Contacts of the helix formed by residues 3748 - 3767 (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 PHE3748 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3747F SER* 1.3 79.7 + - - +
3749F GLU* 1.3 61.2 + - - +
3751F LYS* 3.9 5.6 - - + -
3752F GLU* 3.0 36.5 + - + +
4714F TRP* 3.7 30.3 - - + +
4715F ASP* 4.4 8.7 - - + -
4716F LYS 5.3 0.9 - - - -
4717F PHE* 4.4 26.5 - + - -
4994F ILE* 5.6 17.7 - - + -
5009F TRP* 5.6 14.6 - + - -
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Residues in contact with GLU3749 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747F SER* 3.3 7.5 + - - +
3748F PHE* 1.3 83.1 - - - +
3750F GLU* 1.3 57.1 + - - +
3752F GLU* 3.6 4.4 + - - +
3753F MET* 3.1 29.1 + - - +
4714F TRP 5.3 3.1 + - - +
4716F LYS* 4.2 24.7 - - + -
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Residues in contact with GLU3750 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747F SER* 3.5 22.3 + - - +
3748F PHE 3.3 0.2 - - - -
3749F GLU* 1.3 76.0 - - - +
3751F LYS* 1.3 65.6 + - - +
3753F MET* 3.5 5.0 + - - +
3754F GLU* 3.2 30.6 + - + +
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Residues in contact with LYS3751 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747F SER 3.0 17.9 + - - +
3748F PHE* 3.9 8.7 - - + +
3749F GLU 3.3 0.2 - - - -
3750F GLU* 1.3 77.7 - - - +
3752F GLU* 1.3 61.6 + - - +
3754F GLU* 3.5 4.7 + - - +
3755F LYS* 3.1 23.6 + - - +
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Residues in contact with GLU3752 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3748F PHE* 3.0 28.0 + - + +
3749F GLU* 4.2 4.9 - - - +
3751F LYS* 1.3 77.6 - - - +
3753F MET* 1.3 62.3 + - - +
3755F LYS* 3.6 6.5 + - - +
3756F GLN* 3.2 22.3 + - - +
4717F PHE* 4.4 24.9 - - + -
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Residues in contact with MET3753 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3749F GLU 3.1 19.0 + - - +
3750F GLU* 3.8 6.7 - - - +
3751F LYS 3.2 0.4 - - - -
3752F GLU* 1.3 77.7 - - - +
3754F GLU* 1.3 60.6 + - + +
3756F GLN* 3.3 6.8 + - - +
3757F ARG* 3.0 35.7 + - - +
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Residues in contact with GLU3754 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3750F GLU* 3.2 18.3 + - + +
3751F LYS* 4.1 3.6 - - - +
3753F MET* 1.3 76.0 - - + +
3755F LYS* 1.3 64.6 + - - +
3757F ARG* 3.4 38.2 + - - +
3758F LEU* 3.1 23.0 + - - +
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Residues in contact with LYS3755 (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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3751F LYS 3.1 17.3 + - - +
3752F GLU* 3.8 8.3 - - - +
3753F MET 3.3 0.2 - - - -
3754F GLU* 1.3 79.1 - - - +
3756F GLN* 1.3 61.6 + - - +
3758F LEU* 3.5 11.0 + - - +
3759F LEU* 3.2 19.8 + - - +
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Residues in contact with GLN3756 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3752F GLU 3.2 16.1 + - - +
3753F MET* 3.3 6.0 + - - +
3755F LYS* 1.3 75.4 - - - +
3757F ARG* 1.3 64.4 + - + +
3759F LEU* 3.0 17.9 + - - +
3760F TYR* 3.0 24.9 + - + +
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Residues in contact with ARG3757 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3753F MET* 3.0 24.2 + - + +
3754F GLU* 3.4 38.9 + - - +
3755F LYS 3.4 0.4 - - - -
3756F GLN* 1.3 76.3 - - + +
3758F LEU* 1.3 60.9 + - - +
3760F TYR* 3.4 7.3 + - - +
3761F GLN* 2.9 34.7 + - - +
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Residues in contact with LEU3758 (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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3729F CYS* 4.6 11.7 - - - +
3730F HIS* 5.2 11.7 - - - +
3754F GLU 3.1 17.0 + - - +
3755F LYS* 3.7 8.7 - - - +
3756F GLN 3.2 0.2 - - - -
3757F ARG* 1.3 78.1 - - - +
3759F LEU* 1.3 66.2 + - + +
3761F GLN* 3.4 9.3 + - - +
3762F GLN* 3.1 24.2 + - + +
3798F SER 5.8 2.7 - - - +
3799F ILE 5.4 2.2 - - - +
3801F ASN* 4.7 16.4 - - + +
3802F GLY* 3.6 38.1 - - - +
3804F ASN* 5.6 3.6 - - - +
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Residues in contact with LEU3759 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3755F LYS 3.2 10.4 + - - +
