Contacts of the helix formed by residues 336 - 346 (chain H) in PDB entry 6V3O
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 ASN 336 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335H CYS* 1.3 81.0 - - - +
337H ASP* 1.3 66.0 + - - +
338H GLU* 3.6 19.8 + - - +
339H LEU* 3.6 9.6 - - - +
340H ARG* 3.1 22.3 + - - +
418H LEU* 4.8 2.8 + - - +
421H LYS* 3.8 13.7 - - - +
422H SER* 3.1 37.3 + - - +
425H ASP* 2.7 38.7 + - - +
426H CYS* 3.9 2.0 - - - -
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Residues in contact with ASP 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H CYS 3.9 0.2 + - - -
336H ASN* 1.3 76.3 + - - +
338H GLU* 1.3 62.9 + - - +
340H ARG* 3.2 8.3 + - - +
341H VAL* 3.0 33.1 + - + +
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Residues in contact with GLU 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ASN* 3.3 14.4 + - + +
337H ASP* 1.3 79.2 - - - +
339H LEU* 1.3 61.5 + - - +
341H VAL* 3.2 24.2 - - + +
342H ARG* 3.5 7.6 + - - +
418H LEU* 3.7 27.1 - - + +
421H LYS* 4.7 10.6 - - - +
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Residues in contact with LEU 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H CYS* 3.6 10.3 - - + -
336H ASN* 3.6 6.7 - - + +
337H ASP 3.3 0.6 - - - -
338H GLU* 1.3 76.8 - - - +
340H ARG* 1.3 58.3 + - - +
342H ARG* 3.0 2.4 + - - +
343H ALA* 2.7 36.6 + - + -
370H PRO* 3.3 34.8 - - + +
371H TYR* 3.5 37.0 - - + -
374H ILE* 4.0 14.8 - - + -
418H LEU* 4.2 17.4 - - + +
419H CYS* 4.0 17.5 - - - -
422H SER* 3.8 20.9 - - - +
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Residues in contact with ARG 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H CYS* 3.8 18.2 - - - -
336H ASN 3.1 20.7 + - - +
337H ASP* 3.5 6.7 - - - +
339H LEU* 1.3 79.8 - - - +
341H VAL* 1.3 85.2 + - - +
343H ALA* 3.6 3.7 - - - +
344H GLU* 3.1 51.0 + - + +
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Residues in contact with VAL 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H ASP* 3.0 18.8 + - + +
338H GLU* 3.2 21.8 - - + +
340H ARG* 1.3 99.0 - - - +
342H ARG* 1.3 64.2 + - + +
344H GLU* 3.6 2.2 + - - +
345H GLU* 3.1 37.5 + - - +
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Residues in contact with ARG 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H GLU 3.9 8.5 - - - +
339H LEU 3.0 6.5 + - - +
341H VAL* 1.3 82.2 - - + +
343H ALA* 1.3 68.1 + - - +
345H GLU* 3.2 23.8 + - - +
346H LEU* 3.1 44.9 + - + +
374H ILE* 3.8 20.9 - - + +
377H HIS* 3.9 26.1 + - - -
415H PRO* 5.3 12.3 - - - +
418H LEU* 4.6 14.6 - - + +
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Residues in contact with ALA 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339H LEU* 2.7 23.1 + - + +
340H ARG* 3.6 6.7 - - - +
342H ARG* 1.3 74.5 - - - +
344H GLU* 1.3 65.3 + - + +
346H LEU* 3.2 12.3 + - - +
347H HIS 3.5 8.1 + - - -
367H PRO 5.7 2.9 - - - +
370H PRO* 4.1 19.5 - - + +
373H VAL* 3.5 36.2 - - + +
374H ILE* 3.9 5.0 - - + +
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Residues in contact with GLU 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H ARG* 3.1 40.7 + - + +
341H VAL* 4.4 2.0 - - - +
343H ALA* 1.3 77.1 - - + +
345H GLU* 1.3 65.6 - - - +
347H HIS* 3.1 18.7 + - - +
367H PRO* 3.8 28.3 - - - +
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Residues in contact with GLU 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341H VAL* 3.1 26.6 + - + +
342H ARG* 3.3 34.6 + - - +
344H GLU* 1.3 77.2 - - - +
346H LEU* 1.3 60.6 + - + +
347H HIS* 3.1 24.4 + - - -
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Residues in contact with LEU 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ARG* 3.1 38.7 + - + +
343H ALA 3.2 7.4 + - - +
345H GLU* 1.3 74.8 - - + +
347H HIS* 1.3 80.0 + - - +
373H VAL* 4.0 21.0 - - + +
374H ILE* 4.2 19.3 - - + -
377H HIS* 3.7 52.7 - - + +
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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
------------------------------------------------------------
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