Contacts of the helix formed by residues 3969 - 3978 (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 THR3969 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3967H PRO 5.8 0.4 - - - -
3968H CYS* 1.3 79.8 - - - +
3970H GLY* 1.3 77.2 + - - +
3971H ASN 3.2 2.1 + - - -
3972H GLN* 3.5 2.0 + - - +
3973H GLN* 2.7 37.9 - - - +
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Residues in contact with GLY3970 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3896H ASN* 6.4 1.3 - - - +
3899H ARG* 4.4 20.9 - - - +
3911H ILE* 6.1 0.2 - - - +
3969H THR* 1.3 84.6 + - - +
3971H ASN* 1.3 63.7 + - - +
3972H GLN 3.4 0.2 - - - -
3973H GLN* 4.7 2.3 - - - +
3974H SER* 3.3 27.5 + - - -
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Residues in contact with ASN3971 (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* 4.0 27.2 + - - +
3896H ASN* 5.3 1.0 - - - -
3898H LEU* 5.9 1.0 - - - +
3899H ARG* 5.3 3.8 - - - +
3911H ILE* 4.5 20.3 - - - +
3963H TYR* 3.1 50.0 + - + +
3964H ILE* 4.6 5.1 - - + +
3968H CYS* 3.6 21.3 - - - +
3969H THR 3.2 1.0 - - - -
3970H GLY* 1.3 80.6 + - - +
3972H GLN* 1.3 58.8 + - - +
3974H SER* 4.0 3.0 - - - -
3975H LEU* 3.2 31.4 + - + +
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Residues in contact with GLN3972 (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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3964H ILE* 5.2 6.5 - - + -
3967H PRO* 5.2 2.1 - - - +
3968H CYS* 3.2 41.7 + - - +
3969H THR 3.5 1.4 + - - +
3970H GLY 3.4 0.6 - - - -
3971H ASN* 1.3 76.3 - - - +
3973H GLN* 1.3 76.2 + - - +
3975H LEU* 3.6 3.9 + - - +
3976H ALA* 3.1 25.1 + - - +
4024H SER 5.3 2.4 - - - +
4025H LEU* 4.0 30.1 + - + +
4028H GLY 4.9 7.6 + - - +
4029H ASN* 5.4 9.7 - - - +
4035H ILE* 4.8 24.2 - - + +
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Residues in contact with GLN3973 (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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3969H THR* 2.7 29.2 + - - +
3970H GLY* 4.8 2.0 - - - +
3971H ASN 3.5 0.2 - - - -
3972H GLN* 1.3 86.1 + - - +
3974H SER* 1.3 64.2 + - - +
3976H ALA* 4.6 3.8 - - - -
3977H HIS* 3.1 47.4 + - + +
4034H MET* 6.3 2.2 - - - -
4035H ILE* 4.9 20.0 - - + +
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Residues in contact with SER3974 (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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3899H ARG* 5.3 3.9 - - - +
3909H ASN* 4.4 16.7 + - - -
3911H ILE* 4.2 23.9 - - - +
3912H ILE* 6.1 2.5 - - - -
3970H GLY 3.3 19.7 + - - -
3971H ASN* 4.3 2.5 - - - -
3972H GLN 3.3 0.4 - - - -
3973H GLN* 1.3 77.4 - - - +
3975H LEU* 1.3 63.5 + - - +
3977H HIS* 3.6 4.8 + - - +
3978H SER* 3.1 25.5 + - - -
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Residues in contact with LEU3975 (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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3911H ILE* 5.1 7.1 - - + +
3915H VAL* 5.2 3.4 - - + -
3960H LEU* 4.1 37.2 - - + +
3963H TYR* 6.5 0.2 - - + -
3964H ILE* 5.5 8.1 - - + -
3971H ASN 3.2 20.5 + - - +
3972H GLN* 4.1 3.6 - - - +
3974H SER* 1.3 77.0 - - - +
3976H ALA* 1.3 63.5 + - - +
3978H SER* 2.8 21.3 + - - +
3980H LEU* 3.7 27.4 - - + +
3981H TRP 5.0 1.3 + - - +
4025H LEU* 3.7 29.8 - - + -
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Residues in contact with ALA3976 (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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3972H GLN 3.1 18.6 + - - +
3973H GLN* 4.1 5.4 - - - +
3974H SER 3.3 0.4 - - - -
3975H LEU* 1.3 82.4 - - - +
3977H HIS* 1.3 69.4 + - + +
3978H SER 3.5 6.8 + - - +
3981H TRP* 5.9 2.9 - - - +
4025H LEU* 6.2 3.4 - - + -
4035H ILE* 5.3 13.5 - - + -
4038H GLN* 4.6 27.1 - - + +
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Residues in contact with HIS3977 (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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3973H GLN* 3.1 34.5 + - + +
3974H SER* 4.2 4.7 - - - +
3976H ALA* 1.3 82.1 + - + +
3978H SER* 1.3 65.0 + - - +
4034H MET* 5.7 10.3 - - + -
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Residues in contact with SER3978 (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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3911H ILE* 5.9 0.6 - - - +
3912H ILE* 6.0 2.9 - - - -
3915H VAL* 3.7 28.7 - - - +
3974H SER 3.1 15.9 + - - -
3975H LEU* 2.8 26.3 + - - +
3976H ALA 3.3 8.4 - - - +
3977H HIS* 1.3 81.1 - - - +
3979H ARG* 1.3 59.1 + - - +
3980H LEU* 3.3 11.7 + - - +
3981H TRP* 4.7 3.1 + - - +
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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