Contacts of the helix formed by residues 3715 - 3731 (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 ASP3715 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119H ARG* 5.9 1.1 - - - +
3701H PHE* 6.0 0.7 - - + -
3713H ASP* 3.7 7.9 - - + +
3714H GLU* 1.3 82.0 - - - +
3716H TYR* 1.3 62.0 + - - +
3717H LEU* 3.1 16.8 - - + -
3718H TYR* 2.9 36.0 + - + +
3719H MET* 3.6 5.7 + - - +
3788H MET* 4.0 11.9 - - - +
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Residues in contact with TYR3716 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123H SER* 4.8 14.0 - - - -
2126H HIS* 6.2 4.5 - + - -
2127H ARG* 5.9 4.2 - - + -
3714H GLU* 3.5 15.9 - - + +
3715H ASP* 1.3 77.0 - - - +
3717H LEU* 1.3 78.2 + - + +
3719H MET* 3.7 6.8 + - - +
3720H ALA* 3.3 22.8 + - + +
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Residues in contact with LEU3717 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119H ARG* 3.5 57.7 - - + +
2122H PHE* 5.6 4.5 - - + -
2123H SER* 5.3 13.2 - - - +
2126H HIS* 6.2 0.9 - - - -
3700H HIS* 4.5 10.1 - - + +
3701H PHE* 4.2 15.8 - - + -
3715H ASP* 3.1 20.7 - - + -
3716H TYR* 1.3 96.1 - - + +
3718H TYR* 1.3 72.7 + - - +
3720H ALA* 3.5 6.0 + - - +
3721H TYR* 3.4 34.8 + - + +
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Residues in contact with TYR3718 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3701H PHE* 3.5 53.5 - + + +
3715H ASP* 2.9 20.6 + - + +
3717H LEU* 1.3 83.3 - - - +
3719H MET* 1.3 59.2 + - - +
3720H ALA 3.2 0.2 + - - -
3721H TYR* 3.9 1.3 - - + +
3722H ALA* 3.0 33.7 + - + +
3773H MET* 4.3 14.4 + - - +
3774H VAL* 5.3 3.8 - - - +
3777H MET* 3.8 26.4 - - + +
3788H MET* 3.7 25.1 - - + -
3791H SER* 6.5 0.4 - - - -
3792H THR* 3.4 33.8 - - + +
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Residues in contact with MET3719 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3715H ASP 3.6 6.8 + - - +
3716H TYR* 3.7 7.8 + - - +
3717H LEU 3.5 0.2 - - - -
3718H TYR* 1.3 77.7 - - - +
3720H ALA* 1.3 63.6 + - - +
3722H ALA* 3.8 9.0 - - - +
3723H ASP* 3.6 18.9 + - - +
3787H ALA 6.1 0.4 - - - -
3788H MET* 5.7 7.4 - - + +
3791H SER* 4.0 21.2 - - - +
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Residues in contact with ALA3720 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126H HIS* 3.4 36.7 - - + +
3716H TYR* 3.3 18.7 + - + +
3717H LEU* 3.7 9.4 - - - +
3718H TYR 3.1 0.6 - - - -
3719H MET* 1.3 80.9 - - - +
3721H TYR* 1.3 62.7 + - + +
3722H ALA 3.4 0.2 + - - -
3723H ASP* 3.7 2.6 + - - +
3724H ILE* 3.3 26.5 + - - +
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Residues in contact with TYR3721 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122H PHE* 2.3 50.9 + + + +
2123H SER* 4.9 1.3 - - - -
2125H LEU* 3.3 20.5 - - + +
2126H HIS* 3.3 30.7 + + + -
3673H LEU* 5.4 2.7 - - + -
3697H LEU* 4.3 24.0 - - + -
3701H PHE* 5.2 15.3 - + + -
3717H LEU* 3.4 24.9 + - + +
3718H TYR* 4.4 2.5 - - + +
3720H ALA* 1.3 79.5 - - + +
3722H ALA* 1.3 58.8 - - - +
3723H ASP 3.4 0.2 - - - -
3724H ILE* 3.8 15.9 - - + +
3725H MET* 2.9 42.8 + - + +
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Residues in contact with ALA3722 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3718H TYR* 3.0 29.0 + - + +
3719H MET* 3.9 10.3 - - - +
3720H ALA 3.2 0.4 - - - -
3721H TYR* 1.3 77.9 - - - +
3723H ASP* 1.3 57.9 + - - +
3725H MET* 6.1 0.2 - - - -
3726H ALA* 3.0 31.9 + - - +
3791H SER* 4.3 26.7 - - - +
3792H THR* 5.8 1.6 - - + -
3795H LEU* 3.5 16.1 - - + +
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Residues in contact with ASP3723 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3719H MET 3.6 13.0 + - - +
3720H ALA 4.3 3.4 - - - +
3721H TYR 3.4 0.2 - - - -
3722H ALA* 1.3 79.2 - - - +