3756F GLN* 3.0 27.6 + - - +
3758F LEU* 1.3 79.1 - - + +
3760F TYR* 1.3 61.0 + - - +
3762F GLN* 3.3 7.4 + - - +
3763F ALA* 2.7 30.5 + - - +
3804F ASN* 4.7 15.2 + - + +
3806F ASP* 5.7 0.3 - - - +
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Residues in contact with TYR3760 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3756F GLN* 3.0 14.7 + - + +
3757F ARG* 3.7 11.0 - - - +
3758F LEU 3.2 0.2 - - - -
3759F LEU* 1.3 74.3 - - - +
3761F GLN* 1.3 84.3 + - - +
3763F ALA* 3.3 8.9 + - + +
3764F ARG* 3.0 51.0 + - + +
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Residues in contact with GLN3761 (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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3728F SER 3.5 22.0 - - - +
3729F CYS* 3.4 32.5 - - - +
3731F LEU 5.2 5.6 - - - +
3757F ARG* 2.9 26.5 + - - +
3758F LEU* 3.8 5.3 - - - +
3759F LEU 3.4 0.2 - - - -
3760F TYR* 1.3 104.9 - - - +
3762F GLN* 1.3 61.5 + - - +
3764F ARG* 3.5 37.3 + - - +
3765F LEU* 4.0 7.4 + - - +
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Residues in contact with GLN3762 (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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3729F CYS* 4.0 15.1 - - - -
3758F LEU* 3.1 19.0 + - + +
3759F LEU* 3.7 4.9 - - - +
3760F TYR 3.2 0.4 - - - -
3761F GLN* 1.3 75.5 - - - +
3763F ALA* 1.3 59.4 + - - +
3765F LEU* 3.3 5.2 + - - +
3766F HIS* 2.9 28.2 + - + +
3798F SER 5.3 0.2 - - - +
3799F ILE* 3.9 32.8 - - + +
3804F ASN* 4.1 15.5 - - - +
3806F ASP* 5.7 0.7 - - - +
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Residues in contact with ALA3763 (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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3759F LEU 2.7 20.9 + - - +
3760F TYR* 3.3 12.1 + - + +
3762F GLN* 1.3 72.3 - - - +
3764F ARG* 1.3 63.9 + - - +
3765F LEU 3.2 0.2 - - - -
3766F HIS* 3.6 13.4 - - + -
3767F ASN* 3.1 24.4 + - - +
3806F ASP* 5.2 7.6 + - - +
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Residues in contact with ARG3764 (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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3670F ILE* 3.6 27.9 - - - +
3671F ASP* 3.5 34.4 + - - +
3674F SER* 4.9 11.6 + - - +
3694F LEU* 4.4 15.8 - - + +
3760F TYR* 3.0 45.9 + - + +
3761F GLN* 3.5 31.8 - - - +
3762F GLN 3.2 0.6 - - - -
3763F ALA* 1.3 77.7 - - - +
3765F LEU* 1.3 63.9 + - + +
3767F ASN* 4.4 5.4 + - - +
3768F ARG* 4.5 8.5 + - - +
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Residues in contact with LEU3765 (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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3670F ILE* 5.5 2.9 - - + -
3694F LEU* 4.7 17.0 - - + -
3725F MET* 3.6 52.7 - - + +
3726F ALA* 6.0 0.2 - - - -
3729F CYS* 4.7 7.9 - - + -
3761F GLN 4.4 6.7 - - - +
3762F GLN 3.3 6.8 + - - +
3763F ALA 3.2 0.2 - - - -
3764F ARG* 1.3 84.8 - - + +
3766F HIS* 1.3 64.0 + - - +
3767F ASN 3.3 1.8 - - - -
3768F ARG* 3.3 19.4 + - + +
3770F ALA* 3.3 30.7 + - + +
3771F ALA 4.6 1.1 + - - -
3795F LEU* 5.1 4.9 - - + -
3799F ILE* 3.7 28.5 - - + -
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Residues in contact with HIS3766 (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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3762F GLN* 2.9 18.4 + - + +
3763F ALA* 3.4 13.2 + - + -
3765F LEU* 1.3 76.5 - - - +
3767F ASN* 1.3 66.7 + - - +
3768F ARG 3.2 6.2 - - - +
3771F ALA* 5.4 7.3 - - - +
3799F ILE* 5.6 3.3 - - + +
3806F ASP* 3.1 55.4 + - + +
3807F VAL* 3.9 21.0 - - + +
3809F GLN* 5.0 3.6 + - - -
3810F LYS* 3.5 27.1 - - + +
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Residues in contact with ASN3767 (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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3695F HIS* 5.4 0.7 - - - -
3763F ALA 3.1 16.2 + - - +
3764F ARG 4.6 3.8 - - - +
3765F LEU 3.3 0.2 - - - -
3766F HIS* 1.3 82.2 - - - +
3768F ARG* 1.3 63.8 + - - +
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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
------------------------------------------------------------
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