Contacts of the helix formed by residues 847 - 856 (chain A) in PDB entry 4ZZ0
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 VAL 847 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814A ILE* 4.2 7.9 - - + -
815A SER 3.5 18.2 - - - +
816A GLY* 3.5 24.2 - - - +
842A SER* 3.6 21.5 - - - +
844A LYS* 3.6 21.8 - - + +
845A ALA 3.7 11.4 - - - +
846A ALA* 1.3 80.6 - - - +
848A ALA* 1.3 65.0 + - - +
850A LEU* 3.1 29.9 + - + +
851A ASP* 3.8 6.7 + - - +
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Residues in contact with ALA 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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816A GLY 3.7 2.6 + - - -
817A THR* 3.4 23.5 - - + +
846A ALA 4.2 0.2 + - - -
847A VAL* 1.3 73.2 - - - +
849A GLY* 1.3 62.4 + - - +
851A ASP* 3.0 27.6 + - + +
852A LYS* 3.1 25.5 + - - +
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Residues in contact with GLY 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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814A ILE* 3.6 17.9 - - - -
816A GLY 3.0 17.9 + - - -
817A THR 3.0 15.0 + - - -
818A GLY* 4.0 6.3 - - - -
821A LEU* 3.4 14.0 - - - +
847A VAL 3.2 0.6 - - - -
848A ALA* 1.3 77.4 - - - +
850A LEU* 1.3 60.3 + - - +
852A LYS* 3.3 3.5 + - - +
853A ALA* 3.1 18.7 + - - +
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Residues in contact with LEU 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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814A ILE* 3.8 5.5 - - + +
840A VAL* 4.7 3.4 - - + -
842A SER* 3.8 20.9 - - - +
844A LYS 3.8 14.4 - - - +
846A ALA* 3.8 17.9 - - - +
847A VAL* 3.1 18.6 + - + +
849A GLY* 1.3 75.4 - - - +
851A ASP* 1.3 61.8 + - - +
853A ALA* 3.3 4.5 + - - +
854A GLU* 3.0 42.0 + - - +
860A THR* 3.8 27.6 - - + +
861A ARG 4.8 1.1 - - - +
862A VAL* 3.7 28.0 - - + -
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Residues in contact with ASP 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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846A ALA 6.4 0.2 - - - -
847A VAL 4.4 3.8 - - - +
848A ALA* 3.0 23.9 + - + +
850A LEU* 1.3 79.2 - - - +
852A LYS* 1.3 58.0 + - + +
854A GLU* 3.4 14.0 + - - +
855A ARG* 2.9 31.5 + - - +
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Residues in contact with LYS 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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817A THR* 2.9 33.0 + - - +
818A GLY* 3.4 27.4 - - - +
819A SER* 4.5 4.7 - - - +
821A LEU* 4.6 6.1 - - + -
822A GLN* 3.7 31.1 - - + +
825A ILE* 4.1 5.8 - - + +
848A ALA* 3.1 22.7 + - - +
849A GLY* 3.6 7.2 - - - +
850A LEU 3.2 0.4 - - - -
851A ASP* 1.3 77.0 - - + +
853A ALA* 1.3 63.2 + - - +
855A ARG* 3.5 8.9 + - - +
856A ALA* 3.2 22.9 + - - +
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Residues in contact with ALA 853 (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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821A LEU* 4.3 1.9 - - + +
825A ILE* 4.4 9.9 - - - -
840A VAL* 3.8 26.2 - - + -
849A GLY 3.1 12.7 + - - +
850A LEU 3.7 3.1 - - - +
851A ASP 3.2 0.2 - - - -
852A LYS* 1.3 75.1 - - - +
854A GLU* 1.3 65.5 + - - +
856A ALA* 3.0 9.0 + - - +
858A ILE* 3.0 29.2 + - + +
860A THR* 3.5 26.0 - - + -
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Residues in contact with GLU 854 (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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850A LEU* 3.0 26.9 + - - +
851A ASP* 3.9 14.8 - - - +
853A ALA* 1.3 74.8 - - - +
855A ARG* 1.3 58.8 + - - +
857A GLY* 3.0 19.4 + - - +
858A ILE 4.2 5.6 - - - +
860A THR* 3.9 22.7 + - + +
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Residues in contact with ARG 855 (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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822A GLN* 6.1 1.1 - - - -
851A ASP 2.9 18.0 + - - +
852A LYS* 3.7 9.2 - - - +
854A GLU* 1.3 76.8 - - - +
856A ALA* 1.3 57.3 + - - +
857A GLY 3.3 0.7 + - - -
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Residues in contact with ALA 856 (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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822A GLN* 5.7 1.8 - - - +
825A ILE* 3.9 23.8 - - + -
829A ARG* 2.2 55.2 + - - +
852A LYS 3.2 14.9 + - - +
853A ALA 3.0 6.5 + - - +
855A ARG* 1.3 76.0 - - + +
857A GLY* 1.3 59.3 + - - +
858A ILE* 3.3 3.6 - - + -
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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