Contacts of the helix formed by residues 3769 - 3781 (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 GLY3769 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3695H HIS* 3.8 14.8 + - - -
3698H VAL* 3.5 20.9 - - - +
3699H LEU* 5.5 5.9 - - - +
3768H ARG* 1.3 75.0 - - - +
3770H ALA* 1.3 60.6 + - - +
3771H ALA 3.5 1.6 - - - -
3772H GLU* 3.8 16.6 + - - +
3773H MET* 3.6 16.3 + - - +
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Residues in contact with ALA3770 (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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3698H VAL* 4.0 10.2 - - + +
3725H MET* 5.2 6.3 - - - -
3765H LEU* 3.3 42.2 - - + +
3768H ARG* 3.1 5.8 + - + -
3769H GLY* 1.3 75.5 - - - +
3771H ALA* 1.3 65.8 + - - +
3772H GLU 3.2 0.4 - - - -
3773H MET* 3.4 12.6 + - - +
3774H VAL* 3.5 19.4 + - - +
3795H LEU* 5.3 5.3 - - + +
3799H ILE* 6.1 1.6 - - + -
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Residues in contact with ALA3771 (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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3765H LEU 4.6 3.0 + - - +
3766H HIS* 5.4 8.3 - - - +
3768H ARG 4.6 1.7 + - - +
3769H GLY* 3.5 0.6 - - - -
3770H ALA* 1.3 78.1 - - - +
3772H GLU* 1.3 64.9 + - + +
3773H MET 3.3 0.2 - - - -
3774H VAL* 3.3 22.4 - - - +
3775H LEU* 3.5 13.0 - - - +
3799H ILE* 6.1 0.9 - - + -
3807H VAL* 3.9 28.3 - - + -
3810H LYS* 4.9 15.0 - - + +
3811H MET* 4.4 9.8 - - + +
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Residues in contact with GLU3772 (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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3769H GLY* 3.8 15.8 + - - +
3770H ALA 3.2 0.6 - - - -
3771H ALA* 1.3 79.1 - - + +
3773H MET* 1.3 63.7 + - - +
3774H VAL 3.3 0.2 - - - -
3775H LEU* 3.5 7.1 + - - +
3776H GLN* 3.3 36.5 + - - +
3810H LYS* 3.1 37.5 + - - +
3813H ASP* 4.7 1.0 - - - +
3814H TYR* 3.2 42.0 - - - +
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Residues in contact with MET3773 (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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3698H VAL* 4.3 16.4 - - - +
3701H PHE* 5.4 10.3 - - + -
3702H SER* 5.7 6.5 - - - +
3718H TYR* 4.3 10.3 + - - +
3769H GLY 3.6 11.2 + - - +
3770H ALA* 3.4 11.3 + - - +
3771H ALA 3.3 0.8 - - - -
3772H GLU* 1.3 79.7 - - - +
3774H VAL* 1.3 62.7 + - + +
3776H GLN* 4.2 6.2 - - - +
3777H MET* 3.3 25.3 + - - +
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Residues in contact with VAL3774 (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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3718H TYR* 5.3 5.4 - - - +
3770H ALA 3.5 13.5 - - - +
3771H ALA* 3.3 22.9 - - - +
3773H MET* 1.3 79.2 - - + +
3775H LEU* 1.3 70.5 + - + +
3777H MET* 4.2 4.9 - - - +
3778H ILE* 3.2 26.9 + - - +
3792H THR* 4.7 20.0 - - - +
3795H LEU* 3.9 27.1 - - + -
3796H GLY* 4.9 12.1 - - - -
3799H ILE* 6.3 0.7 - - + -
3811H MET* 4.5 8.1 - - + -
3823H PHE* 4.8 0.2 - - - -
3882H PHE* 5.3 6.1 - - + -
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Residues in contact with LEU3775 (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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3771H ALA 3.5 16.6 - - - +
3772H GLU* 3.5 10.6 + - - +
3773H MET 3.2 0.6 - - - -
3774H VAL* 1.3 91.2 - - + +
3776H GLN* 1.3 64.7 + - - +
3777H MET 3.3 0.4 - - - -
3778H ILE 3.5 0.5 + - - -
