Contacts of the helix formed by residues 394 - 407 (chain A) in PDB entry 6B0O
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 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ARG* 3.6 39.6 - - + +
375A ARG* 3.8 11.0 - - - +
383A PHE* 3.4 8.6 - - - -
392A PHE* 3.3 3.4 - - - +
393A SER* 1.3 94.4 + - - +
395A SER* 1.3 59.3 + - - +
396A ASP* 3.0 34.1 + - - +
397A HIS* 3.4 30.8 + - + +
398A LEU* 3.1 26.0 + - - +
6B G 3.5 21.6 + - - +
7B G 2.8 50.9 + - - -
6C T 6.3 0.2 - - + -
7C C 3.7 2.0 - - - +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PHE* 3.4 38.9 - - - -
394A ARG* 1.3 71.1 - - - +
396A ASP* 1.3 62.9 + - - +
398A LEU* 3.3 7.9 + - - +
399A LYS* 3.0 28.7 + - - +
5C C 4.7 15.7 + - - +
6C T 3.5 25.0 + - - +
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ARG* 3.0 47.0 + - - +
395A SER* 1.3 78.2 + - - +
397A HIS* 1.3 73.5 + - - -
399A LYS* 3.3 12.2 + - - +
400A THR* 3.2 28.3 + - + +
6C T 3.9 22.5 - - + +
7C C 3.1 30.1 + - + -
8C C 4.1 1.7 + - - -
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PHE* 4.5 12.3 - - + -
393A SER* 5.1 1.6 - - - +
394A ARG* 3.4 31.7 + - + +
395A SER 3.3 0.4 - - - -
396A ASP* 1.3 98.4 + - - +
398A LEU* 1.3 63.9 + - - +
400A THR* 3.3 7.5 + - - +
401A HIS* 3.0 23.9 + - - +
4B G 4.5 3.2 + - + -
5B T 3.4 53.5 - + + +
6B G 2.7 45.0 + - - -
8C C 4.9 1.8 - - - -
9C C 5.2 0.7 - - - -
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Residues in contact with LEU 398 (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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383A PHE* 3.6 28.0 - - + -
384A GLN 3.9 14.6 - - - +
385A CYS* 3.6 34.3 - - + +
386A LYS* 6.3 0.7 - - - +
392A PHE* 3.7 25.4 - - + +
394A ARG 3.1 14.0 + - - +
395A SER* 3.5 9.6 - - - +
396A ASP 3.3 0.2 - - - -
397A HIS* 1.3 77.2 - - - +
399A LYS* 1.3 63.4 + - - +
401A HIS* 3.1 2.4 + - - +
402A THR* 3.0 38.4 + - + +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A SER 3.0 13.6 + - - +
396A ASP* 3.6 14.1 - - - +
397A HIS 3.3 0.4 - - - -
398A LEU* 1.3 78.3 - - - +
400A THR* 1.3 63.0 + - + +
402A THR* 2.5 27.7 + - - +
403A ARG* 3.6 27.8 + - - +
6C T 3.1 48.7 + - - +
7C C 3.8 20.7 + - - +
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Residues in contact with THR 400 (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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396A ASP* 3.2 13.3 + - + +
397A HIS* 3.3 14.7 + - - +
399A LYS* 1.3 78.1 - - + +
401A HIS* 1.3 65.5 + - - +
403A ARG* 3.3 45.0 + - - +
404A THR* 4.1 5.4 + - - +
423A ALA* 5.2 2.9 - - - +
424A ARG* 3.8 32.3 - - + +
3B C 6.1 0.5 - - - +
4B G 4.7 2.6 + - - -
5B T 4.3 8.7 - - - +
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Residues in contact with HIS 401 (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 CYS* 3.7 7.8 - - + -
388A CYS* 3.5 8.5 - - - -
390A ARG* 4.6 7.2 - - - -
392A PHE* 3.2 36.3 - + + -
397A HIS 3.0 20.7 + - - +
398A LEU* 3.1 6.3 + - + +
400A THR* 1.3 77.5 + - - +
402A THR* 1.3 59.3 + - - +
404A THR* 2.5 41.8 + - - +
405A HIS* 3.3 7.6 + + - -
502A ZN 2.1 37.2 - - - -
4B G 2.7 38.0 + - - +
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Residues in contact with THR 402 (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 CYS* 4.1 16.2 - - - -
386A LYS 5.7 0.4 - - - +
387A THR* 6.0 0.4 - - - +
398A LEU* 3.0 32.7 + - + +
399A LYS* 2.5 24.9 + - - +
401A HIS* 1.3 74.6 - - - +
403A ARG* 1.3 57.7 + - - +
404A THR 3.1 0.2 - - - -
405A HIS* 3.0 29.6 + - - +
406A THR* 3.2 21.3 + - - +
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Residues in contact with ARG 403 (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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399A LYS* 3.8 32.9 + - - +
400A THR* 3.4 34.1 - - - +
401A HIS 3.0 1.2 - - - -
402A THR* 1.3 76.0 + - - +
404A THR* 1.3 58.9 - - - +
406A THR* 3.4 8.7 - - - +
407A GLY* 2.9 28.3 + - - -
408A GLU* 3.7 30.9 + - + +
410A PRO* 4.2 15.7 - - - +
411A PHE* 4.0 14.3 - - - -
423A ALA* 2.6 46.1 + - + +
424A ARG* 4.5 0.8 - - - +
3B C 5.9 0.2 - - - -
7C C 5.0 5.7 + - - -
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Residues in contact with THR 404 (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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400A THR 4.3 5.2 - - - +
401A HIS* 2.5 36.4 + - - +
403A ARG* 1.3 79.1 - - + +
405A HIS* 1.3 66.4 + - - +
407A GLY* 4.5 1.7 + - - -
423A ALA* 6.3 1.1 - - + -
3B C 3.2 57.6 + - + +
4B G 4.3 4.3 - - - +
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Residues in contact with HIS 405 (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 CYS* 3.7 4.5 - - - -
387A THR* 3.7 34.7 - - + +
388A CYS* 3.9 17.0 - - + +
401A HIS* 3.3 5.5 + + - -
402A THR* 3.0 19.8 + - - +
404A THR* 1.3 88.5 + - - +
406A THR* 1.3 66.5 + - + +
407A GLY* 3.3 1.0 + - - -
502A ZN 2.1 36.9 - - - -
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Residues in contact with THR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A THR* 3.2 14.5 + - - +
403A ARG* 3.4 13.7 - - - +
405A HIS* 1.3 79.1 - - + +
407A GLY* 1.3 61.9 + - - +
408A GLU* 3.2 24.9 + - - +
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Residues in contact with GLY 407 (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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403A ARG 2.9 13.4 + - - -
404A THR 4.5 2.0 + - - -
405A HIS 3.3 3.6 + - - +
406A THR* 1.3 77.2 - - - +
408A GLU* 1.3 64.9 + - - +
409A LYS* 3.3 21.2 + - - +
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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