Contacts of the helix formed by residues 822 - 836 (chain A) in PDB entry 5ZR1
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 LEU 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A PHE* 3.8 21.3 - - + -
820A GLN 3.5 0.4 + - - -
821A GLU* 1.3 75.3 - - - +
823A GLY* 1.3 60.1 + - - +
825A ILE* 3.4 11.1 + - + +
826A VAL* 3.3 26.8 + - - +
866A TRP* 3.7 33.2 - - + -
870A LEU* 4.3 5.8 - - + -
881A LYS* 4.3 21.5 - - + +
887A ASP* 3.6 24.2 - - + +
888A ARG* 4.2 1.3 - - - +
890A CYS* 2.6 26.1 + - + +
892A VAL* 3.7 21.3 - - + -
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Residues in contact with GLY 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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821A GLU* 3.2 2.7 - - - -
822A LEU* 1.3 71.8 - - - +
824A ASP* 1.3 64.3 + - - +
825A ILE 3.3 0.4 - - - -
826A VAL* 3.6 4.8 + - - +
827A ASP* 3.1 32.2 + - - +
862A ARG* 5.9 0.4 - - - -
888A ARG* 2.7 51.2 + - - -
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Residues in contact with ASP 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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811A LEU* 4.0 26.3 - - + +
815A ASN* 5.9 0.9 + - - -
820A GLN* 5.1 3.4 + - - +
821A GLU* 3.1 45.0 + - - +
823A GLY* 1.3 77.6 - - - +
825A ILE* 1.3 64.3 + - - +
827A ASP* 3.8 7.6 + - - +
828A GLU* 3.2 22.9 + - - +
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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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804A PHE* 3.7 40.6 - - + +
807A ALA* 4.3 12.6 - - + -
808A LEU* 3.7 30.3 - - + +
811A LEU* 5.1 4.9 - - + -
820A GLN* 4.3 11.0 - - + -
821A GLU 3.3 15.0 + - - +
822A LEU* 3.6 25.6 - - + +
823A GLY 3.3 0.4 - - - -
824A ASP* 1.3 76.9 - - - +
826A VAL* 1.3 59.3 + - + +
828A GLU* 3.2 6.1 + - - +
829A ILE* 3.0 34.6 + - + +
892A VAL* 4.3 11.4 - - + -
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Residues in contact with VAL 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A LEU 3.3 17.6 + - - +
823A GLY* 4.0 8.3 - - - +
824A ASP 3.4 0.2 - - - -
825A ILE* 1.3 77.2 - - + +
827A ASP* 1.3 61.6 + - - +
829A ILE* 3.4 9.5 + - - +
830A LYS* 3.1 23.2 + - + +
861A LEU 4.0 12.1 - - - +
862A ARG* 3.7 50.9 - - - +
866A TRP* 3.9 21.5 - - + +
888A ARG* 4.5 1.6 - - - +
512D GLU* 4.2 10.1 - - - +
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Residues in contact with ASP 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 GLY 3.1 10.7 + - - +
824A ASP* 4.3 7.5 - - - +
826A VAL* 1.3 77.9 - - - +
828A GLU* 1.3 57.6 + - - +
830A LYS* 3.6 7.0 + - - +
831A LEU* 3.0 29.3 + - - +
888A ARG* 2.7 32.2 + - - -
509D ILE* 4.4 7.6 - - - +
512D GLU* 3.9 11.6 - - - +
515D ARG* 5.6 1.4 + - - -
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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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807A ALA* 3.7 22.2 - - + +
810A ASN* 4.1 17.7 + - + +
811A LEU* 3.6 21.4 - - + +
814A LYS* 2.7 32.6 + - - -
824A ASP 3.2 19.9 + - - +
825A ILE 3.5 5.2 - - - +
826A VAL 3.2 0.2 - - - -
827A ASP* 1.3 75.0 - - - +
829A ILE* 1.3 60.1 + - - +
831A LEU* 3.3 18.9 + - - +
832A LEU* 2.8 39.3 + - + +
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Residues in contact with ILE 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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803A LEU* 3.7 27.5 - - + +
804A PHE* 4.1 31.9 - - + +
