Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 6O0Z
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A LEU* 3.8 19.3 - - + -
380A LEU* 3.1 48.2 + - + +
383A MET* 4.2 13.4 + - + -
384A ASP* 3.5 17.9 - - - +
385A GLY* 1.3 77.4 - - - +
387A GLU* 1.3 63.9 + - - +
388A GLU* 3.6 2.9 - - - -
389A LEU* 3.7 13.9 + - - -
390A LEU* 3.3 25.8 + - - +
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Residues in contact with GLU 387 (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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385A GLY* 3.5 8.0 - - - +
386A THR* 1.3 81.7 - - - +
388A GLU* 1.3 64.9 + - - +
390A LEU* 3.0 10.1 + - - +
391A VAL* 2.9 30.9 + - + +
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Residues in contact with GLU 388 (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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334A LEU* 4.4 17.7 - - + +
385A GLY 3.9 11.6 - - - +
386A THR 5.0 0.2 - - - -
387A GLU* 1.3 82.6 + - - +
389A LEU* 1.3 71.0 + - + +
391A VAL* 3.5 12.7 - - + +
392A LYS* 2.9 40.9 + - - +
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Residues in contact with LEU 389 (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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331A ASP* 4.4 16.8 - - + +
334A LEU* 4.3 29.6 - - + -
335A LEU* 4.1 32.1 - - + -
338A LEU* 5.0 5.2 - - + -
380A LEU* 4.1 24.5 - - + -
386A THR* 3.7 16.5 + - - +
387A GLU 3.2 0.8 - - - -
388A GLU* 1.3 85.3 - - + +
390A LEU* 1.3 58.6 + - - +
392A LYS* 3.3 8.9 + - + +
393A LEU* 2.9 29.1 + - - +
398A LEU* 4.0 26.9 - - + +
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Residues in contact with LEU 390 (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 LYS* 3.5 30.5 - - + +
380A LEU* 4.0 29.8 - - + +
381A GLU* 4.6 16.2 - - + +
386A THR* 3.3 26.6 + - - +
387A GLU* 3.0 11.0 + - - +
389A LEU* 1.3 77.2 - - - +
391A VAL* 1.3 58.0 + - - +
393A LEU* 3.8 12.9 - - + +
394A ASN* 2.4 47.0 + - - +
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Residues in contact with VAL 391 (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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387A GLU* 2.9 21.0 + - + +
388A GLU* 3.3 16.1 + - + +
390A LEU* 1.3 78.3 - - + +
392A LYS* 1.3 62.6 + - + +
394A ASN* 3.5 8.5 + - - +
395A ARG* 3.3 26.3 + - + +
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Residues in contact with LYS 392 (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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327A GLU* 4.0 12.1 + - - +
330A GLN* 5.8 1.4 + - - -
331A ASP* 2.9 42.1 + - - +
388A GLU* 2.9 26.2 + - - +
389A LEU* 3.7 12.9 - - + +
391A VAL* 1.3 78.2 - - + +
393A LEU* 1.3 58.3 + - - +
395A ARG* 3.1 6.2 + - - -
396A GLU 3.0 9.2 + - - -
397A ASP* 3.0 50.2 + - + +
398A LEU* 4.1 7.0 - - + -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A TYR* 4.4 32.2 - - + +
376A ILE* 4.0 21.8 - - + -
377A LYS* 3.9 40.2 - - + +
380A LEU* 4.5 10.3 - - + -
389A LEU 2.9 16.4 + - - +
390A LEU* 3.9 10.8 - - + +
391A VAL 3.3 0.2 - - - -
392A LYS* 1.3 73.9 - - - +
394A ASN* 1.3 65.5 + - - +
396A GLU* 3.5 14.2 + - - +
398A LEU* 3.8 28.7 - - + +
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Residues in contact with ASN 394 (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 LYS* 4.2 15.0 + - - -
390A LEU* 2.4 40.4 + - - +
391A VAL* 3.8 9.5 - - - +
392A LYS 3.3 0.2 - - - -
393A LEU* 1.3 77.5 - - - +
395A ARG* 1.3 65.9 + - - +
396A GLU* 3.0 14.7 - - - +
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Residues in contact with ARG 395 (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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391A VAL* 3.3 18.4 + - + +
392A LYS* 3.1 7.8 + - - +
394A ASN* 1.3 84.3 - - - +
396A GLU* 1.3 73.7 + - - +
397A ASP* 3.4 9.2 + - + +
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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