Contacts of the helix formed by residues 827 - 834 (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 MET 827 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A ARG* 1.3 72.3 - - - +
828A GLU* 1.3 62.2 + - - +
830A ILE* 3.2 6.6 + - - +
831A LYS* 3.1 24.8 + - + +
839A GLU* 3.8 46.2 - - + +
842A ILE* 3.7 32.5 - - + -
843A ARG* 4.5 4.5 - - + -
846A LEU* 3.9 10.3 - - + -
860A ASN 4.2 5.2 + - - +
862A TRP* 3.4 46.0 - - + +
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Residues in contact with GLU 828 (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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826A ARG* 3.2 23.9 + - + +
827A MET* 1.3 80.1 - - - +
829A ASP* 1.3 60.6 + - - +
831A LYS* 3.9 5.4 - - + +
832A LYS* 3.0 33.2 + - + +
858A ASP 5.3 2.6 - - - +
859A SER* 4.7 11.1 + - - -
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Residues in contact with ASP 829 (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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810A PHE* 4.3 5.6 - - - -
814A LEU* 4.8 18.3 - - + +
825A ILE* 5.6 1.6 - - + +
826A ARG* 3.4 50.7 + - - +
827A MET 3.2 1.0 - - - -
828A GLU* 1.3 82.3 - - - +
830A ILE* 1.3 61.8 + - - +
832A LYS* 3.8 24.1 + - - +
833A ALA* 3.5 19.8 + - - +
861A TRP* 5.8 0.5 - - - -
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Residues in contact with ILE 830 (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* 3.9 20.2 - - + -
810A PHE* 4.4 9.0 - - + -
811A ILE* 3.8 22.4 - - + -
814A LEU* 3.8 21.3 - - + -
825A ILE* 3.9 25.1 - - + -
826A ARG 3.8 7.2 + - - +
827A MET* 3.2 7.9 + - - +
829A ASP* 1.3 74.4 - - - +
831A LYS* 1.3 53.9 + - - +
833A ALA* 3.2 3.5 + - - +
834A PHE* 2.8 38.5 + - + +
842A ILE* 3.7 27.6 - - + -
846A LEU* 4.0 17.3 - - + -
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Residues in contact with LYS 831 (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* 3.1 20.0 + - + +
828A GLU* 4.0 7.4 - - - +
830A ILE* 1.3 77.5 - - - +
832A LYS* 1.3 61.1 + - - +
834A PHE 3.2 23.4 - - - +
835A PRO* 3.1 39.1 + - - +
837A HIS 3.4 24.0 - - - +
838A SER* 5.3 0.7 - - - +
839A GLU* 5.3 9.2 - - + +
842A ILE* 4.5 12.3 - - + +
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Residues in contact with LYS 832 (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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828A GLU* 3.0 22.6 + - + +
829A ASP* 3.8 28.6 + - - +
830A ILE 3.3 0.2 - - - -
831A LYS* 1.3 77.4 - - - +
833A ALA* 1.3 60.0 + - - +
835A PRO* 4.1 8.0 - - - +
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Residues in contact with ALA 833 (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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605A THR* 2.9 33.1 + - + +
606A HIS* 3.3 13.5 - - - +
810A PHE* 3.7 36.8 - - + -
829A ASP 3.5 6.2 + - - +
830A ILE 3.2 4.5 + - - +
832A LYS* 1.3 79.9 - - - +
834A PHE* 1.3 65.3 + - + +
835A PRO* 3.4 1.5 - - - +
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Residues in contact with PHE 834 (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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605A THR* 3.2 36.1 - - - -
606A HIS* 4.6 4.7 - + + -
803A ILE* 5.5 1.1 - - + -
806A PHE* 3.6 31.0 - + - -
807A LEU* 3.6 45.5 - - + -
810A PHE* 4.4 14.8 - + + -
830A ILE* 2.8 24.1 + - + +
831A LYS* 3.2 18.4 - - - +
833A ALA* 1.3 81.8 - - - +
835A PRO* 1.3 63.9 - - - +
836A SER 3.2 3.3 + - - -
837A HIS* 3.4 43.2 + + + +
842A ILE* 4.9 1.1 - - + +
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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