Contacts of the helix formed by residues 3748 - 3767 (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 PHE3748 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747H SER* 1.3 80.1 + - - +
3749H GLU* 1.3 60.0 + - - +
3751H LYS* 3.9 6.0 - - + +
3752H GLU* 3.0 36.3 + - + +
4714H TRP* 3.7 31.6 - - + +
4715H ASP* 4.4 8.7 - - + -
4716H LYS 5.3 0.9 - - - -
4717H PHE* 4.4 26.5 - + - -
4994H ILE* 5.6 17.7 - - + -
5009H TRP* 5.6 14.8 - + - -
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Residues in contact with GLU3749 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747H SER* 3.3 7.9 + - - +
3748H PHE* 1.3 83.2 - - - +
3750H GLU* 1.3 57.2 + - - +
3752H GLU* 3.6 3.7 + - - +
3753H MET* 3.1 28.9 + - - +
4714H TRP 5.3 2.6 + - - +
4716H LYS* 4.2 24.9 - - + -
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Residues in contact with GLU3750 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747H SER 3.5 22.8 + - - +
3748H PHE 3.3 0.2 - - - -
3749H GLU* 1.3 76.9 - - - +
3751H LYS* 1.3 64.9 + - - +
3753H MET* 3.8 4.7 - - - +
3754H GLU* 3.2 30.5 + - + +
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Residues in contact with LYS3751 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747H SER 3.0 19.0 + - - +
3748H PHE* 3.9 8.7 - - + +
3750H GLU* 1.3 78.5 - - - +
3752H GLU* 1.3 60.7 + - - +
3754H GLU* 3.5 4.7 + - - +
3755H LYS* 3.1 24.3 + - - +
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Residues in contact with GLU3752 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3748H PHE* 3.0 28.4 + - + +
3749H GLU* 4.2 4.5 - - - +
3751H LYS* 1.3 76.6 - - - +
3753H MET* 1.3 62.0 + - - +
3755H LYS* 3.6 6.5 + - - +
3756H GLN* 3.2 22.3 + - - +
4717H PHE* 4.4 25.4 - - + -
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Residues in contact with MET3753 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3749H GLU 3.1 19.5 + - - +
3750H GLU* 3.8 7.2 - - - +
3751H LYS 3.2 0.4 - - - -
3752H GLU* 1.3 78.2 - - - +
3754H GLU* 1.3 59.4 + - + +
3756H GLN* 3.3 6.1 + - - +
3757H ARG* 3.0 36.7 + - - +
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Residues in contact with GLU3754 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3750H GLU* 3.2 18.4 + - + +
3751H LYS* 4.1 4.5 - - - +
3753H MET* 1.3 76.9 - - + +
3755H LYS* 1.3 64.4 + - - +
3757H ARG* 3.4 38.0 + - - +
3758H LEU* 3.1 23.7 + - - +
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Residues in contact with LYS3755 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3751H LYS 3.1 18.4 + - - +
3752H GLU* 3.8 8.5 - - - +
3753H MET 3.3 0.2 - - - -
3754H GLU* 1.3 77.7 - - - +
3756H GLN* 1.3 61.4 + - - +
3758H LEU* 3.5 10.8 + - - +
3759H LEU* 3.2 19.4 + - - +
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Residues in contact with GLN3756 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3752H GLU 3.2 14.8 + - - +
3753H MET* 3.3 5.8 + - - +
3755H LYS* 1.3 77.8 - - - +
3757H ARG* 1.3 65.1 + - + +
3759H LEU* 3.0 18.5 + - - +
3760H TYR* 3.0 24.7 + - + +
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Residues in contact with ARG3757 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3753H MET* 3.0 24.5 + - - +
3754H GLU* 3.4 37.6 + - - +
3755H LYS 3.4 0.2 - - - -
3756H GLN* 1.3 75.5 - - + +
3758H LEU* 1.3 61.7 + - - +
3760H TYR* 3.4 7.2 + - - +
3761H GLN* 2.9 34.9 + - - +
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Residues in contact with LEU3758 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729H CYS* 4.6 12.0 - - - +
3730H HIS* 5.2 11.4 - - - +
3754H GLU 3.1 16.7 + - - +
3755H LYS* 3.7 8.7 - - - +
3756H GLN 3.2 0.2 - - - -
3757H ARG* 1.3 79.0 - - - +
3759H LEU* 1.3 65.9 + - + +
3761H GLN* 3.4 7.9 + - - +
3762H GLN* 3.1 24.1 + - + +
3798H SER 5.8 3.1 - - - +
3799H ILE 5.4 2.9 - - - +
3801H ASN* 4.7 16.8 - - + +
3802H GLY* 3.6 37.5 - - - +
3804H ASN* 5.6 3.4 - - - +
