Contacts of the helix formed by residues 3748 - 3767 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747B SER* 1.3 81.0 + - - +
3749B GLU* 1.3 60.2 + - - +
3751B LYS* 3.4 5.7 + - + +
3752B GLU* 3.0 34.7 + - + +
4714B TRP* 3.7 31.4 - - + +
4715B ASP* 4.4 9.0 - - + -
4716B LYS 5.3 0.7 - - - -
4717B PHE* 4.4 26.2 - + - -
4994B ILE* 5.6 17.7 - - + -
5009B TRP* 5.6 14.6 - + - -
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Residues in contact with GLU3749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747B SER* 3.3 7.7 + - - +
3748B PHE* 1.3 83.2 - - - +
3750B GLU* 1.3 57.2 + - - +
3752B GLU* 4.0 4.2 - - - +
3753B MET* 3.1 28.8 + - - +
4714B TRP 5.3 3.1 + - - +
4716B LYS* 4.2 24.0 - - + +
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Residues in contact with GLU3750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747B SER* 3.5 23.2 + - - +
3748B PHE 3.3 0.6 - - - -
3749B GLU* 1.3 75.2 - - - +
3751B LYS* 1.3 65.0 + - - +
3753B MET* 3.5 5.0 + - - +
3754B GLU* 3.2 30.7 + - + +
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Residues in contact with LYS3751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747B SER 3.0 18.1 + - - +
3748B PHE* 3.9 8.5 - - + +
3750B GLU* 1.3 76.9 - - - +
3752B GLU* 1.3 61.7 + - - +
3754B GLU* 3.5 4.4 + - - +
3755B LYS* 3.1 24.1 + - - +
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Residues in contact with GLU3752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3748B PHE* 3.0 29.0 + - + +
3749B GLU* 4.2 4.3 - - - +
3751B LYS* 1.3 76.9 - - - +
3753B MET* 1.3 61.0 + - - +
3755B LYS* 3.6 7.0 + - - +
3756B GLN* 3.2 22.2 + - - +
4717B PHE* 4.4 24.7 - - + -
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Residues in contact with MET3753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3749B GLU 3.1 19.3 + - - +
3750B GLU* 3.8 7.0 - - - +
3751B LYS 3.2 0.2 - - - -
3752B GLU* 1.3 77.9 - - - +
3754B GLU* 1.3 60.8 + - + +
3756B GLN* 3.3 6.5 + - - +
3757B ARG* 3.0 36.1 + - - +
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Residues in contact with GLU3754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3750B GLU* 3.2 18.1 + - + +
3751B LYS* 4.1 4.3 - - - +
3753B MET* 1.3 77.2 - - + +
3755B LYS* 1.3 65.0 + - - +
3757B ARG* 3.4 37.6 + - - +
3758B LEU* 3.1 23.4 + - - +
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Residues in contact with LYS3755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3751B LYS 3.1 18.6 + - - +
3752B GLU* 3.8 8.1 - - - +
3753B MET 3.3 0.2 - - - -
3754B GLU* 1.3 78.3 - - - +
3756B GLN* 1.3 60.4 + - - +
3758B LEU* 3.5 10.6 + - - +
3759B LEU* 3.2 20.4 + - - +
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Residues in contact with GLN3756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3752B GLU 3.2 15.0 + - - +
3753B MET* 3.3 6.0 + - - +
3755B LYS* 1.3 77.4 - - - +
3757B ARG* 1.3 65.6 + - + +
3759B LEU* 3.0 17.3 + - - +
3760B TYR* 3.0 24.5 + - + +
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Residues in contact with ARG3757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3753B MET* 3.0 25.0 + - + +
3754B GLU* 3.4 38.9 + - - +
3755B LYS 3.4 0.2 - - - -
3756B GLN* 1.3 75.8 - - + +
3758B LEU* 1.3 61.1 + - - +
3760B TYR* 3.4 7.9 + - - +
3761B GLN* 2.9 34.5 + - - +
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Residues in contact with LEU3758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729B CYS* 4.6 10.9 - - - +
3730B HIS* 5.2 12.1 - - - +
3754B GLU 3.1 16.9 + - - +
3755B LYS* 3.7 9.4 - - - +
3756B GLN 3.2 0.4 - - - -
3757B ARG* 1.3 76.9 - - - +
3759B LEU* 1.3 65.2 + - + +
3761B GLN* 3.4 7.5 + - - +
3762B GLN* 3.1 23.8 + - + +
3798B SER 5.8 3.1 - - - +
3799B ILE 5.4 2.9 - - - +
3801B ASN* 4.7 16.8 - - + +
3802B GLY* 3.6 37.2 - - - +
