Contacts of the helix formed by residues 818 - 829 (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 GLY 818 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814A ILE* 5.1 7.6 - - - -
816A GLY 3.3 2.0 - - - -
817A THR* 1.3 79.1 - - - +
819A SER* 1.3 61.3 + - - +
820A ASN 3.2 1.8 - - - -
821A LEU* 3.3 13.3 + - - +
822A GLN 2.9 23.4 + - - -
849A GLY* 4.0 12.3 - - - -
852A LYS* 3.4 12.5 - - - +
893A ALA 5.4 0.4 - - - -
1101A GAR 2.9 14.1 + - - -
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Residues in contact with SER 819 (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* 3.6 9.1 + - - +
818A GLY* 1.3 73.9 - - - +
820A ASN* 1.3 62.1 + - - +
822A GLN* 3.3 8.6 + - - +
823A ALA* 3.1 17.8 + - - +
852A LYS* 4.7 4.7 - - - +
977A LYS* 3.7 12.6 - - - +
981A HIS* 2.8 40.5 + - - -
1101A GAR 2.6 27.9 + - - -
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Residues in contact with ASN 820 (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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819A SER* 1.3 78.9 + - - +
821A LEU* 1.3 67.0 + - - +
823A ALA* 3.2 3.5 + - - +
824A LEU* 3.0 27.3 + - - +
893A ALA* 4.0 16.6 - - + -
914A ILE* 4.1 11.7 - - - +
977A LYS* 5.2 0.8 - - - +
980A GLU* 2.8 51.4 + - - +
981A HIS* 3.5 12.7 + - - -
984A PHE* 3.9 13.8 - - + +
1101A GAR 3.0 33.6 + - - +
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Residues in contact with LEU 821 (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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812A VAL* 3.8 23.8 - - + -
814A ILE* 4.3 14.8 - - + -
818A GLY* 3.3 13.7 + - - +
820A ASN* 1.3 78.1 - - - +
822A GLN* 1.3 58.0 + - - +
824A LEU* 3.1 9.6 + - - +
825A ILE* 2.8 53.0 + - + +
837A ILE* 4.6 2.5 - - + -
840A VAL* 3.8 39.0 - - + -
849A GLY* 3.4 31.4 - - - +
852A LYS* 4.6 4.3 - - + -
853A ALA* 4.3 6.1 - - + +
893A ALA* 4.3 3.6 - - - +
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Residues in contact with GLN 822 (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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818A GLY 2.9 14.3 + - - +
819A SER* 3.6 9.9 - - - +
820A ASN 3.2 0.2 - - - -
821A LEU* 1.3 76.2 - - - +
823A ALA* 1.3 58.0 + - - +
825A ILE* 3.2 20.9 + - - +
826A ASP* 2.8 66.0 + - - +
852A LYS* 3.7 36.6 - - + +
855A ARG* 6.1 1.2 - - - -
856A ALA* 5.7 1.6 - - - +
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Residues in contact with ALA 823 (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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819A SER 3.1 11.5 + - - +
820A ASN* 3.2 7.8 + - - +
822A GLN* 1.3 76.2 - - - +
824A LEU* 1.3 58.0 + - - +
826A ASP* 3.5 9.6 + - - +
827A SER* 3.0 29.3 + - - -
981A HIS* 3.7 44.6 - - + +
985A PRO* 3.7 7.8 - - + +
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Residues in contact with LEU 824 (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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812A VAL* 4.2 18.6 - - + -
820A ASN 3.0 20.1 + - - +
821A LEU* 3.5 6.5 - - - +
823A ALA* 1.3 74.4 - - - +
825A ILE* 1.3 63.6 + - - +
827A SER* 3.1 4.0 + - - +
828A THR* 2.8 31.5 + - - +
837A ILE* 3.7 13.2 - - + -
891A CYS* 4.2 17.9 - - + -
893A ALA* 4.5 0.9 - - + -
984A PHE* 3.8 34.3 - - + +
985A PRO* 3.7 33.9 - - + -
988A LEU* 3.9 21.3 - - + -
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Residues in contact with ILE 825 (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* 2.8 47.6 + - + +
822A GLN* 3.5 26.7 - - - +
824A LEU* 1.3 74.9 - - - +
826A ASP* 1.3 64.3 - - - +
828A THR* 3.3 5.9 + - - -
829A ARG* 3.2 46.2 + - - +
837A ILE* 3.8 3.6 - - + -
852A LYS* 4.1 11.4 - - + +
853A ALA* 4.4 1.8 - - - -
856A ALA* 3.9 26.9 - - + -
858A ILE* 3.8 25.4 - - + -
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Residues in contact with ASP 826 (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* 2.8 50.7 + - - +
823A ALA* 3.7 7.8 - - - +
825A ILE* 1.3 79.8 - - - +
827A SER* 1.3 61.4 + - - +
829A ARG* 3.4 11.4 + - - +
830A GLU* 3.7 18.4 + - - +
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Residues in contact with SER 827 (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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823A ALA 3.0 15.3 + - - -
824A LEU* 3.1 12.6 + - - +
826A ASP* 1.3 76.7 - - - +
828A THR* 1.3 70.5 + - - +
829A ARG 3.1 1.3 + - - -
830A GLU* 3.2 24.7 + - - +
833A SER* 3.6 6.8 - - - -
985A PRO* 3.4 32.4 + - - +
988A LEU* 5.4 0.2 - - - +
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Residues in contact with THR 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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824A LEU 2.8 25.9 + - - +
825A ILE* 3.3 7.1 + - - -
827A SER* 1.3 80.7 + - - +
829A ARG* 1.3 62.3 + - - +
830A GLU 3.4 1.0 - - - +
833A SER* 3.2 22.9 + - - +
835A ALA* 3.3 28.3 - - + +
836A GLN* 4.6 3.4 - - - +
837A ILE* 3.5 25.7 + - + +
988A LEU* 3.8 29.2 - - + -
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Residues in contact with ARG 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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825A ILE* 3.2 29.1 + - + +
826A ASP* 3.4 6.7 + - - +
827A SER 3.1 1.0 - - - -
828A THR* 1.3 82.2 - - - +
830A GLU* 1.3 63.9 + - - +
831A PRO* 3.7 3.8 - - - +
856A ALA* 2.2 55.5 + - - +
857A GLY 4.8 0.4 - - - -
858A ILE* 4.0 13.5 - - - +
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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