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Residues in contact with LEU3759 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3755H LYS 3.2 10.7 + - - +
3756H GLN* 3.0 26.7 + - - +
3758H LEU* 1.3 79.3 - - + +
3760H TYR* 1.3 60.9 + - - +
3762H GLN* 3.3 7.8 + - - +
3763H ALA* 2.7 30.7 + - - +
3804H ASN* 4.7 15.0 + - + +
3806H ASP* 5.7 0.3 - - - +
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Residues in contact with TYR3760 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3756H GLN* 3.0 15.2 + - + +
3757H ARG* 3.7 11.4 - - - +
3758H LEU 3.2 0.4 - - - -
3759H LEU* 1.3 74.8 - - - +
3761H GLN* 1.3 85.2 + - - +
3763H ALA* 3.3 9.5 + - + +
3764H ARG* 3.0 49.9 + - + +
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Residues in contact with GLN3761 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3728H SER 3.5 21.8 - - - +
3729H CYS* 3.4 33.8 - - - +
3731H LEU 5.2 5.3 - - - +
3757H ARG* 2.9 27.5 + - - +
3758H LEU* 3.8 5.3 - - - +
3760H TYR* 1.3 105.3 - - - +
3762H GLN* 1.3 61.0 + - - +
3764H ARG* 3.5 37.7 + - - +
3765H LEU* 4.0 6.8 + - - +
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Residues in contact with GLN3762 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729H CYS* 4.0 14.1 - - - -
3758H LEU* 3.1 19.2 + - + +
3759H LEU* 3.7 4.9 - - - +
3760H TYR 3.2 0.2 - - - -
3761H GLN* 1.3 76.1 - - - +
3763H ALA* 1.3 59.7 + - - +
3765H LEU* 3.3 5.4 + - - +
3766H HIS* 2.9 28.2 + - + +
3799H ILE* 3.9 33.5 - - + +
3804H ASN* 4.1 15.9 - - - +
3806H ASP* 5.7 0.4 - - - -
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Residues in contact with ALA3763 (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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3759H LEU 2.7 21.0 + - - +
3760H TYR* 3.3 12.5 + - + +
3762H GLN* 1.3 71.1 - - - +
3764H ARG* 1.3 65.3 + - - +
3766H HIS* 3.6 13.0 - - + -
3767H ASN* 3.1 25.1 + - - +
3806H ASP* 5.2 7.4 + - - +
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Residues in contact with ARG3764 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670H ILE* 3.6 27.9 - - - +
3671H ASP* 3.5 34.4 + - - +
3674H SER* 4.9 11.6 + - - +
3694H LEU* 4.4 16.5 - - + +
3760H TYR* 3.0 45.8 + - + +
3761H GLN* 3.5 32.4 - - - +
3762H GLN 3.2 0.4 - - - -
3763H ALA* 1.3 77.5 - - - +
3765H LEU* 1.3 64.3 + - + +
3767H ASN* 4.4 5.6 + - - +
3768H ARG* 4.5 8.5 + - - +
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Residues in contact with LEU3765 (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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3670H ILE* 5.5 3.4 - - + -
3694H LEU* 4.7 17.9 - - + -
3725H MET* 3.6 51.4 - - + +
3726H ALA* 6.0 0.2 - - - -
3729H CYS* 4.7 7.4 - - + -
3761H GLN 4.4 6.5 - - - +
3762H GLN 3.3 6.2 + - - +
3764H ARG* 1.3 83.0 - - + +
3766H HIS* 1.3 64.6 + - - +
3767H ASN 3.3 2.7 - - - -
3768H ARG* 3.3 21.0 + - + +
3770H ALA* 3.3 28.6 + - + +
3771H ALA 4.6 0.7 + - - -
3795H LEU* 5.1 5.2 - - + -
3799H ILE* 3.7 28.3 - - + -
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Residues in contact with HIS3766 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3762H GLN 2.9 20.0 + - - +
3763H ALA* 3.4 12.1 + - + -
3765H LEU* 1.3 74.6 - - - +
3767H ASN* 1.3 66.5 + - - +
3768H ARG 3.2 6.8 - - - +
3771H ALA* 5.4 7.7 - - - +
3799H ILE* 5.6 3.3 - - + +
3806H ASP* 3.1 55.2 + - + +
3807H VAL* 3.9 19.2 - - + +
3809H GLN* 5.0 4.2 + - - -
3810H LYS* 3.5 27.1 - - + +
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Residues in contact with ASN3767 (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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3695H HIS* 5.4 1.0 - - - -
3763H ALA 3.1 16.6 + - - +
3764H ARG 4.6 4.5 - - - +
3765H LEU 3.3 0.2 - - - -
3766H HIS* 1.3 82.6 - - - +
3768H ARG* 1.3 62.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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