Contacts of the helix formed by residues 801 - 814 (chain E) in PDB entry 5ZOJ
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 GLN 801 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798E ILE* 4.3 13.2 - - - +
799E GLY* 4.9 3.8 - - - -
800E ASP* 1.3 95.1 + - - +
802E TRP* 1.3 67.8 + - - +
803E HIS 3.2 3.6 + - - -
804E LEU* 3.3 27.9 + - + +
805E ALA* 4.0 1.9 + - - +
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Residues in contact with TRP 802 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792E PHE* 3.6 44.9 - + - -
794E PRO* 4.7 5.6 - - + -
797E GLU* 3.3 45.8 + - + +
798E ILE 3.0 30.6 - - - +
799E GLY 2.7 23.0 + - - -
800E ASP* 4.3 1.9 - - - +
801E GLN* 1.3 81.5 - - + +
803E HIS* 1.3 85.9 + - + +
805E ALA* 2.9 21.1 + - + +
806E ILE* 3.2 33.0 - - + +
825E VAL* 5.1 2.0 - - + -
827E LYS* 4.1 31.9 - - + -
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Residues in contact with HIS 803 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800E ASP* 2.6 34.1 + - + +
802E TRP* 1.3 99.1 - - + +
804E LEU* 1.3 84.9 + - + +
806E ILE* 3.4 5.6 + - - +
807E GLN* 3.1 46.6 + - - +
825E VAL* 3.5 25.5 - - + +
827E LYS* 5.2 16.9 - - + -
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Residues in contact with LEU 804 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800E ASP 4.3 0.2 - - - +
801E GLN* 3.3 22.4 + - + +
802E TRP 3.1 0.8 - - - -
803E HIS* 1.3 111.5 - - + +
805E ALA* 1.3 53.9 + - - +
807E GLN* 3.1 13.0 + - - +
808E GLU* 2.7 40.8 + - - +
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Residues in contact with ALA 805 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E LYS* 5.5 9.6 - - + -
801E GLN 4.0 1.5 + - - +
802E TRP* 2.9 17.2 + - + +
804E LEU* 1.3 79.4 - - - +
806E ILE* 1.3 59.8 + - + +
808E GLU* 3.3 7.7 + - - +
809E ALA* 2.7 29.5 + - - +
856E PHE* 6.1 0.4 - - - -
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Residues in contact with ILE 806 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E LYS* 4.2 22.9 - - - -
791E MET* 4.0 23.3 - - + +
792E PHE* 4.2 23.1 - - + -
797E GLU* 4.6 1.6 - - - +
802E TRP* 3.2 49.5 + - + +
803E HIS* 3.7 6.3 - - - +
804E LEU 3.2 0.2 - - - -
805E ALA* 1.3 74.6 - - + +
807E GLN* 1.3 66.3 + - - +
809E ALA* 3.1 7.5 + - - +
810E ILE* 2.9 24.7 + - + +
825E VAL* 4.1 9.6 - - + -
834E VAL* 3.8 28.9 - - + -
856E PHE* 4.9 2.2 - - + -
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Residues in contact with GLN 807 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803E HIS* 3.1 36.9 + - - +
804E LEU* 3.3 13.4 - - - +
806E ILE* 1.3 76.6 - - - +
808E GLU* 1.3 61.3 + - - +
810E ILE* 3.3 5.2 + - - +
811E LEU* 3.1 34.2 + - + +
823E ILE* 3.7 46.4 + - + +
824E ALA* 4.7 1.0 - - - +
825E VAL* 3.8 17.7 - - + +
885E LEU* 5.7 4.3 - - - +
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Residues in contact with GLU 808 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 2.7 23.8 + - - +
805E ALA* 3.6 8.1 - - - +
807E GLN* 1.3 70.6 - - - +
809E ALA* 1.3 61.7 + - - +
811E LEU* 3.1 9.7 + - - +
812E GLU* 2.9 52.8 + - + +
886E LYS 4.2 1.7 - - - +
887E PRO* 3.2 7.1 - - - +
888E SER* 2.4 49.0 + - - +
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Residues in contact with ALA 809 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E TRP* 3.3 17.1 + - - +
791E MET* 4.6 3.6 - - + -
805E ALA 2.7 21.4 + - - +
806E ILE* 3.1 7.6 + - - +
808E GLU* 1.3 72.5 - - - +
810E ILE* 1.3 62.2 + - - +
812E GLU* 4.3 6.5 - - - +
813E LYS* 3.3 17.2 + - - +
856E PHE* 3.5 38.8 - - + -
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Residues in contact with ILE 810 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E TRP* 4.7 2.9 - - + -
788E ILE* 4.4 11.9 - - + -
791E MET* 3.6 36.8 - - + -
806E ILE* 2.9 21.2 + - + +
807E GLN* 3.6 8.5 - - - +
808E GLU 3.2 0.2 - - - -
809E ALA* 1.3 77.3 - - - +
811E LEU* 1.3 65.6 + - + +
813E LYS* 3.5 3.3 + - - +
814E CYS* 3.2 26.0 + - + +
820E ILE* 5.8 4.3 - - + -
823E ILE* 4.8 8.3 - - + -
834E VAL* 4.5 14.8 - - + -
836E VAL* 4.5 18.2 - - + -
851E LEU* 4.0 31.4 - - + -
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Residues in contact with LEU 811 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807E GLN* 3.1 22.1 + - + +
808E GLU* 3.1 12.4 + - - +
810E ILE* 1.3 77.3 - - + +
812E GLU* 1.3 59.5 + - - +
814E CYS* 3.1 6.7 - - - +
815E SER* 3.0 26.3 + - - -
820E ILE* 4.2 16.4 - - + -
823E ILE* 3.6 28.0 - - + -
885E LEU* 4.1 33.2 - - + +
886E LYS* 3.6 20.2 - - - +
887E PRO* 3.7 20.9 - - + +
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Residues in contact with GLU 812 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E TRP* 5.8 2.0 - - + +
808E GLU* 2.9 36.6 + - + +
809E ALA* 4.3 6.1 - - - +
811E LEU* 1.3 73.9 - - - +
813E LYS* 1.3 66.5 + - - +
815E SER* 3.2 20.7 + - - -
887E PRO* 3.7 22.2 - - + -
888E SER 4.9 6.7 - - - +
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Residues in contact with LYS 813 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E TRP* 3.4 57.1 - - + +
768E GLN* 5.9 2.2 - - - +
809E ALA 3.3 17.2 + - - +
810E ILE 3.8 4.7 - - - +
811E LEU 3.3 0.2 - - - -
812E GLU* 1.3 78.6 - - - +
814E CYS* 1.3 58.2 + - - +
815E SER* 3.5 0.9 + - - -
850E ALA* 3.0 49.6 + - - +
851E LEU* 4.2 6.5 - - + -
854E SER* 4.0 8.7 + - - -
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Residues in contact with CYS 814 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810E ILE* 3.2 17.3 + - - +
811E LEU* 3.1 7.1 - - - +
812E GLU 3.1 0.4 - - - -
813E LYS* 1.3 80.0 - - - +
815E SER* 1.3 63.0 + - - +
816E ASP 3.3 3.1 - - - -
817E ASN* 3.1 25.3 + - + +
820E ILE* 3.6 23.6 - - + +
847E ALA* 3.9 29.6 - - - -
850E ALA* 3.9 14.1 - - - -
851E LEU* 4.1 17.5 - - - -
886E LYS* 6.0 0.2 - - - +
887E PRO* 5.5 0.3 - - - +
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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