Contacts of the helix formed by residues 373 - 382 (chain A) in PDB entry 6B0Z
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 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A SER* 3.4 21.8 - - - +
327A THR 3.7 21.1 - - - +
328A ASN* 3.5 19.9 + - - -
372A MET* 1.3 79.8 - - - +
374A LYS* 1.3 65.8 + - - +
375A ASP* 2.5 21.2 + - - -
376A LEU* 3.1 15.4 + - - +
377A ALA 3.2 9.4 + - - -
391A TYR* 3.7 3.7 - - - +
392A LEU 3.7 2.7 - - - +
394A THR* 4.9 2.5 - - - -
397A PHE* 4.0 33.1 - - + -
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A SER* 2.8 22.9 + - - +
373A THR* 1.3 73.8 - - - +
375A ASP* 1.3 58.4 + - - +
377A ALA* 3.2 1.6 + - - +
378A ALA* 2.9 29.7 + - - +
383A LEU* 3.6 34.2 - - + +
386A VAL* 4.2 8.5 - - + -
391A TYR* 3.6 55.1 - - + +
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 4.1 22.1 - - - +
287A SER* 5.5 0.7 - - - -
289A GLY* 4.5 5.9 + - - -
290A MET* 5.0 0.9 - - - +
326A SER 4.6 3.1 + - - +
328A ASN* 2.7 33.5 + - - +
373A THR* 2.5 30.0 + - - -
374A LYS* 1.3 74.0 - - - +
376A LEU* 1.3 65.9 + - - +
378A ALA* 3.3 7.6 + - - +
379A CYS* 3.0 26.7 + - - +
501A NDP 4.1 20.0 - - + +
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Residues in contact with LEU 376 (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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117A ILE* 4.1 27.8 - - + +
287A SER* 6.4 0.7 - - - -
290A MET* 3.7 28.5 - - + -
328A ASN* 3.6 21.5 - - - +
367A ILE* 3.6 29.4 - - + -
372A MET* 3.6 28.5 - - + -
373A THR* 3.1 13.4 + - - +
375A ASP* 1.3 83.5 + - - +
377A ALA* 1.3 62.7 + - - +
379A CYS* 3.1 15.9 + - + +
380A ILE* 3.2 17.2 + - - +
397A PHE* 5.1 2.2 - - + -
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Residues in contact with ALA 377 (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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372A MET* 3.4 12.0 - - - -
373A THR 3.2 11.9 + - - +
374A LYS 3.7 6.3 - - - +
376A LEU* 1.3 76.7 - - - +
378A ALA* 1.3 57.6 + - - +
380A ILE* 3.1 6.8 + - - +
381A LYS* 2.9 35.1 + - + +
386A VAL* 4.0 8.3 - - + -
390A ASP* 3.8 34.5 - - + +
391A TYR* 4.2 7.6 - - + -
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Residues in contact with ALA 378 (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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374A LYS 2.9 16.9 + - - +
375A ASP* 3.6 8.1 - - - +
377A ALA* 1.3 75.0 - - - +
379A CYS* 1.3 58.7 + - - +
382A GLY* 2.7 27.6 + - - +
383A LEU* 3.9 32.0 + - + +
386A VAL* 3.6 14.0 - - + +
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Residues in contact with CYS 379 (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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117A ILE* 3.9 14.8 - - + -
118A PRO* 3.4 31.3 - - - +
285A TYR* 3.6 43.2 + - - +
286A GLY 5.2 5.4 - - - +
287A SER* 5.7 2.9 - - - -
375A ASP 3.0 13.4 + - - +
376A LEU* 3.1 15.0 + - + +
378A ALA* 1.3 76.6 - - - +
380A ILE* 1.3 63.0 + - - +
382A GLY 4.9 0.2 + - - -
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Residues in contact with ILE 380 (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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116A ASN* 3.6 29.8 - - + +
117A ILE* 3.7 10.3 - - + -
118A PRO* 3.9 15.4 - - + +
372A MET* 3.7 33.9 - - + -
376A LEU 3.4 8.1 - - - +
377A ALA* 3.1 7.5 + - - +
379A CYS* 1.3 79.3 - - - +
381A LYS* 1.3 80.9 + - + +
382A GLY 3.6 0.2 - - - -
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Residues in contact with LYS 381 (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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377A ALA* 2.9 17.0 + - + +
380A ILE* 1.3 97.0 - - + +
382A GLY* 1.3 65.3 + - - +
385A ASN* 3.1 34.4 + - + +
386A VAL* 4.5 3.6 - - + -
390A ASP* 3.5 43.5 - - + +
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Residues in contact with GLY 382 (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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378A ALA 2.7 23.3 + - - -
379A CYS 4.9 0.2 + - - -
380A ILE 3.6 0.6 - - - -
381A LYS* 1.3 75.6 - - - +
383A LEU* 1.3 66.7 + - - -
384A PRO* 3.3 7.2 - - - -
385A ASN* 2.9 16.4 + - - -
386A VAL* 3.3 11.0 + - - +
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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