Contacts of the helix formed by residues 831 - 841 (chain A) in PDB entry 2Z5K
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 ASP 831 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791A GLN* 4.6 5.2 - - - +
794A ILE* 3.9 26.6 - - + +
795A ARG* 3.5 43.7 + - + +
827A GLY 5.2 2.5 + - - +
828A VAL* 2.7 14.3 + - - +
830A GLN* 1.3 89.4 - - - +
832A PHE* 1.3 61.8 + - - +
833A ILE* 3.1 6.7 - - - -
834A PHE* 3.0 32.2 + - + +
835A PHE* 3.8 2.8 + - - +
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Residues in contact with PHE 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 VAL* 2.8 28.5 + - + +
829A ILE* 3.7 11.7 + - + +
830A GLN 3.7 0.6 + - - -
831A ASP* 1.3 76.6 - - - +
833A ILE* 1.3 56.5 + - - +
835A PHE* 3.2 33.3 + + - +
836A CYS* 3.0 54.1 + - - -
856A ILE* 4.2 3.8 - - + -
857A LEU* 3.8 15.3 - - + -
860A PHE* 3.5 51.8 - + + -
869A TRP* 4.1 14.1 - + - -
872A PHE* 3.8 22.1 - + + -
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Residues in contact with ILE 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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830A GLN 5.5 1.3 - - - +
831A ASP* 4.3 5.6 - - - +
832A PHE* 1.3 78.6 - - - +
834A PHE* 1.3 89.6 + - + +
836A CYS* 3.5 5.0 + - - +
837A ASP* 3.1 26.5 + - + +
872A PHE* 3.4 25.2 - - + -
875A GLN* 5.0 14.4 - - + +
876A PHE* 4.4 19.5 - - + -
880A LEU* 5.0 4.7 - - + +
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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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794A ILE* 4.8 4.5 - - + +
795A ARG* 3.3 62.4 - - + -
798A CYS* 3.5 20.4 - - + +
799A THR* 4.0 15.7 - - - -
831A ASP* 3.0 24.9 + - + +
833A ILE* 1.3 100.3 - - + +
835A PHE* 1.3 58.4 + - - +
837A ASP* 3.5 7.7 + - - +
838A ALA* 3.0 28.6 + - - +
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Residues in contact with PHE 835 (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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794A ILE* 4.8 9.6 - - + +
797A TRP* 5.8 0.2 - + - -
798A CYS* 3.8 12.9 - - - -
814A PHE* 5.3 2.2 - + - -
817A ILE* 4.2 22.9 - - + -
818A CYS* 4.9 0.7 - - - -
821A ILE* 3.6 30.1 - - + -
828A VAL* 5.3 3.1 - - + -
831A ASP 3.8 2.5 + - - +
832A PHE* 3.2 39.6 + + + +
834A PHE* 1.3 76.0 - - - +
836A CYS* 1.3 56.0 + - - +
838A ALA* 3.1 2.4 + - + -
839A VAL* 2.7 60.2 + - + +
853A PHE* 4.5 10.3 - + - -
856A ILE* 3.6 34.5 - - + -
857A LEU* 4.3 9.6 - - + -
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Residues in contact with CYS 836 (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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832A PHE* 3.0 50.0 + - - -
833A ILE 3.7 7.2 - - - +
834A PHE 3.4 0.2 - - - -
835A PHE* 1.3 77.3 - - - +
837A ASP* 1.3 57.1 + - - +
839A VAL* 3.7 6.0 - - - +
840A ALA* 3.0 30.0 + - - +
857A LEU* 3.9 13.7 - - + -
869A TRP* 4.8 2.2 - - - -
872A PHE* 4.2 11.9 - - - -
876A PHE* 4.2 15.0 - - + -
880A LEU* 3.6 5.2 - - + +
884A LEU* 4.3 19.2 - - + +
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Residues in contact with ASP 837 (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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798A CYS* 5.2 1.0 - - - +
802A ARG* 3.1 47.2 + - - +
833A ILE* 3.1 21.6 + - + +
834A PHE* 3.8 7.3 - - - +
836A CYS* 1.3 77.1 - - - +
838A ALA* 1.3 61.1 + - - +
840A ALA* 3.6 2.4 + - - +
841A SER* 3.2 20.6 + - - -
880A LEU* 3.7 26.3 - - + +
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Residues in contact with ALA 838 (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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797A TRP* 5.0 0.2 - - + -
798A CYS* 3.8 31.9 - - + +
802A ARG* 4.2 5.8 - - + +
814A PHE* 3.8 23.3 - - + -
834A PHE 3.0 17.7 + - - +
835A PHE* 3.1 4.2 + - + +
837A ASP* 1.3 75.4 + - - +
839A VAL* 1.3 64.5 + - - +
841A SER* 2.8 25.1 + - - -
842A TRP* 3.7 8.0 - - - -
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Residues in contact with VAL 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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814A PHE* 4.3 2.0 - - + -
835A PHE* 2.7 58.3 + - + +
836A CYS* 3.7 6.3 - - - +
838A ALA* 1.3 71.1 - - - +
840A ALA* 1.3 63.3 - - - +
842A TRP* 3.1 28.9 + - - +
853A PHE* 3.7 27.1 - - + -
857A LEU* 4.4 6.1 - - + -
884A LEU* 4.2 7.2 - - + -
888A TYR* 3.6 36.9 + - + +
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Residues in contact with ALA 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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836A CYS 3.0 18.1 + - - +
837A ASP* 3.9 4.0 - - - +
839A VAL* 1.3 73.8 - - - +
841A SER* 1.3 53.6 + - - +
842A TRP 2.9 14.4 + - - +
880A LEU* 3.4 23.3 - - + -
883A ARG* 2.7 54.9 + - + +
884A LEU* 4.5 6.5 - - + -
888A TYR* 5.4 2.7 - - - -
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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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802A ARG* 3.4 41.7 - - - -
804A ILE 5.3 0.2 - - - +
806A ASP* 3.9 1.6 - - - +
810A LYS* 3.4 24.5 + - - -
814A PHE* 4.9 0.2 - - - -
837A ASP 3.2 12.7 + - - -
838A ALA 2.8 17.8 + - - -
839A VAL 3.2 1.0 - - - -
840A ALA* 1.3 75.5 - - - +
842A TRP* 1.3 58.6 + - - +
843A ILE* 3.7 10.2 + - - +
883A ARG* 4.8 2.7 - - - +
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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