Contacts of the helix formed by residues 3786 - 3800 (chain F) in PDB entry 6X34
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 GLY3786 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3785F THR* 1.3 75.1 - - - +
3787F ALA* 1.3 65.4 + - - -
3788F MET* 3.2 3.6 - - - -
3789F VAL* 3.2 22.5 + - - +
3790F SER* 3.5 10.4 + - - -
3875F PHE* 5.2 3.9 - - - -
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Residues in contact with ALA3787 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3714F GLU* 5.5 6.5 - - - +
3719F MET* 6.1 0.7 - - - -
3786F GLY* 1.3 72.8 - - - -
3788F MET* 1.3 60.5 + - - +
3790F SER* 2.9 18.8 + - - +
3791F SER* 2.9 18.8 + - - -
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Residues in contact with MET3788 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3712F LEU* 4.6 8.7 - - + -
3713F ASP* 3.4 28.0 - - + +
3714F GLU 3.8 22.0 - - - +
3715F ASP* 4.0 9.9 - - - +
3718F TYR* 3.7 36.6 - - + -
3719F MET* 5.7 6.3 - - + +
3777F MET* 3.7 26.9 - - + +
3786F GLY* 3.2 1.0 - - - -
3787F ALA* 1.3 75.6 - - - +
3789F VAL* 1.3 69.5 + - + +
3791F SER* 3.3 9.6 + - - -
3792F THR* 3.2 24.0 + - + +
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Residues in contact with VAL3789 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3777F MET* 6.5 0.7 - - + -
3778F ILE* 4.8 10.1 - - + -
3781F CYS* 4.4 16.8 - - + -
3784F GLU 3.4 25.6 - - - +
3785F THR 4.4 0.2 - - - -
3786F GLY* 3.2 21.4 + - - +
3788F MET* 1.3 84.2 - - + +
3790F SER* 1.3 58.9 + - - +
3792F THR* 3.0 17.6 + - - -
3793F LEU* 3.4 17.9 + - + +
3830F LEU* 4.3 25.4 - - + -
3875F PHE* 4.4 12.3 - - + -
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Residues in contact with SER3790 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3786F GLY 3.5 6.5 + - - -
3787F ALA* 2.9 19.4 + - - +
3788F MET 3.3 0.2 - - - -
3789F VAL* 1.3 78.5 - - - +
3791F SER* 1.3 63.2 + - - +
3793F LEU* 3.7 5.0 + - - +
3794F LYS* 3.1 22.9 + - - +
3874F GLU 5.1 8.7 - - - -
3875F PHE* 4.3 24.1 - - - -
3878F ASP* 6.0 0.7 - - - +
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Residues in contact with SER3791 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718F TYR* 6.5 0.4 - - - -
3719F MET* 4.0 20.1 - - - +
3722F ALA* 4.3 23.6 - - - +
3787F ALA 2.9 15.9 + - - -
3788F MET* 3.3 10.8 + - - -
3789F VAL 3.3 0.6 - - - -
3790F SER* 1.3 78.7 + - - +
3792F THR* 1.3 65.9 + - - +
3794F LYS* 3.3 15.4 + - - +
3795F LEU* 3.3 14.0 + - - +
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Residues in contact with THR3792 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718F TYR* 3.4 42.4 - - + +
3722F ALA* 5.8 2.5 - - + -
3774F VAL* 4.7 15.8 - - + +
3777F MET* 3.7 19.0 - - + +
3778F ILE* 4.0 16.7 - - - +
3788F MET 3.2 10.8 + - - +
3789F VAL* 3.0 20.3 + - - -
3791F SER* 1.3 77.0 - - - +
3793F LEU* 1.3 58.2 + - - +
3795F LEU* 3.4 7.0 + - - +
3796F GLY* 3.1 22.9 + - - -
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Residues in contact with LEU3793 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3778F ILE* 3.8 25.8 - - + -
3789F VAL* 3.4 21.9 + - + +
3790F SER* 4.1 5.4 - - - +
3791F SER 3.3 0.6 - - - -
3792F THR* 1.3 76.4 + - - +
3794F LYS* 1.3 64.6 + - - +
3796F GLY* 4.4 2.0 - - - +
3797F ILE* 3.3 29.5 + - + +
3830F LEU* 4.9 5.4 - - + -
3875F PHE* 4.7 19.1 - - + +
3878F ASP* 4.9 15.3 - - + +
3879F LEU* 4.7 28.9 - - + +
3882F PHE* 4.6 28.6 - - + -
