Contacts of the helix formed by residues 3789 - 3797 (chain J) in PDB entry 2ZLE
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 SER3789 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3740J GLU* 3.1 22.9 - - - -
3756J GLY 3.9 4.4 - - - -
3757J ALA* 4.2 4.9 - - - -
3787J ILE* 3.5 3.0 + - - +
3788J SER* 1.3 83.8 + - - +
3790J PHE* 1.3 69.0 + - - +
3791J ALA* 3.5 9.9 - - - +
3792J ALA* 2.9 32.3 + - - +
3793J LEU* 3.1 10.2 + - - +
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Residues in contact with PHE3790 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3736J ILE* 3.0 39.9 - - + -
3737J MET* 4.4 3.4 - - - -
3738J GLY 3.3 33.2 - - - -
3739J THR* 3.7 18.8 - - + +
3740J GLU* 2.5 17.1 + - + +
3757J ALA* 3.7 25.8 - - + +
3758J PHE 4.7 0.9 - - - -
3789J SER* 1.3 68.3 - - - +
3791J ALA* 1.3 54.5 + - - +
3793J LEU* 2.8 11.4 + - + +
3794J ARG* 2.7 70.3 + - + +
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Residues in contact with ALA3791 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3740J GLU* 3.6 2.5 + - - +
3789J SER* 3.5 12.8 - - - +
3790J PHE* 1.3 81.4 - - - +
3792J ALA* 1.3 64.6 + - - +
3794J ARG* 3.1 9.4 + - - +
3795J ALA* 3.0 24.6 + - - +
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Residues in contact with ALA3792 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3786J PRO 5.4 1.6 - - - +
3787J ILE* 4.8 8.3 - - + -
3788J SER* 4.5 11.9 - - - +
3789J SER* 2.9 28.3 + - - +
3791J ALA* 1.3 76.4 - - - +
3793J LEU* 1.3 57.7 + - - +
3795J ALA* 3.5 5.5 + - - +
3796J GLN* 3.0 37.3 + - - +
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Residues in contact with LEU3793 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3734J LEU* 4.4 15.5 - - + -
3736J ILE* 5.4 7.0 - - + -
3757J ALA* 3.8 22.9 - - + -
3779J ILE* 4.2 26.7 - - + -
3782J LEU* 4.5 9.2 - - + -
3787J ILE* 3.8 21.3 - - + +
3789J SER 3.1 6.0 + - - +
3790J PHE* 2.8 23.2 + - + +
3792J ALA* 1.3 71.5 - - - +
3794J ARG* 1.3 66.3 + - - +
3795J ALA 3.1 1.8 - - - -
3796J GLN* 3.1 5.5 + - - +
3797J VAL* 2.9 52.7 + - + +
3808J LEU* 5.1 0.7 - - + -
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Residues in contact with ARG3794 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3610J ARG* 2.6 78.7 + - - +
3790J PHE* 2.7 53.2 + - + +
3791J ALA* 3.7 8.0 - - - +
3793J LEU* 1.3 71.5 - - - +
3795J ALA* 1.3 59.9 + - - +
3797J VAL* 3.0 18.5 - - + +
3798J GLY 3.5 3.1 + - - -
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Residues in contact with ALA3795 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3610J ARG* 5.0 4.5 - - - +
3665J GLU* 4.3 21.9 - - - +
3791J ALA 3.0 16.5 + - - +
3792J ALA* 3.7 5.2 - - - +
3794J ARG* 1.3 77.9 - - - +
3796J GLN* 1.3 63.7 + - + +
3798J GLY* 3.2 13.3 + - - -
3799J THR* 3.6 11.1 + - - -
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Residues in contact with GLN3796 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3782J LEU* 3.0 43.8 + - + +
3785J LYS* 4.7 19.0 + - - +
3786J PRO 4.3 6.2 - - - +
3787J ILE* 3.6 17.5 - - - +
3792J ALA* 3.0 23.3 + - + +
3793J LEU* 3.1 5.1 + - - +
3795J ALA* 1.3 73.8 - - + +
3797J VAL* 1.3 61.9 + - - +
3798J GLY 3.0 5.2 - - - -
3799J THR* 3.1 13.9 + - - -
3800J MET* 2.9 28.8 - - + +
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Residues in contact with VAL3797 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3610J ARG* 4.4 5.8 - - - +
3731J ARG* 5.9 0.2 - - - +
3732J GLY 3.5 22.8 - - - +
3733J GLU* 5.9 1.1 - - - -
3734J LEU* 4.3 23.1 - - + +
3782J LEU* 4.3 2.7 - - + -
3793J LEU* 2.9 41.2 + - + +
3794J ARG* 3.0 22.9 - - + +
3796J GLN* 1.3 76.5 - - - +
3798J GLY* 1.3 57.6 + - - +
3799J THR 3.2 2.3 + - - -
3800J MET* 3.7 22.0 + - - +
3806J LEU* 4.0 23.3 - - + -
3821J LEU* 4.7 2.9 - - + +
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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