Contacts of the helix formed by residues 845 - 852 (chain A) in PDB entry 2N8Z
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 845 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844A THR* 1.3 74.3 - - - +
846A ASP* 1.3 60.8 + - - +
848A LEU* 3.6 12.6 - - - +
849A ARG* 3.1 25.5 + - - +
861A ILE* 3.8 38.7 - - + +
874A PRO 4.7 3.1 - - - +
875A GLY* 2.8 40.9 + - - +
877A LEU* 3.8 19.3 - - + +
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Residues in contact with ASP 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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844A THR* 3.1 9.7 + - - +
845A MET* 1.3 79.5 - - - +
847A GLU* 1.3 71.1 + - - +
849A ARG* 3.3 14.4 + - - +
850A ARG* 3.6 10.6 + - - +
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Residues in contact with GLU 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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836A LEU* 3.6 29.6 - - + +
840A LYS* 2.8 36.7 + - - -
843A ILE* 3.8 3.8 - - + -
844A THR* 3.0 43.9 + - - +
846A ASP* 1.3 84.3 - - - +
848A LEU* 1.3 59.2 + - - +
850A ARG* 3.0 56.4 + - - +
851A GLU* 4.2 2.1 - - - +
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Residues in contact with LEU 848 (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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833A PHE* 3.8 23.1 - - + -
836A LEU* 5.2 0.2 - - - -
843A ILE* 4.1 10.2 - - + +
844A THR 3.0 18.9 + - - +
845A MET* 3.6 12.6 - - - +
847A GLU* 1.3 76.9 - - - +
849A ARG* 1.3 62.6 + - - +
850A ARG 3.1 0.2 - - - -
851A GLU* 3.1 20.7 + - - +
852A LEU* 3.4 10.7 + - + +
857A ALA* 3.7 37.0 - - + +
860A CYS* 4.0 11.0 - - + -
861A ILE* 4.1 6.7 - - + -
864A MET* 4.1 15.9 - - - -
877A LEU* 3.7 28.9 - - + -
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Residues in contact with ARG 849 (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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845A MET 3.1 19.4 + - - +
846A ASP* 3.6 7.9 - - - +
847A GLU 3.2 0.6 - - - -
848A LEU* 1.3 77.7 - - - +
850A ARG* 1.3 60.9 + - - +
851A GLU 3.2 0.2 - - - -
852A LEU 4.1 0.4 - - - -
853A PRO* 3.1 52.2 + - + +
854A PRO* 3.3 17.0 + - - +
855A ASP* 4.2 4.9 + - - +
857A ALA* 3.7 18.3 - - + +
858A GLU* 3.0 44.6 + - - +
861A ILE* 5.2 1.2 - - - +
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Residues in contact with ARG 850 (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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836A LEU* 4.3 22.8 - - - +
846A ASP* 3.6 8.3 + - - +
847A GLU* 3.0 47.0 + - - +
849A ARG* 1.3 79.9 - - - +
851A GLU* 1.3 71.1 + - + +
853A PRO* 4.2 6.5 - - - +
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Residues in contact with GLU 851 (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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740A GLY* 2.9 51.7 + - - +
741A SER* 4.2 1.9 + - - -
832A SER* 3.1 32.1 - - - -
833A PHE* 3.5 9.8 + - + -
836A LEU* 3.2 34.8 - - + +
847A GLU 4.2 1.1 - - - +
848A LEU* 3.1 14.3 + - - +
850A ARG* 1.3 86.8 - - + +
852A LEU* 1.3 69.0 + - + +
853A PRO* 4.0 3.7 - - - +
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Residues in contact with LEU 852 (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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740A GLY* 4.2 4.5 - - - -
741A SER* 3.7 31.2 - - - +
824A ASP* 4.8 4.3 - - + -
828A GLN* 4.6 4.7 - - - +
829A VAL* 4.2 20.2 - - + -
833A PHE* 4.6 5.4 - - + -
848A LEU* 3.4 15.7 + - + +
849A ARG 3.6 2.5 - - - -
851A GLU* 1.3 89.4 - - + +
853A PRO* 1.3 67.4 - - - +
854A PRO* 3.3 5.9 - - + +
856A GLN* 3.7 30.7 - - + +
857A ALA* 3.2 25.1 - - - +
860A CYS* 3.8 25.4 - - - -
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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