Contacts of the helix formed by residues 3939 - 3964 (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 GLU3939 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3846H ASN* 5.8 3.1 - - - +
3932H TYR* 3.5 31.5 - - + +
3937H VAL* 4.3 0.8 + - - +
3938H ILE* 1.3 83.0 - - - +
3940H GLU* 1.3 66.2 + - - +
3941H GLN* 4.3 4.9 - - + +
3942H GLY* 3.4 7.9 + - - +
3943H LYS* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3940 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938H ILE 3.7 1.6 + - - -
3939H GLU* 1.3 70.8 - - - +
3941H GLN* 1.3 70.0 + - + +
3943H LYS* 3.3 15.9 + - - +
3944H ARG* 3.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3941 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842H PHE* 4.5 1.8 - - + -
3846H ASN* 3.9 27.1 - - - +
3939H GLU* 3.3 4.1 - - + +
3940H GLU* 1.3 80.4 - - + +
3942H GLY* 1.3 62.4 + - - +
3944H ARG* 3.4 38.1 + - - +
3945H ASN* 3.1 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3942 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842H PHE* 3.8 24.1 - - - -
3928H PHE* 3.5 21.1 - - - -
3932H TYR* 4.6 5.8 - - - -
3938H ILE* 5.4 1.6 - - - -
3939H GLU* 3.4 9.8 + - - +
3940H GLU 3.3 0.4 - - - -
3941H GLN* 1.3 76.9 - - - +
3943H LYS* 1.3 59.0 + - - +
3945H ASN* 3.6 1.3 + - - +
3946H PHE* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3943 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938H ILE* 4.9 5.3 - - + +
3939H GLU 3.3 12.2 + - - +
3940H GLU* 3.6 12.3 - - - +
3941H GLN 3.2 1.0 - - - -
3942H GLY* 1.3 78.3 - - - +
3944H ARG* 1.3 57.8 + - - +
3946H PHE* 4.0 1.7 - - - +
3947H SER* 3.1 28.1 + - - -
4004H GLN* 6.5 0.9 - - + -
4007H LEU* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3944 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3867H GLU* 4.9 18.0 - - - +
3869H VAL* 5.1 4.2 - - - +
3940H GLU 3.5 8.0 + - - +
3941H GLN* 3.4 29.2 + - - +
3942H GLY 3.3 0.6 - - - -
3943H LYS* 1.3 77.4 - - - +
3945H ASN* 1.3 91.9 + - - +
3947H SER* 3.4 6.6 + - - -
3948H LYS* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3945 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842H PHE* 3.2 21.4 - - + -
3867H GLU* 6.1 1.0 - - - +
3869H VAL* 3.4 43.0 - - + +
3870H MET* 4.8 9.8 - - + +
3928H PHE* 5.8 2.7 - - + -
3941H GLN* 3.1 18.2 + - - +
3942H GLY* 4.1 4.7 - - - +
3943H LYS 3.4 0.2 - - - -
3944H ARG* 1.3 103.0 + - - +
3946H PHE* 1.3 57.2 + - - +
3948H LYS* 3.5 6.8 + - - +
3949H ALA* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3946 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925H ILE* 3.7 30.5 - - + -
3928H PHE* 3.9 29.6 - + + -
3942H GLY 3.1 18.1 + - - +
3943H LYS* 4.0 5.2 - - - +
3944H ARG 3.3 0.2 - - - -
3945H ASN* 1.3 75.7 - - - +
3947H SER* 1.3 62.9 + - - +
3949H ALA* 3.3 8.8 + - + +
3950H MET* 2.8 40.5 + - + +
3991H PHE* 5.4 4.0 - + - -
3994H MET* 3.5 26.9 - - + -
4007H LEU* 4.0 25.4 - - + -
4011H LEU* 3.5 28.0 - - + -
4014H LEU* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER3947 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3943H LYS 3.1 18.9 + - - -
3944H ARG* 3.7 6.5 - - - -
3945H ASN 3.4 0.4 - - - -
3946H PHE* 1.3 79.7 - - - +
3948H LYS* 1.3 58.6 + - - +
3950H MET* 3.4 7.9 + - - +
3951H SER* 3.0 25.8 + - - -
4007H LEU* 6.1 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3948 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870H MET* 4.8 13.5 - - + -
3873H ASP* 5.6 10.1 - - + -
3944H ARG* 3.2 13.5 + - + +
3945H ASN* 3.8 11.0 - - - +
3947H SER* 1.3 77.2 - - - +
