Contacts of the helix formed by residues 742 - 751 (chain E) in PDB entry 1M2Z
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 ASN 742 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593D MET* 3.9 5.4 - - - +
597D GLN* 2.8 43.9 + - - +
755D GLU* 3.1 34.0 + - - +
756D ILE* 3.8 6.3 - - - +
759D ASN* 3.1 17.1 + - - +
740E LYS* 3.7 0.8 - - - +
741E GLU* 1.3 88.4 + - - +
743E ALA* 1.3 62.5 + - - +
744E LEU 3.5 1.3 - - - -
745E LEU* 4.2 14.8 - - + +
746E ARG* 3.6 27.8 + - - -
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Residues in contact with ALA 743 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755D GLU* 3.6 9.5 + - - +
740E LYS* 4.9 23.3 - - + +
741E GLU 3.8 0.8 - - - +
742E ASN* 1.3 73.3 - - - +
744E LEU* 1.3 64.9 + - - +
746E ARG* 3.5 11.5 + - - +
747E TYR* 3.3 19.9 + - - +
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Residues in contact with LEU 744 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ILE* 6.0 1.3 - - + -
751D GLU* 3.8 32.5 - - + +
752D MET* 4.0 21.8 - - + +
755D GLU* 4.5 16.5 + - + +
742E ASN* 3.5 0.4 - - - +
743E ALA* 1.3 76.4 - - - +
745E LEU* 1.3 66.2 + - - +
747E TYR* 3.2 21.0 + - + +
748E LEU* 3.2 37.3 + - + +
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Residues in contact with LEU 745 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575D VAL* 4.5 9.0 - - + -
593D MET* 3.9 10.5 - - + +
596D LEU* 4.1 20.6 - - + -
597D GLN* 3.8 38.1 - - + +
752D MET* 4.1 22.7 - - + -
755D GLU* 5.4 1.3 - - + +
756D ILE* 4.6 13.7 - - + -
742E ASN* 4.0 19.3 + - + +
743E ALA 3.4 0.6 - - - -
744E LEU* 1.3 79.3 - - - +
746E ARG* 1.3 63.4 + - - +
748E LEU* 3.2 13.3 + - - +
749E LEU* 3.2 36.0 + - + +
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Residues in contact with ARG 746 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589D LEU* 4.0 10.2 - - + +
590D ASP* 4.4 15.8 + - - -
593D MET* 3.3 42.0 - - + +
742E ASN* 3.6 17.6 + - - +
743E ALA* 3.5 11.8 + - - +
744E LEU 3.3 0.4 - - - -
745E LEU* 1.3 77.8 - - - +
747E TYR* 1.3 62.6 + - - +
749E LEU* 3.0 11.8 + - - +
750E ASP* 2.7 36.3 + - - +
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Residues in contact with TYR 747 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743E ALA 3.3 9.1 + - - +
744E LEU* 3.2 18.8 + - + +
746E ARG* 1.3 79.8 - - - +
748E LEU* 1.3 84.7 + - + +
750E ASP* 3.2 16.7 + - + +
751E LYS* 3.7 43.0 + - + +
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Residues in contact with LEU 748 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ILE* 4.3 28.7 - - + -
575D VAL* 4.0 25.0 - - + +
576D LYS* 6.0 0.9 - - - +
579D LYS* 2.9 24.8 + - - +
752D MET* 4.0 17.7 - - + -
744E LEU* 3.2 33.0 + - + +
745E LEU* 3.2 7.6 + - - +
747E TYR* 1.3 97.4 - - + +
749E LEU* 1.3 56.5 - - - +
750E ASP 3.6 0.2 + - - -
751E LYS* 4.0 12.8 - - + +
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Residues in contact with LEU 749 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575D VAL* 3.6 20.9 - - + -
579D LYS* 3.5 23.1 - - + -
584D PHE* 4.6 2.2 - - + -
585D ARG* 2.9 28.8 + - - -
589D LEU* 4.5 10.3 - - + +
592D GLN* 3.9 24.2 - - + +
593D MET* 3.5 34.8 - - + +
596D LEU* 3.9 12.1 - - + -
745E LEU* 3.2 30.6 + - + +
746E ARG* 3.0 9.9 + - - +
748E LEU* 1.3 77.1 - - - +
750E ASP* 1.3 64.6 + - - +
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Residues in contact with ASP 750 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D ARG* 4.4 10.9 + - - +
589D LEU* 3.3 32.8 - - - +
746E ARG* 2.7 29.4 - - - +
747E TYR* 3.2 9.9 + - + +
749E LEU* 1.3 77.4 - - - +
751E LYS* 1.3 72.3 + - - +
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Residues in contact with LYS 751 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D LYS* 3.3 8.0 + - - +
585D ARG* 5.5 1.2 - - - -
747E TYR* 3.7 51.3 + - + +
748E LEU* 4.0 17.3 - - + +
750E ASP* 1.3 87.0 - - - +
752E ASP* 1.3 85.7 + - - +
754E THR* 6.5 0.7 - - - -
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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
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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