Contacts of the helix formed by residues 3875 - 3885 (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 PHE3875 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3785B THR* 4.9 10.8 - - + -
3786B GLY 5.2 3.1 - - - -
3789B VAL* 4.4 19.1 - - + -
3790B SER* 4.3 23.3 - - - -
3793B LEU* 4.7 11.3 - - + +
3830B LEU* 3.9 42.4 - - + -
3833B THR* 4.8 8.3 - - - -
3834B CYS* 5.1 6.5 - - - -
3872B ASP* 3.3 17.3 + - + +
3874B GLU* 1.3 79.0 - - - +
3876B THR* 1.3 73.3 + - - +
3877B GLN 3.3 1.6 - - - -
3878B ASP* 3.5 4.9 + - - +
3879B LEU* 3.3 34.2 + - + +
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Residues in contact with THR3876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3834B CYS* 3.7 25.0 - - + +
3835B SER 5.2 0.7 + - - -
3870B MET* 6.2 0.2 - - - +
3872B ASP* 3.1 27.8 + - - +
3875B PHE* 1.3 77.7 - - - +
3877B GLN* 1.3 64.2 + - - +
3878B ASP 3.3 0.5 + - - -
3879B LEU* 3.4 12.0 + - + -
3880B PHE* 3.7 39.7 + - + +
3917B TYR* 3.9 4.9 - - - +
3952B VAL* 3.7 29.9 - - + +
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Residues in contact with GLN3877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3794B LYS* 5.6 8.7 - - - +
3797B ILE* 5.6 5.2 - - - +
3872B ASP 4.6 0.2 + - - -
3873B ASP 3.2 26.0 + - - +
3874B GLU* 4.1 14.6 + - - +
3876B THR* 1.3 78.5 - - - +
3878B ASP* 1.3 72.2 + - - +
3880B PHE* 5.5 0.2 - - - +
3881B ARG* 3.2 24.3 + - - +
3952B VAL* 5.6 9.5 - - + +
3955B GLN* 5.0 16.1 - - + +
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Residues in contact with ASP3878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3790B SER 6.0 0.7 - - - +
3793B LEU* 4.9 21.9 - - + +
3794B LYS* 5.5 4.3 - - + +
3797B ILE* 4.1 17.4 - - + +
3874B GLU 4.7 6.1 - - - +
3875B PHE 3.5 7.0 + - - +
3876B THR 3.2 0.2 - - - -
3877B GLN* 1.3 96.4 - - - +
3879B LEU* 1.3 64.7 + - - +
3881B ARG* 3.8 7.3 - - - +
3882B PHE* 3.2 22.9 + - - +
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Residues in contact with LEU3879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3793B LEU* 4.7 13.9 - - + +
3827B ILE* 5.5 6.1 - - + +
3830B LEU* 3.7 40.2 - - + +
3831B MET* 3.7 22.9 - - - +
3834B CYS* 4.5 10.1 - - - -
3875B PHE* 3.3 29.5 + - + +
3876B THR* 3.4 6.7 + - - +
3878B ASP* 1.3 80.4 - - - +
3880B PHE* 1.3 92.1 + - + +
3882B PHE* 3.4 10.1 + - - +
3883B LEU* 3.7 19.7 + - + +
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Residues in contact with PHE3880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3831B MET* 3.6 35.7 - - + -
3834B CYS* 4.5 1.3 - - - -
3876B THR* 3.7 34.4 + - + +
3877B GLN 5.5 0.2 - - - +
3879B LEU* 1.3 87.1 - - + +
3881B ARG* 1.3 62.8 + - - +
3882B PHE 3.3 0.2 - - - -
3883B LEU* 3.5 12.4 + - + +
3884B GLN* 3.1 24.4 + - - +
3914B THR* 5.0 7.4 - - + -
3917B TYR* 3.6 43.1 - + + -
3952B VAL* 5.3 3.6 - - + -
3955B GLN* 4.6 21.8 - - + +
3956B VAL* 4.4 21.8 - - + -
3959B SER* 4.5 12.9 - - - -
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Residues in contact with ARG3881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3797B ILE* 4.5 18.3 - - + +
3801B ASN* 4.8 8.9 + - - -
3877B GLN* 3.2 26.2 + - - +
3878B ASP* 3.6 8.6 + - - +
3879B LEU 3.2 0.8 - - - -
3880B PHE* 1.3 75.8 - - - +
3882B PHE* 1.3 63.5 + - - +
3884B GLN* 3.5 7.0 + - - +
3885B LEU* 3.2 63.8 + - + +
3955B GLN* 3.6 37.2 + - + +
3958B ASN* 5.3 4.0 - - - +
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Residues in contact with PHE3882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3774B VAL* 5.3 6.1 - - + -
3775B LEU* 5.2 7.6 - - + -
3778B ILE* 6.3 3.6 - - + -
3793B LEU* 4.6 22.9 - - + -
3796B GLY* 3.9 38.4 - - - -
3797B ILE* 3.8 14.3 - - + +
3800B LEU* 4.7 7.7 - - + +
3811B MET* 4.9 13.5 - - + -
3823B PHE* 5.2 13.2 - + - -
3878B ASP 3.2 18.1 + - - +
3879B LEU 3.8 5.2 - - - +
3880B PHE 3.3 0.4 - - - -
3881B ARG* 1.3 78.9 - - - +
3883B LEU* 1.3 73.9 + - + +
3885B LEU* 3.7 4.3 + - - +
3886B LEU* 3.3 48.3 + - + +
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Residues in contact with LEU3883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3827B ILE* 4.6 20.9 - - + -
3831B MET* 5.3 12.8 - - + -
3879B LEU* 3.8 16.2 - - + +
3880B PHE* 3.5 14.8 + - + +
3881B ARG 3.3 0.2 - - - -
3882B PHE* 1.3 88.6 - - + +
3884B GLN* 1.3 64.4 + - - +
3886B LEU* 3.5 35.4 + - + +
3887B CYS* 4.4 1.2 + - - +
3898B LEU* 5.5 5.1 - - + +
3910B ILE* 3.8 29.8 - - + -
3914B THR* 5.6 2.2 - - + +
3959B SER* 5.8 0.4 - - - -
3963B TYR* 3.4 32.5 + - - +
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Residues in contact with GLN3884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3880B PHE 3.1 18.1 + - - +
3881B ARG* 4.0 10.8 - - - +
3882B PHE 3.3 0.6 - - - -
3883B LEU* 1.3 78.3 - - - +
3885B LEU* 1.3 66.6 + - + +
3886B LEU 3.2 1.1 + - - -
3887B CYS* 3.6 8.1 + - - +
3888B GLU* 3.9 5.9 + - - +
3955B GLN 5.4 2.2 - - - +
3958B ASN* 4.3 10.3 - - + +
3959B SER* 4.1 26.0 - - - +
3962B GLU* 4.0 22.2 - - + +
3963B TYR* 4.6 1.8 + - - -
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Residues in contact with LEU3885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3797B ILE* 4.5 9.6 - - + +
3800B LEU* 3.1 49.2 - - + +
3801B ASN* 3.7 25.4 - - - +
3803B GLY* 5.6 0.7 - - - -
3804B ASN 5.8 0.2 - - - +
3881B ARG* 3.2 64.4 + - + +
3882B PHE* 4.2 4.3 - - - +
3883B LEU 3.4 0.2 - - - -
3884B GLN* 1.3 80.3 - - + +
3886B LEU* 1.3 64.2 + - - +
3887B CYS 3.3 1.3 + - - -
3888B GLU* 3.6 23.0 + - + +
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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