3724H ILE* 1.3 62.7 + - + +
3726H ALA* 4.4 3.5 - - - +
3727H LYS* 3.2 26.7 + - - +
3794H LYS* 6.2 3.4 - - - -
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Residues in contact with ILE3724 (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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2126H HIS* 3.7 25.6 - - + +
3665H PHE* 3.6 28.5 - - + -
3666H GLU* 3.2 41.7 - - + +
3669H MET* 4.4 14.6 - - + -
3670H ILE* 4.8 7.4 - - + -
3720H ALA 3.3 19.7 - - - +
3721H TYR* 3.5 15.6 + - + +
3722H ALA 3.3 0.6 - - - -
3723H ASP* 1.3 80.2 - - + +
3725H MET* 1.3 59.8 + - - +
3728H SER* 3.0 16.3 + - - -
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Residues in contact with MET3725 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670H ILE* 4.4 18.4 - - + +
3694H LEU* 5.8 6.7 - - + -
3697H LEU* 5.1 20.9 - - + -
3698H VAL* 6.1 0.9 - - - +
3701H PHE* 6.3 2.5 - - + -
3721H TYR* 2.9 28.0 + - + +
3724H ILE* 1.3 78.4 - - - +
3726H ALA* 1.3 59.8 + - - +
3728H SER* 2.7 18.6 + - - +
3729H CYS* 3.5 12.1 + - - +
3765H LEU* 3.6 41.5 - - + +
3770H ALA* 5.2 7.0 - - - -
3795H LEU* 3.8 20.2 - - + -
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Residues in contact with ALA3726 (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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3722H ALA 3.0 19.1 + - - +
3723H ASP* 4.4 3.8 - - - +
3725H MET* 1.3 76.5 - - - +
3727H LYS* 1.3 63.2 + - - +
3729H CYS* 3.4 1.3 + - - -
3730H HIS* 3.3 12.8 + - - +
3765H LEU* 6.0 0.2 - - - -
3794H LYS* 4.2 14.8 - - + +
3795H LEU* 3.8 32.3 - - + +
3798H SER* 3.2 25.9 + - - -
3799H ILE* 6.5 0.2 - - - -
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Residues in contact with LYS3727 (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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3666H GLU* 3.9 16.6 - - + -
3723H ASP 3.2 20.6 + - - +
3725H MET 3.4 0.2 - - - -
3726H ALA* 1.3 77.6 - - - +
3728H SER* 1.3 58.4 + - - +
3730H HIS* 5.0 2.2 - - - -
3731H LEU* 2.9 35.5 + - + +
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Residues in contact with SER3728 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3666H GLU* 3.2 30.7 - - - +
3667H ASP* 4.5 8.7 - - - +
3670H ILE* 3.5 16.0 - - - +
3724H ILE 3.0 10.0 + - - -
3725H MET* 2.7 26.7 + - - +
3727H LYS* 1.3 79.3 - - - +
3729H CYS* 1.3 59.5 + - - +
3731H LEU 3.8 12.4 - - - -
3761H GLN* 3.5 16.3 - - - +
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Residues in contact with CYS3729 (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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3725H MET 4.0 8.5 - - - +
3726H ALA* 3.4 3.2 + - - +
3727H LYS 3.3 0.6 - - - -
3728H SER* 1.3 82.5 + - - +
3730H HIS* 1.3 61.4 + - - +
3731H LEU 4.9 0.2 - - - +
3758H LEU* 4.6 13.4 - - - +
3761H GLN* 3.4 26.7 - - - +
3762H GLN* 4.0 25.8 - - - -
3765H LEU* 4.7 4.3 - - + -
3798H SER* 3.2 35.7 - - - +
3799H ILE* 3.9 19.7 - - + -
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Residues in contact with HIS3730 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3726H ALA 3.3 13.0 + - - +
3727H LYS* 4.4 2.5 - - - +
3729H CYS* 1.3 83.5 - - - +
3731H LEU* 1.3 61.0 + - + +
3758H LEU* 5.2 11.8 - - - +
3798H SER* 3.8 13.0 + - - +
3801H ASN* 5.0 14.6 - - - +
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Residues in contact with LEU3731 (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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3667H ASP* 6.0 3.8 - - - -
3727H LYS* 2.9 23.2 + - + +
3728H SER* 3.8 13.9 - - - +
3729H CYS 4.9 0.7 - - - +
3730H HIS* 1.3 81.2 - - + +
3761H GLN* 5.2 5.7 - - - +
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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