASN* 1.3 72.6 - - - +
437C ILE* 1.3 60.5 + - - +
439C TYR* 4.3 10.4 + - - +
474C ILE* 2.8 40.8 - - + +
489C ILE* 4.4 9.9 - - + -
493C ARG* 3.6 27.4 + - - +
220D PHE* 5.4 1.0 - - - -
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Residues in contact with ILE 437 (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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433C VAL* 3.2 33.9 - - + +
434C ALA* 3.2 8.3 - - - +
435C ASN 2.7 0.6 + - - -
436C ASN* 1.3 80.1 - - - +
438C ALA* 1.3 54.8 + - - +
439C TYR 3.4 0.2 - - - -
440C ALA* 2.8 31.9 - - - +
450C ILE* 4.2 11.9 - - + -
453C ALA* 4.7 3.6 - - + -
454C ALA* 4.5 16.8 - - + -
470C LEU* 5.7 2.5 - - + -
489C ILE* 4.0 12.3 - - + -
492C ALA* 3.9 24.5 - - + -
493C ARG* 3.4 24.9 - - - +
496C LEU* 3.8 23.5 - - + +
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Residues in contact with ALA 438 (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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434C ALA* 2.6 23.1 + - + +
435C ASN* 2.6 22.7 + - - +
437C ILE* 1.3 66.7 - - - +
439C TYR* 1.3 51.0 + - + +
440C ALA* 2.4 21.9 + - - +
441C ARG 4.7 0.2 - - - +
443C GLU* 2.8 38.3 + - - +
444C GLU* 4.2 5.3 + - - +
445C TYR* 5.6 5.6 - - + +
450C ILE* 4.7 7.8 - - + +
496C LEU* 4.6 8.7 - - - -
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Residues in contact with TYR 439 (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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429C PHE* 3.7 17.7 - + + -
431C ASP* 3.0 35.7 + - + -
435C ASN* 2.5 40.2 + - + +
436C ASN* 4.6 4.7 - - - +
437C ILE 3.4 0.6 - - - -
438C ALA* 1.3 68.6 - - + +
440C ALA* 1.3 52.5 + - - +
441C ARG 3.6 0.5 + - - -
443C GLU* 2.4 39.2 - - + +
220D PHE* 2.7 60.3 - + + -
225D VAL* 5.0 14.4 - - + +
226D GLU* 4.9 3.8 - - - -
229D ARG* 3.7 28.1 + - - -
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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