Contacts of the helix formed by residues 816 - 828 (chain A) in PDB entry 3ZNS
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 SER 816 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A ASP* 2.6 35.0 + - - -
803A ALA* 5.9 0.2 - - - -
804A GLU* 5.9 2.2 - - - -
814A HIS 3.5 3.6 + - - -
815A VAL* 1.3 73.4 - - - +
817A ALA* 1.3 64.1 + - - +
818A LYS* 3.7 9.8 + - - +
819A CYS* 3.2 20.1 + - - +
820A PHE* 3.2 18.4 + - - -
872A TRP* 4.5 0.3 + - - -
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Residues in contact with ALA 817 (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 ALA* 6.1 0.6 - - - +
815A VAL 4.1 0.2 + - - -
816A SER* 1.3 73.5 - - - +
818A LYS* 1.3 62.1 + - - +
820A PHE* 3.3 5.6 + - - +
821A GLY 3.1 9.5 + - - -
850A ASP* 3.6 46.2 - - + +
851A ALA* 3.7 10.3 - - - +
854A ALA* 3.0 22.5 - - + +
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Residues in contact with LYS 818 (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 SER* 3.2 9.5 - - - +
817A ALA* 1.3 78.6 - - - +
819A CYS* 1.3 57.5 + - - +
821A GLY* 3.4 2.1 + - - +
822A TYR* 3.0 28.1 + - - +
854A ALA* 4.7 4.7 - - - -
864A VAL* 3.9 33.6 - - + +
865A ASP 5.6 0.2 - - - +
868A SER* 2.8 33.5 + - - -
869A GLU* 2.9 33.2 + - + +
872A TRP* 4.1 9.6 - - + -
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Residues in contact with CYS 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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771A ASP* 3.3 47.1 - - - +
774A TYR* 4.4 5.6 - - - -
775A LEU* 4.1 21.1 - - - -
815A VAL* 3.9 5.6 - - + -
816A SER* 3.2 9.3 + - - +
818A LYS* 1.3 77.7 - - - +
820A PHE* 1.3 59.3 + - - +
822A TYR* 3.3 2.6 + - - +
823A MET* 2.9 51.0 + - - +
872A TRP* 3.8 11.1 - - + -
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Residues in contact with PHE 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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706A TRP* 3.7 37.0 - + + -
774A TYR* 6.1 1.3 - + - -
799A GLY 3.9 1.3 - - - -
800A PHE* 3.6 35.7 - + + -
802A ALA* 4.4 6.7 - - + -
803A ALA* 3.9 23.8 - - + -
815A VAL* 3.5 38.1 - - + -
816A SER 3.2 21.3 + - - -
817A ALA 3.3 6.7 + - - +
819A CYS* 1.3 78.1 - - - +
821A GLY* 1.3 57.0 + - - +
823A MET* 3.4 15.1 + - + +
824A THR* 2.9 30.2 + - - -
851A ALA* 3.8 15.5 - - + +
855A CYS* 3.8 13.9 - - - -
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Residues in contact with GLY 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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817A ALA 3.1 9.7 + - - -
818A LYS 3.8 2.7 - - - -
820A PHE* 1.3 77.9 - - - +
822A TYR* 1.3 57.7 + - - +
824A THR* 3.5 4.4 + - - -
825A GLN* 3.0 23.2 + - - +
854A ALA* 3.4 30.6 - - - +
855A CYS* 4.2 0.6 - - - -
858A ALA* 3.1 13.8 - - - +
864A VAL* 4.6 7.4 - - - +
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Residues in contact with TYR 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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775A LEU* 3.6 23.6 - - + -
818A LYS 3.0 17.8 + - - +
819A CYS 3.6 4.3 - - - +
820A PHE 3.3 0.2 - - - -
821A GLY* 1.3 75.2 - - - +
823A MET* 1.3 60.0 + - - +
825A GLN* 3.2 29.5 + - - +
826A GLN* 2.9 60.9 + - + +
