Contacts of the helix formed by residues 844 - 860 (chain B) 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 ASP 844 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804B GLU 4.5 0.3 - - - +
805B GLY* 3.6 34.3 - - - +
806B HIS* 3.5 6.8 + - + +
843B HIS* 1.3 81.8 - - + +
845B LEU* 1.3 66.7 + - - +
846B THR* 2.8 35.0 - - - +
847B ALA* 3.0 21.4 + - + +
848B ILE* 3.0 23.8 + - - +
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Residues in contact with LEU 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B HIS* 3.9 31.6 - - + +
546B GLY* 4.0 9.2 - - - +
547B ARG* 4.0 9.6 - - + -
550B SER* 3.8 27.8 - - - +
843B HIS 3.0 17.1 + - - +
844B ASP* 1.3 71.7 - - - +
846B THR* 1.3 62.4 + - - +
848B ILE* 3.6 7.5 - - + +
849B CYS* 3.0 32.0 + - - -
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Residues in contact with THR 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ARG* 4.6 7.9 + - - +
844B ASP* 2.8 24.6 + - - +
845B LEU* 1.3 78.1 - - - +
847B ALA* 1.3 58.8 + - + +
849B CYS* 3.8 3.4 - - - +
850B ASP* 2.9 47.4 + - - +
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Residues in contact with ALA 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B ALA* 4.0 11.7 - - + +
804B GLU* 3.2 28.5 - - + +
806B HIS* 3.8 10.1 - - + -
844B ASP* 3.0 19.8 + - + +
846B THR* 1.3 83.9 - - + +
848B ILE* 1.3 58.6 + - - +
850B ASP* 3.2 8.2 + - - +
851B ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B ARG* 3.9 38.1 - - + +
551B ILE* 3.9 16.2 - - + -
800B PHE* 3.9 26.0 - - + +
806B HIS* 4.4 4.7 - - - +
839B LEU* 5.6 1.6 - - + -
841B GLY 4.8 0.9 - - - +
842B GLY* 3.5 42.6 - - - +
843B HIS 3.8 1.8 - - - +
844B ASP 3.0 18.1 + - - +
845B LEU* 3.6 14.4 - - + +
847B ALA* 1.3 75.3 - - - +
849B CYS* 1.3 58.9 + - - +
851B ALA* 3.9 1.0 - - - +
852B SER* 2.8 36.7 + - - -
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Residues in contact with CYS 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B SER* 3.6 46.0 - - - -
551B ILE* 3.6 13.2 - - - +
554B ARG* 3.4 33.9 + - + +
845B LEU* 3.0 25.8 + - - +
846B THR* 3.8 2.2 - - - +
848B ILE* 1.3 76.6 - - - +
850B ASP* 1.3 60.3 + - - +
852B SER* 3.9 1.8 - - - -
853B GLU* 3.0 31.2 + - - +
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Residues in contact with ASP 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ARG* 2.8 31.3 + - - +
817B ALA* 3.3 24.6 - - + +
846B THR* 2.9 29.8 + - - +
847B ALA* 3.6 6.3 - - - +
849B CYS* 1.3 74.2 - - - +
851B ALA* 1.3 63.9 + - - +
853B GLU* 3.8 5.0 - - - +
854B ALA* 3.1 17.2 + - - +
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Residues in contact with ALA 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B PHE* 3.3 40.8 - - + -
803B ALA* 5.4 1.6 - - + -
817B ALA* 3.8 12.2 - - - +
820B PHE* 3.8 15.5 - - + -
847B ALA 2.9 16.7 + - - +
848B ILE 4.0 0.9 - - - +
850B ASP* 1.3 77.4 - - - +
852B SER* 1.3 57.3 + - - +
854B ALA* 3.2 4.0 + - - +
855B CYS* 2.9 32.2 + - - -
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Residues in contact with SER 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B ILE* 3.7 36.1 - - - +
554B ARG* 6.2 0.4 - - - -
555B LEU* 4.6 2.5 - - - -
661B PHE* 3.8 12.4 - - - -
800B PHE* 3.5 21.5 - - - -
848B ILE 2.8 23.5 + - - -
849B CYS 3.9 2.9 - - - -
851B ALA* 1.3 73.4 - - - +
853B GLU* 1.3 59.6 + - - +
855B CYS* 3.2 2.1 + - - +
856B VAL* 2.9 37.6 + - - +
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Residues in contact with GLU 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ARG* 2.9 35.7 + - + +