3804B ASN* 5.6 3.6 - - - +
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Residues in contact with LEU3759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3755B LYS 3.2 11.0 + - - +
3756B GLN* 3.0 26.8 + - - +
3758B LEU* 1.3 78.7 - - + +
3760B TYR* 1.3 59.8 - - - +
3762B GLN* 3.3 8.1 + - - +
3763B ALA* 2.7 30.5 + - - +
3804B ASN* 4.7 14.8 + - + +
3806B ASP* 5.7 0.5 - - - +
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Residues in contact with TYR3760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3756B GLN* 3.0 16.0 + - + +
3757B ARG* 3.7 11.4 - - - +
3758B LEU 3.2 0.4 - - - -
3759B LEU* 1.3 75.2 - - - +
3761B GLN* 1.3 84.3 + - - +
3763B ALA* 3.3 9.3 + - + +
3764B ARG* 3.0 50.7 + - + +
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Residues in contact with GLN3761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3728B SER 3.5 22.2 - - - +
3729B CYS* 3.4 33.7 - - - +
3731B LEU 5.2 6.0 - - - +
3757B ARG* 2.9 26.6 + - - +
3758B LEU* 3.8 5.2 - - - +
3759B LEU 3.4 0.4 - - - -
3760B TYR* 1.3 107.0 - - - +
3762B GLN* 1.3 60.4 + - - +
3764B ARG* 3.5 37.0 + - - +
3765B LEU* 4.0 7.1 + - - +
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Residues in contact with GLN3762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729B CYS* 4.0 14.1 - - - -
3758B LEU* 3.1 18.6 + - + +
3759B LEU* 3.7 4.7 - - - +
3760B TYR 3.2 0.2 - - - -
3761B GLN* 1.3 76.5 - - - +
3763B ALA* 1.3 59.6 + - - +
3765B LEU* 3.3 5.2 + - - +
3766B HIS* 2.9 27.5 + - - +
3799B ILE* 3.9 32.9 - - + +
3804B ASN* 4.1 16.4 - - - +
3806B ASP* 5.7 0.4 - - - -
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Residues in contact with ALA3763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3759B LEU 2.7 21.4 + - - +
3760B TYR* 3.3 12.3 + - + +
3762B GLN* 1.3 70.1 - - - +
3764B ARG* 1.3 64.0 + - - +
3765B LEU 3.2 0.2 - - - -
3766B HIS* 3.6 13.5 - - + -
3767B ASN* 3.1 25.1 + - - +
3806B ASP* 5.2 7.1 + - - +
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Residues in contact with ARG3764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670B ILE* 3.6 27.9 - - - +
3671B ASP* 3.5 34.6 + - - +
3674B SER* 4.9 10.6 + - - +
3694B LEU* 4.4 16.6 - - + +
3760B TYR* 3.0 45.5 + - + +
3761B GLN* 3.5 33.0 - - - +
3762B GLN 3.2 0.6 - - - -
3763B ALA* 1.3 78.4 - - - +
3765B LEU* 1.3 63.1 + - + +
3767B ASN* 4.4 5.1 + - - +
3768B ARG* 4.5 9.2 + - - +
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Residues in contact with LEU3765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670B ILE* 5.5 3.4 - - + -
3694B LEU* 4.7 16.6 - - + -
3725B MET* 3.6 52.3 - - + +
3729B CYS* 4.7 7.4 - - + -
3761B GLN 4.4 6.7 - - - +
3762B GLN 3.3 6.0 + - - +
3764B ARG* 1.3 84.2 - - + +
3766B HIS* 1.3 64.6 + - - +
3767B ASN 3.3 1.8 - - - -
3768B ARG* 3.3 20.1 + - + +
3770B ALA* 3.3 29.2 + - + +
3771B ALA 4.6 1.0 + - - -
3795B LEU* 5.1 4.7 - - + -
3799B ILE* 3.7 28.9 - - + -
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Residues in contact with HIS3766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3762B GLN* 2.9 19.3 + - + +
3763B ALA* 3.4 12.5 + - + -
3765B LEU* 1.3 76.3 - - - +
3767B ASN* 1.3 67.1 + - - +
3768B ARG 3.2 7.0 - - - +
3771B ALA* 5.4 7.0 - - - +
3799B ILE* 5.6 2.9 - - + +
3806B ASP* 3.1 55.0 + - + +
3807B VAL* 3.9 20.9 - - + +
3809B GLN* 5.0 3.8 + - - -
3810B LYS* 3.5 27.6 - - + +
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Residues in contact with ASN3767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3695B HIS* 5.4 0.9 - - - -
3763B ALA 3.1 16.4 + - - +
3764B ARG* 4.6 4.5 - - - +
3765B LEU 3.3 0.2 - - - -
3766B HIS* 1.3 81.8 - - - +
3768B ARG* 1.3 61.9 + - - +
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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