Contacts of the helix formed by residues 3891 - 3900 (chain H) 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 ASN3891 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3805H ALA* 5.4 10.0 - - + +
3808H GLN* 4.8 11.1 - - - +
3812H LEU* 5.9 1.0 - - - +
3886H LEU 4.1 8.7 + - - +
3887H CYS* 3.4 28.1 - - - +
3889H GLY* 3.2 8.3 + - - +
3890H HIS* 1.3 74.9 + - - +
3892H ASN* 1.3 61.3 + - - +
3893H ASP* 3.2 23.0 + - - +
3894H PHE* 3.4 19.5 - - - +
3895H GLN* 3.6 17.5 + - - +
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Residues in contact with ASN3892 (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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3890H HIS 3.7 3.7 + - - +
3891H ASN* 1.3 70.1 - - - +
3893H ASP* 1.3 55.4 + - - +
3894H PHE 3.2 2.5 - - - -
3895H GLN* 3.8 8.4 - - + +
3896H ASN* 2.5 39.4 + - - +
3967H PRO 4.7 14.8 - - - +
3968H CYS* 6.1 2.2 - - + -
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Residues in contact with ASP3893 (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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3812H LEU* 4.1 24.6 - - + +
3891H ASN* 3.2 27.7 + - - +
3892H ASN* 1.3 74.0 - - - +
3894H PHE* 1.3 63.6 + - - -
3896H ASN* 2.8 23.9 + - - +
3897H TYR* 4.3 3.8 + - - +
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Residues in contact with PHE3894 (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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3808H GLN* 4.8 10.8 - - + -
3811H MET* 5.0 9.6 - - + -
3812H LEU* 4.1 35.4 - - + -
3815H LEU* 5.2 7.4 - - + -
3824H PHE* 6.3 1.1 - + - -
3886H LEU* 3.6 46.0 - - + -
3887H CYS* 3.7 17.0 - - - -
3891H ASN* 3.4 22.4 + - - +
3893H ASP* 1.3 82.3 + - - +
3895H GLN* 1.3 63.1 + - - +
3896H ASN 3.3 2.5 - - - -
3897H TYR* 3.4 22.4 + + + +
3898H LEU* 3.6 36.5 - - + +
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Residues in contact with GLN3895 (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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3887H CYS* 3.8 15.4 - - + -
3891H ASN 3.6 17.6 + - - +
3892H ASN* 3.5 9.0 + - - +
3894H PHE* 1.3 79.1 - - - +
3896H ASN* 1.3 59.5 + - - +
3897H TYR 3.5 0.3 + - - -
3898H LEU* 3.5 15.2 + - - +
3899H ARG* 3.7 7.1 + - - +
3962H GLU 6.0 0.4 - - - +
3963H TYR* 4.8 10.1 - - + +
3968H CYS* 5.6 4.5 - - + -
3971H ASN* 4.0 28.0 + - - +
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Residues in contact with ASN3896 (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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3892H ASN* 2.5 27.2 + - - +
3893H ASP* 2.8 19.6 - - - +
3895H GLN* 1.3 77.2 - - - +
3897H TYR* 1.3 81.6 + - - +
3899H ARG* 3.4 8.2 + - - +
3900H THR* 3.2 22.3 + - - +
3970H GLY* 6.4 0.9 - - - -
3971H ASN* 5.3 1.1 - - - -
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Residues in contact with TYR3897 (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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3812H LEU* 5.6 6.3 - - + -
3815H LEU* 3.2 43.5 + - + +
3816H LYS* 3.4 42.2 - - + -
3819H LYS* 5.6 0.7 - - - -
3824H PHE* 3.5 35.4 - + - -
3893H ASP 4.4 4.0 - - - +
3894H PHE* 3.4 21.2 + + + +
3895H GLN 3.3 1.2 - - - -
3896H ASN* 1.3 87.3 + - - +
3898H LEU* 1.3 57.4 + - + +
3900H THR 3.0 9.7 - - - +
3901H GLN* 2.3 54.9 + - + +
3903H GLY* 5.7 2.6 - - - -
3904H ASN* 5.4 5.4 + - - +
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Residues in contact with LEU3898 (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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3824H PHE* 5.0 12.1 - - + -
3883H LEU* 5.5 3.4 - - + +
3886H LEU* 5.4 8.3 - - + -
3887H CYS* 5.9 2.2 - - - -
3894H PHE* 3.6 43.7 - - + +
3895H GLN* 3.5 11.3 + - - +
3896H ASN 3.3 0.8 - - - -
3897H TYR* 1.3 84.5 - - + +
3899H ARG* 1.3 62.5 + - - +
3901H GLN* 3.4 9.2 + - - +
3909H ASN* 3.9 1.0 - - - +
3910H ILE* 3.7 49.0 + - + +
3911H ILE* 4.4 9.8 - - + +
3963H TYR* 4.2 32.3 - - + +
3971H ASN* 5.9 0.9 - - - +
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Residues in contact with ARG3899 (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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3895H GLN 3.7 8.4 + - - +
3896H ASN* 3.4 10.6 + - - +
3897H TYR 3.3 0.4 - - - -
3898H LEU* 1.3 80.2 - - - +
3900H THR* 1.3 62.5 + - - +
3901H GLN* 4.1 0.2 - - - -
3909H ASN* 3.1 34.8 + - - +
3911H ILE* 4.7 8.7 - - + +
3970H GLY* 4.4 29.8 - - - +
3971H ASN* 5.3 3.8 - - - +
3974H SER* 5.3 2.9 - - - +
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Residues in contact with THR3900 (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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3896H ASN 3.2 12.4 + - - +
3897H TYR* 3.0 16.8 - - - +
3899H ARG* 1.3 82.4 - - - +
3901H GLN* 1.3 69.2 + - - +
3902H THR 4.0 2.0 + - - -
3907H THR* 5.8 7.0 - - - -
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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