3949H ALA* 1.3 60.9 + - - +
3951H SER* 3.3 16.6 + - - -
3952H VAL* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3949 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837H LEU* 5.3 9.0 - - + -
3870H MET* 4.7 17.6 - - + +
3921H LEU* 5.4 5.9 - - + +
3925H ILE* 5.1 15.3 - - + +
3945H ASN 3.1 17.9 + - - +
3946H PHE* 3.3 11.2 + - + +
3948H LYS* 1.3 74.0 - - - +
3950H MET* 1.3 60.5 + - - +
3952H VAL* 3.3 10.7 + - - +
3953H ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3950 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925H ILE* 6.3 0.7 - - - -
3946H PHE* 2.8 32.0 + - + +
3947H SER* 3.6 9.9 - - - +
3948H LYS 3.2 0.4 - - - -
3949H ALA* 1.3 74.8 - - - +
3951H SER* 1.3 58.3 + - - +
3953H ALA* 3.3 7.7 + - - +
3954H LYS* 2.9 29.5 + - - +
4010H GLU* 5.2 15.5 - - + +
4011H LEU* 5.9 2.0 - - - -
4014H LEU* 5.2 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3951 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3947H SER* 3.0 15.5 + - - -
3948H LYS* 3.3 10.0 + - - -
3949H ALA 3.3 0.4 - - - -
3950H MET* 1.3 79.5 - - - +
3952H VAL* 1.3 62.3 + - - +
3954H LYS* 3.4 9.2 + - - +
3955H GLN* 3.3 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3952 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870H MET* 4.9 13.7 - - + -
3872H ASP 5.9 1.3 - - - +
3873H ASP* 6.0 5.6 - - - -
3876H THR* 3.7 30.1 - - + +
3877H GLN* 5.6 9.0 - - + +
3880H PHE* 5.3 3.7 - - + -
3917H TYR* 3.5 27.8 - - + +
3921H LEU* 4.9 5.2 - - + -
3948H LYS 3.3 16.4 - - - +
3949H ALA* 3.3 10.3 + - - +
3950H MET 3.3 0.4 - - - -
3951H SER* 1.3 77.1 - - - +
3953H ALA* 1.3 63.4 + - - +
3954H LYS 3.4 0.5 + - - -
3955H GLN* 3.5 4.7 + - - +
3956H VAL* 3.3 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3953 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3921H LEU* 4.1 16.7 - - + +
3925H ILE* 4.4 12.6 - - + -
3949H ALA 2.9 16.8 + - - +
3950H MET* 3.3 7.2 + - - +
3952H VAL* 1.3 76.5 - - - +
3954H LYS* 1.3 58.5 + - - +
3956H VAL* 3.3 12.0 - - + +
3957H PHE* 3.1 31.6 - - + -
3987H PHE* 5.8 2.0 - - + -
4014H LEU* 3.4 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3954 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3950H MET 2.9 16.9 + - - +
3951H SER* 3.7 10.3 - - - +
3952H VAL 3.2 0.4 - - - -
3953H ALA* 1.3 78.5 - - - +
3955H GLN* 1.3 72.0 + - + +
3957H PHE* 3.6 5.3 + - - +
3958H ASN* 3.0 36.1 + - - +
4013H ASP* 5.2 14.9 - - + +
4014H LEU* 4.2 11.7 - - + -
4016H LYS* 5.6 4.5 - - - +
4017H ASP* 3.5 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3955 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3876H THR 6.2 0.2 - - - +
3877H GLN* 5.0 18.8 - - + +
3880H PHE* 4.6 14.5 - - + +
3881H ARG* 3.6 37.5 + - - +
3884H GLN* 5.4 1.6 - - - +
3951H SER 3.3 16.1 + - - +
3952H VAL* 3.5 3.5 + - - +
3954H LYS* 1.3 86.1 - - + +
3956H VAL* 1.3 63.3 + - - +
3957H PHE 3.4 0.2 - - - -
3958H ASN* 2.8 41.3 + - - +
3959H SER* 3.5 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3956 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880H PHE* 4.4 21.3 - - + +
3914H THR* 5.2 2.2 - - + +
3917H TYR* 4.3 16.2 - - + -
3918H LEU* 3.8 35.9 - - + -
3921H LEU* 4.3 9.4 - - + -
3952H VAL 3.3 15.0 + - - +
3953H ALA* 3.3 22.4 - - - +
3955H GLN* 1.3 75.6 - - - +
3957H PHE* 1.3 69.8 + - + +
3959H SER* 2.3 37.3 + - - +
3960H LEU* 3.1 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3957 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918H LEU* 3.9 17.3 - - + -
3921H LEU* 6.3 0.4 - - + -
3953H ALA* 3.1 25.8 - - + +