864A VAL* 3.7 30.0 - - + +
866A PRO* 3.2 24.4 - - + +
872A TRP* 3.8 21.5 - + + -
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Residues in contact with MET 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TRP* 3.7 23.8 - - + -
774A TYR* 4.3 22.9 - - + +
775A LEU* 5.4 3.6 - - + -
778A PHE* 3.7 42.2 - - + -
815A VAL* 4.1 13.0 - - + -
819A CYS* 2.9 51.4 + - - +
820A PHE* 3.7 21.8 - - + +
822A TYR* 1.3 72.5 - - - +
824A THR* 1.3 60.1 + - - +
826A GLN* 3.2 9.1 + - - +
827A LEU* 3.0 32.6 + - - +
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Residues in contact with THR 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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706A TRP* 3.4 17.6 - - - -
820A PHE 2.9 16.2 + - - -
821A GLY* 3.5 9.6 - - - -
823A MET* 1.3 77.8 - - - +
825A GLN* 1.3 62.5 + - - +
827A LEU* 3.2 7.5 + - - +
828A MET* 3.0 23.5 + - + +
835A VAL* 5.1 1.6 - - + -
837A LEU* 3.9 14.7 - - + +
855A CYS* 3.4 22.9 - - - +
858A ALA* 3.9 6.7 - - + -
859A LEU* 3.3 34.1 - - + -
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Residues in contact with GLN 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 GLY 3.0 13.0 + - - +
822A TYR* 3.4 31.5 - - - +
824A THR* 1.3 76.5 - - - +
826A GLN* 1.3 59.9 + - - +
828A MET* 3.3 29.2 + - + +
829A ASN* 3.7 12.1 + - - +
858A ALA* 4.1 6.2 - - + +
862A ASN 4.4 4.7 - - - +
863A ARG* 3.5 44.1 - - + +
864A VAL* 2.9 32.6 + - - +
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Residues in contact with GLN 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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775A LEU* 4.3 9.1 + - - +
778A PHE* 3.9 25.1 - - + +
779A ARG* 4.9 4.9 + - - +
783A MET* 3.2 49.4 - - + +
822A TYR* 2.9 59.1 + - + +
823A MET* 3.6 8.8 - - - +
824A THR 3.2 0.4 - - - -
825A GLN* 1.3 75.4 - - + +
827A LEU* 1.3 64.0 + - - +
829A ASN* 3.3 21.0 + - - +
830A LEU 4.4 0.2 + - - -
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Residues in contact with LEU 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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702A LEU* 4.5 1.3 - - + -
704A VAL* 4.0 30.5 - - + -
706A TRP* 3.9 21.3 - - + -
778A PHE* 4.0 16.6 - - + -
782A VAL* 4.4 4.7 - - + -
783A MET* 4.1 7.2 - - - -
794A VAL* 4.4 9.4 - - + +
796A VAL* 3.6 28.9 - - + -
823A MET 3.0 16.1 + - - +
824A THR* 3.2 6.0 + - - +
826A GLN* 1.3 75.5 - - - +
828A MET* 1.3 56.9 + - - +
829A ASN 3.2 1.1 - - - -
830A LEU* 3.2 44.5 + - + +
835A VAL* 3.5 18.0 - - + +
837A LEU* 5.7 0.2 - - + -
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Residues in contact with MET 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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658A LYS* 5.1 10.5 - - - -
659A ASN* 4.0 9.6 - - - +
824A THR 3.0 19.6 + - - +
825A GLN* 3.4 20.4 - - + +
826A GLN 3.2 1.0 - - - -
827A LEU* 1.3 76.3 - - - +
829A ASN* 1.3 60.5 + - - +
830A LEU 3.2 1.3 - - - -
833A GLY* 3.4 22.9 + - - +
835A VAL* 3.8 18.6 - - + -
858A ALA 3.1 36.1 - - - +
859A LEU* 3.8 30.1 - - + +
861A GLY* 4.7 7.4 - - - +
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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