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Residues in contact with LYS3794 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3723F ASP* 6.2 3.1 - - - -
3726F ALA* 4.2 11.3 - - + +
3790F SER 3.1 15.0 + - - +
3791F SER* 3.5 12.8 - - - +
3792F THR 3.2 0.4 - - - -
3793F LEU* 1.3 78.9 - - - +
3795F LEU* 1.3 59.8 + - - +
3797F ILE* 3.3 31.1 - - + +
3798F SER* 3.7 8.3 + - - -
3877F GLN* 5.6 8.3 - - - +
3878F ASP* 5.5 4.9 - - + +
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Residues in contact with LEU3795 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3722F ALA* 3.5 30.5 - - + +
3725F MET* 3.8 36.6 - - + -
3726F ALA* 3.8 17.7 - - + +
3765F LEU* 5.1 2.5 - - + -
3770F ALA* 5.3 6.7 - - + +
3774F VAL* 3.9 24.5 - - + -
3791F SER 3.3 10.8 + - - +
3792F THR* 3.4 7.4 + - - +
3793F LEU 3.3 0.2 - - - -
3794F LYS* 1.3 78.3 - - - +
3796F GLY* 1.3 63.8 + - - +
3797F ILE 3.4 0.2 - - - -
3798F SER* 3.4 10.6 + - - -
3799F ILE* 3.5 24.4 - - + +
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Residues in contact with GLY3796 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3774F VAL* 4.9 12.8 - - - -
3792F THR 3.1 14.6 + - - -
3793F LEU 3.5 2.2 + - - -
3794F LYS 3.4 0.6 - - - -
3795F LEU* 1.3 79.7 - - - +
3797F ILE* 1.3 60.1 + - - +
3798F SER 3.3 0.7 + - - -
3799F ILE* 3.4 13.0 + - - +
3800F LEU* 3.5 22.1 - - - +
3882F PHE* 3.9 20.6 - - - -
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Residues in contact with ILE3797 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3793F LEU 3.3 15.2 + - - +
3794F LYS* 3.3 36.3 - - + +
3796F GLY* 1.3 75.9 - - - +
3798F SER* 1.3 61.8 + - - +
3799F ILE 3.3 0.4 - - - -
3800F LEU* 4.0 4.1 - - - +
3801F ASN* 3.3 25.6 + - - +
3877F GLN* 5.6 5.4 - - - +
3878F ASP* 4.1 17.3 - - + +
3881F ARG* 4.5 17.5 - - + +
3882F PHE* 3.8 37.9 - - + +
3885F LEU* 4.5 7.8 - - + +
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Residues in contact with SER3798 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3726F ALA* 3.2 30.5 + - - -
3729F CYS* 3.2 28.6 - - - +
3730F HIS* 3.8 11.8 + - - -
3758F LEU* 5.8 2.8 - - - +
3794F LYS 3.9 10.1 - - - -
3795F LEU 3.4 11.6 + - - -
3796F GLY 3.2 1.2 - - - -
3797F ILE* 1.3 83.2 - - - +
3799F ILE* 1.3 61.3 + - - +
3801F ASN* 3.9 14.3 - - - +
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Residues in contact with ILE3799 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3726F ALA* 6.5 0.2 - - - -
3729F CYS* 3.9 17.3 - - + -
3758F LEU* 5.4 2.3 - - - +
3762F GLN* 3.9 28.1 - - + +
3765F LEU* 3.7 35.7 - - + -
3766F HIS* 5.6 3.8 - - + +
3770F ALA* 6.1 1.8 - - + -
3771F ALA* 6.1 0.7 - - + -
3774F VAL* 6.3 0.7 - - + -
3795F LEU* 3.5 24.7 - - + +
3796F GLY* 3.4 8.7 + - - +
3797F ILE 3.3 0.6 - - - -
3798F SER* 1.3 81.9 - - - +
3800F LEU* 1.3 60.6 + - + +
3801F ASN 3.2 4.5 + - - -
3802F GLY 4.6 2.4 + - - -
3804F ASN* 3.7 11.3 + - - +
3807F VAL* 3.9 31.6 - - + -
3811F MET* 6.3 0.2 - - + -
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Residues in contact with LEU3800 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3796F GLY 3.5 19.5 + - - +
3797F ILE* 3.8 2.0 + - - +
3799F ILE* 1.3 80.3 - - + +
3801F ASN* 1.3 63.4 + - - +
3802F GLY 3.3 2.7 - - - -
3803F GLY* 3.1 15.3 + - - -
3804F ASN* 4.2 13.0 - - - +
3807F VAL* 3.7 26.5 - - + -
3808F GLN* 5.0 8.5 - - + -
3811F MET* 4.2 20.4 - - + -
3882F PHE* 4.7 8.7 - - + +
3885F LEU* 3.1 47.3 - - + +
3886F LEU* 3.9 25.4 - - + +
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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