555B LEU* 4.3 5.8 - - + +
558B ARG* 3.4 31.8 + - + +
560B LEU* 3.5 21.8 - - + +
849B CYS 3.0 16.8 + - - +
850B ASP* 3.8 5.4 - - - +
852B SER* 1.3 75.3 - - - +
854B ALA* 1.3 58.1 + - - +
857B ALA* 3.0 32.1 + - + +
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Residues in contact with ALA 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817B ALA* 3.0 34.3 - - + +
818B LYS* 4.3 4.7 - - + +
821B GLY* 3.7 9.1 - - - -
850B ASP 3.1 14.3 + - - +
851B ALA 3.4 6.7 - - - +
853B GLU* 1.3 79.4 - - - +
855B CYS* 1.3 57.4 + - - +
857B ALA* 3.4 7.3 + - - +
858B ALA* 2.9 27.7 + - - +
862B ASN* 5.5 0.2 - - - +
864B VAL* 6.4 0.4 - - + -
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Residues in contact with CYS 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B PHE* 5.8 3.1 - - + -
706B TRP* 4.1 6.3 - - - -
800B PHE* 3.8 26.9 - - + -
820B PHE* 3.7 17.5 - - - -
821B GLY* 4.3 2.7 - - - -
824B THR* 3.3 26.3 - - - +
837B LEU* 4.1 11.9 - - + -
851B ALA 2.9 20.3 + - - +
852B SER* 3.2 6.0 + - - +
854B ALA* 1.3 73.5 - - - +
856B VAL* 1.3 62.7 + - + +
858B ALA* 3.1 4.5 + - - +
859B LEU* 2.9 32.2 + - + +
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Residues in contact with VAL 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B THR* 5.3 0.9 - - - +
522B LEU* 4.3 16.2 - - + -
555B LEU* 3.7 22.7 - - + -
560B LEU* 4.0 17.7 - - + -
564B CYS* 4.4 7.6 - - - -
661B PHE* 3.5 39.3 - - + -
852B SER 2.9 19.6 + - - +
855B CYS* 1.3 73.4 - - + +
857B ALA* 1.3 65.1 + - - +
859B LEU* 3.3 10.1 + - + +
860B LEU* 3.1 33.8 + - + +
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Residues in contact with ALA 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B LEU* 4.0 14.3 - - + +
853B GLU* 3.0 21.9 + - + +
854B ALA* 3.5 7.9 - - - +
856B VAL* 1.3 78.9 - - - +
858B ALA* 1.3 60.6 + - - +
860B LEU* 3.4 14.0 + - - +
861B GLY 3.6 0.2 + - - -
862B ASN* 3.2 42.2 + - + +
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Residues in contact with ALA 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821B GLY* 3.3 27.4 - - - +
824B THR* 3.8 12.3 - - + -
825B GLN* 4.1 8.0 - - + +
828B MET* 3.1 16.7 - - - +
854B ALA 2.9 12.9 + - - +
855B CYS 3.3 8.7 - - - +
857B ALA* 1.3 75.9 - - - +
859B LEU* 1.3 62.5 + - - +
861B GLY* 2.9 14.0 + - - -
862B ASN* 3.6 16.0 + - - +
864B VAL* 6.3 1.1 - - + -
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Residues in contact with LEU 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B THR* 3.1 13.0 - - + +
521B GLY 5.3 0.4 - - - +
522B LEU* 5.6 0.9 - - + -
658B LYS* 4.1 3.5 - - - -
659B ASN* 2.8 51.6 + - + +
660B GLY* 3.5 36.3 - - - +
661B PHE* 3.8 15.7 - - + +
824B THR* 3.8 19.5 - - + -
828B MET* 3.8 12.5 - - + +
835B VAL* 4.6 9.4 - - + -
837B LEU* 4.7 6.1 - - + -
855B CYS* 2.9 18.3 + - + +
856B VAL* 3.3 15.2 + - + +
858B ALA* 1.3 75.5 - - - +
860B LEU* 1.3 60.3 + - - +
861B GLY 3.2 0.9 + - - -
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Residues in contact with LEU 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B THR* 3.1 33.4 - - + +
560B LEU* 3.5 31.4 - - + -
563B GLN* 3.5 43.7 - - + +
564B CYS* 3.9 5.2 - - - -
658B LYS* 5.4 4.7 - - - -
856B VAL* 3.1 26.5 + - + +
857B ALA* 3.8 6.5 - - - +
858B ALA 3.2 0.6 - - - -
859B LEU* 1.3 75.6 - - - +
861B GLY* 1.3 55.8 + - - +
862B ASN* 3.6 2.2 - - + +
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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