Contacts of the helix formed by residues 838 - 847 (chain A) in PDB entry 6MZL
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 SER 838 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831A LYS* 5.3 1.1 - - - +
836A SER 4.1 1.6 + - - -
837A HIS* 1.3 75.6 - - - +
839A GLU* 1.3 62.7 + - - +
840A SER* 3.7 8.9 + - - -
841A SER* 2.7 42.7 + - - -
842A ILE* 3.4 9.3 + - - +
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Residues in contact with GLU 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A MET* 3.8 39.1 - - + +
831A LYS* 5.3 8.1 - - + +
837A HIS 4.0 0.6 + - - -
838A SER* 1.3 72.2 - - - +
840A SER* 1.3 58.4 + - - +
842A ILE* 3.2 11.2 + - - +
843A ARG* 2.8 52.6 + - - +
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Residues in contact with SER 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A SER* 3.2 9.0 - - - -
839A GLU* 1.3 79.1 - - - +
841A SER* 1.3 61.1 + - - +
843A ARG* 3.2 32.4 + - - +
844A LYS* 3.2 33.9 + - - +
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Residues in contact with SER 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A LEU* 4.3 3.6 - - - +
837A HIS* 3.6 21.4 - - - +
838A SER* 2.7 37.6 + - - -
840A SER* 1.3 77.9 - - - +
842A ILE* 1.3 60.8 + - - +
844A LYS* 3.5 26.8 + - - +
845A ARG* 3.8 12.8 + - - +
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Residues in contact with ILE 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A LEU* 4.7 16.2 - - + -
811A ILE* 4.8 0.9 - - + -
827A MET* 3.7 28.9 - - - -
830A ILE* 3.7 33.4 - - + -
831A LYS* 4.5 20.0 - - + -
834A PHE* 4.9 1.8 - - + +
837A HIS* 4.2 15.5 - - + -
838A SER 3.4 17.0 - - - +
839A GLU* 3.2 11.3 + - - +
841A SER* 1.3 77.0 - - - +
843A ARG* 1.3 65.4 + - - +
844A LYS 3.2 0.2 - - - -
845A ARG* 3.3 3.9 + - - +
846A LEU* 3.3 36.2 + - + +
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Residues in contact with ARG 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A MET* 4.5 4.9 - - + +
839A GLU* 2.8 47.2 + - - +
840A SER* 3.2 43.1 + - - +
842A ILE* 1.3 78.1 - - - +
844A LYS* 1.3 59.4 + - - +
846A LEU* 4.2 4.6 - - - +
847A LYS* 3.4 26.4 + - - +
862A TRP* 4.5 22.6 - - + -
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Residues in contact with LYS 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A SER* 3.2 24.6 + - - +
841A SER* 3.6 17.8 - - - +
842A ILE 3.2 0.8 - - - -
843A ARG* 1.3 78.3 - - - +
845A ARG* 1.3 78.4 + - - +
847A LYS* 3.3 27.1 - - + +
848A LEU* 4.7 5.5 + - - +
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Residues in contact with ARG 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A ARG* 3.1 65.6 + - - +
807A LEU* 3.7 26.0 - - + -
808A GLN* 3.3 38.0 + - - +
811A ILE* 3.8 19.0 - - + +
841A SER 3.8 7.2 + - - +
842A ILE 3.3 5.2 + - - +
844A LYS* 1.3 92.2 + - - +
846A LEU* 1.3 61.7 + - - +
847A LYS 3.6 0.4 - - - -
848A LEU* 4.7 12.2 + - - +
849A CYS* 3.8 13.9 + - - -
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Residues in contact with LEU 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A ILE* 3.8 36.1 - - + -
815A PHE* 4.6 3.4 - - + -
825A ILE* 4.1 14.6 - - + -
827A MET* 3.9 4.9 - - + -
830A ILE* 4.0 7.4 - - + -
842A ILE* 3.3 34.8 + - + +
843A ARG 3.7 0.6 + - - +
844A LYS 3.3 0.4 - - - -
845A ARG* 1.3 77.9 - - - +
847A LYS* 1.3 58.7 + - - +
848A LEU 3.3 3.1 - - - -
849A CYS* 4.1 8.3 - - - -
850A ALA* 3.1 33.0 + - + +
862A TRP* 3.5 52.1 - - + +
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Residues in contact with LYS 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A ARG 3.4 13.8 + - - +
844A LYS* 3.3 25.8 - - + +
846A LEU* 1.3 78.5 - - - +
848A LEU* 1.3 84.3 + - + +
850A ALA 3.8 4.9 - - - +
862A TRP* 4.7 5.2 - - + -
865A LYS* 3.5 16.5 + - - -
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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