3954H LYS 3.6 7.5 + - - +
3956H VAL* 1.3 86.9 - - + +
3958H ASN* 1.3 62.3 + - - +
3959H SER 3.1 0.7 + - - -
3960H LEU* 3.6 12.6 + - + +
3961H THR* 3.3 22.7 + - - +
3983H ALA* 5.7 2.0 - - + -
3984H VAL* 4.6 13.2 - - + -
3987H PHE* 3.6 39.9 - + - -
4014H LEU* 3.9 17.3 - - + -
4017H ASP* 4.3 19.9 - - + +
4018H MET* 3.7 31.6 - - + -
4021H MET* 5.3 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3958 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3881H ARG* 5.3 4.1 - - - +
3884H GLN* 4.3 6.2 - - + +
3954H LYS* 3.0 28.2 + - - +
3955H GLN* 2.8 37.5 + - - +
3956H VAL 3.1 0.6 - - - -
3957H PHE* 1.3 77.6 - - - +
3959H SER* 1.3 57.0 + - - +
3961H THR* 3.3 13.7 - - + +
3962H GLU* 3.2 26.9 - - - +
4017H ASP* 4.1 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3959 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880H PHE* 4.5 16.9 - - - -
3883H LEU* 5.8 0.2 - - - -
3884H GLN* 4.1 19.1 - - - -
3914H THR* 4.7 5.5 - - - +
3955H GLN 3.5 7.5 + - - -
3956H VAL* 2.3 33.9 + - - +
3958H ASN* 1.3 78.9 - - - +
3960H LEU* 1.3 67.9 + - - +
3961H THR 3.3 0.4 - - - -
3962H GLU* 3.5 2.4 + - - +
3963H TYR* 3.2 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3960 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914H THR* 5.0 8.5 - - + -
3915H VAL* 3.7 30.1 - - + -
3918H LEU* 4.1 27.6 - - + -
3956H VAL* 3.1 28.7 - - + +
3957H PHE* 3.6 19.3 + - + +
3959H SER* 1.3 85.7 + - - +
3961H THR* 1.3 62.8 + - - +
3963H TYR* 3.3 21.0 + - + +
3964H ILE* 3.5 12.8 + - - +
3975H LEU* 4.1 27.4 - - + +
3980H LEU* 4.9 6.5 - - + -
4021H MET* 5.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR3961 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957H PHE 3.3 19.1 + - - +
3958H ASN* 3.3 19.7 - - + +
3960H LEU* 1.3 78.5 - - - +
3962H GLU* 1.3 64.5 + - + +
3964H ILE* 3.1 4.9 + - - +
3965H GLN* 2.8 48.8 + - - +
4017H ASP 5.5 2.9 - - - +
4020H VAL* 4.9 9.4 + - + +
4021H MET* 4.7 16.4 - - - +
4024H SER* 3.5 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3962 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884H GLN* 4.0 26.9 - - + +
3887H CYS* 3.2 34.5 - - + +
3888H GLU* 3.9 9.8 - - - +
3890H HIS* 4.0 8.9 + - - -
3895H GLN* 6.0 0.7 - - - +
3958H ASN 3.2 20.0 - - - +
3959H SER* 3.5 7.3 + - - +
3960H LEU 3.3 0.4 - - - -
3961H THR* 1.3 80.4 - - + +
3963H TYR* 1.3 64.1 + - + +
3964H ILE 3.5 0.3 + - - -
3965H GLN* 3.6 31.0 + - - +
4999H THR* 4.6 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3963 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3883H LEU* 3.4 48.1 - - - +
3884H GLN* 5.0 2.7 - - - -
3887H CYS* 5.1 12.8 - - + -
3895H GLN* 4.8 10.1 - - + +
3898H LEU* 4.2 24.3 - - + +
3910H ILE* 5.5 1.7 - - + +
3911H ILE* 3.7 24.7 - - + -
3914H THR* 4.3 21.4 + - + +
3959H SER* 3.2 31.3 + - - -
3960H LEU* 3.3 12.5 + - + +
3961H THR 3.2 0.6 - - - -
3962H GLU* 1.3 80.0 - - + +
3964H ILE* 1.3 57.9 + - + +
3965H GLN 3.6 0.2 - - - -
3968H CYS* 3.7 5.0 - - - +
3971H ASN* 3.1 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3964 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960H LEU 3.5 9.7 + - - +
3961H THR* 3.1 8.4 + - - +
3963H TYR* 1.3 77.5 - - + +
3965H GLN* 1.3 67.2 + - - +
3966H GLY 3.6 6.5 - - - +
3968H CYS* 3.6 17.8 - - - -
3971H ASN* 4.6 7.9 - - + +
3972H GLN* 5.2 6.5 - - + -
3975H LEU* 5.5 8.5 - - + -
4021H MET 6.0 0.7 - - - +
4024H SER* 3.2 26.7 - - - +
4025H LEU* 5.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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