807A ALA* 3.7 17.0 - - + -
825A ILE* 3.0 25.7 + - + +
826A VAL* 3.4 9.4 + - - +
828A GLU* 1.3 75.0 - - - +
830A LYS* 1.3 62.1 + - - +
832A LEU* 3.4 5.9 + - - +
833A ILE* 3.3 26.2 + - + +
850A PHE* 5.8 0.2 - - - -
863A ILE* 3.7 40.8 - - + -
866A TRP* 4.7 7.2 - - + +
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Residues in contact with LYS 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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826A VAL* 3.1 17.2 + - + +
827A ASP* 3.9 7.2 - - - +
828A GLU 3.2 0.2 - - - -
829A ILE* 1.3 79.4 - - - +
831A LEU* 1.3 56.7 + - - +
833A ILE* 3.5 1.8 + - + -
834A GLU* 2.9 40.6 + - + +
850A PHE* 3.6 38.6 - - + -
859A GLU* 3.3 14.9 + - - -
860A GLN 5.1 1.9 + - - +
861A LEU 5.9 4.5 - - - +
515D ARG* 3.1 48.1 - - - +
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Residues in contact with LEU 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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814A LYS* 5.3 6.1 - - - +
827A ASP 3.0 19.5 + - - +
828A GLU* 3.3 23.8 + - - +
830A LYS* 1.3 77.6 - - - +
832A LEU* 1.3 60.2 + - + +
834A GLU* 3.2 14.6 - - + +
835A VAL* 3.1 49.4 + - + +
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Residues in contact with LEU 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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803A LEU* 3.7 24.5 - - + -
806A TYR* 3.6 30.7 - - + -
807A ALA* 4.9 5.4 - - + -
810A ASN* 3.8 13.2 - - - +
828A GLU* 2.8 28.8 + - + +
829A ILE* 3.4 5.4 + - - +
830A LYS 3.2 0.2 - - - -
831A LEU* 1.3 81.2 - - - +
833A ILE* 1.3 65.6 + - + +
835A VAL* 5.1 1.3 - - - -
836A ASN* 3.3 36.8 + - - +
842A VAL* 5.1 0.2 - - - +
914A LEU* 3.6 28.4 - - + +
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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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799A PHE* 4.9 10.1 - - + -
803A LEU* 4.2 24.2 - - + -
829A ILE* 3.3 19.1 + - + +
830A LYS* 4.1 2.9 - - + +
832A LEU* 1.3 86.0 - - + +
834A GLU* 1.3 65.4 + - - +
836A ASN 4.0 1.7 + - - -
837A GLY* 4.0 13.5 + - - -
842A VAL* 3.7 32.2 - - + +
845A ILE* 5.4 2.9 - - + -
846A ALA* 3.8 24.9 - - + -
849A LEU* 4.8 8.1 - - + -
850A PHE* 4.2 23.3 - - + -
914A LEU* 6.0 0.2 - - + -
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Residues in contact with GLU 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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830A LYS* 2.9 32.2 + - + +
831A LEU* 3.2 22.5 - - - +
833A ILE* 1.3 78.5 - - - +
835A VAL* 1.3 68.8 + - + +
837A GLY* 3.7 7.3 + - - -
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Residues in contact with VAL 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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831A LEU* 3.1 35.6 + - + +
832A LEU* 4.8 2.2 - - - +
834A GLU* 1.3 86.0 - - + +
836A ASN* 1.3 69.3 + - - +
837A GLY 2.9 7.0 + - - -
838A SER* 4.6 1.9 + - - -
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Residues in contact with ASN 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 LEU* 3.3 31.8 + - - +
833A ILE 4.0 4.3 - - - -
834A GLU 3.5 0.4 - - - -
835A VAL* 1.3 84.5 - - - +
837A GLY* 1.3 59.9 + - - +
838A SER* 3.3 5.4 - - - +
839A ASN* 3.5 15.6 + - + +
842A VAL* 3.4 27.4 - - + +
914A LEU* 3.4 46.8 + - + +
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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