3779H SER* 3.5 9.0 + - - -
3811H MET* 3.8 53.4 - - + +
3814H TYR* 4.5 17.3 - - + -
3815H LEU* 4.4 19.7 - - + -
3823H PHE* 3.2 47.2 - - + -
3882H PHE* 5.2 6.1 - - + -
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Residues in contact with GLN3776 (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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462H GLU* 4.1 17.6 + - - +
3702H SER* 4.1 21.4 - - - -
3705H ALA* 4.4 5.9 - - + +
3706H LEU* 3.4 33.1 - - + +
3772H GLU* 3.3 25.2 + - - +
3773H MET* 4.3 5.0 - - - +
3775H LEU* 1.3 77.2 - - - +
3777H MET* 1.3 60.0 + - - +
3779H SER* 3.5 6.4 + - - -
3780H ALA* 3.1 26.9 + - - +
3814H TYR* 2.9 40.4 + - + +
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Residues in contact with MET3777 (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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3701H PHE* 5.9 0.9 - - - +
3704H THR* 5.8 2.2 - - - -
3705H ALA* 4.5 15.9 - - + +
3712H LEU* 5.8 3.8 - - + -
3718H TYR* 3.8 19.3 - - + +
3773H MET 3.3 18.6 + - - +
3774H VAL 4.6 2.9 - - - +
3775H LEU 3.3 0.2 - - - -
3776H GLN* 1.3 76.1 - - - +
3778H ILE* 1.3 66.4 + - - +
3780H ALA* 3.2 26.0 + - + +
3781H CYS* 3.4 14.4 + - + +
3788H MET* 3.7 29.8 - - + +
3789H VAL* 6.5 0.7 - - + -
3792H THR* 3.7 32.8 - - + +
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Residues in contact with ILE3778 (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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3774H VAL 3.2 18.6 - - - +
3775H LEU 3.5 0.8 + - - +
3776H GLN 3.3 0.4 - - - -
3777H MET* 1.3 78.6 - - + +
3779H SER* 1.3 60.6 + - - +
3781H CYS* 3.2 20.3 - - - -
3789H VAL* 4.8 11.7 - - + -
3792H THR* 4.0 20.0 - - - +
3793H LEU* 3.8 31.9 - - + -
3823H PHE* 3.8 30.5 - - + +
3826H SER* 3.1 31.4 + - - +
3827H ILE* 4.8 7.0 - - + -
3830H LEU* 5.4 8.1 - - + -
3882H PHE* 6.3 2.9 - - + -
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Residues in contact with SER3779 (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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3775H LEU 3.5 8.9 + - - -
3776H GLN* 3.5 9.5 + - - -
3777H MET 3.3 0.4 - - - -
3778H ILE* 1.3 78.5 - - - +
3780H ALA* 1.3 61.0 + - - +
3781H CYS 3.3 0.7 + - - -
3782H LYS* 3.6 11.2 + - - +
3821H VAL 4.6 2.6 + - - -
3822H GLY* 3.7 26.2 - - - +
3823H PHE* 3.7 23.7 + - - +
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Residues in contact with ALA3780 (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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3705H ALA* 3.9 25.4 - - + +
3710H SER 4.5 4.0 - - - +
3711H LYS 2.9 19.6 - - - +
3776H GLN 3.1 17.2 + - - +
3777H MET* 3.2 25.6 + - + +
3779H SER* 1.3 76.7 - - - +
3781H CYS* 1.3 61.6 + - - +
3782H LYS* 3.2 4.2 + - - +
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Residues in contact with CYS3781 (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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3711H LYS* 4.1 11.1 - - - +
3712H LEU* 5.2 5.2 - - + -
3777H MET* 3.4 14.7 + - + +
3778H ILE* 3.2 21.8 - - - +
3779H SER 3.3 0.8 - - - -
3780H ALA* 1.3 78.7 - - - +
3782H LYS* 1.3 65.3 + - - +
3783H GLY* 3.2 18.2 + - - -
3784H GLU* 3.4 40.1 + - + +
3789H VAL* 4.4 19.7 - - + -
3826H SER* 3.7 11.7 - - - -
3830H LEU* 5.3 5.6 - - - -
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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