Contacts of the helix formed by residues 796 - 808 (chain N) in PDB entry 1CZA
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 ALA 796 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249N GLU* 6.0 0.7 - - - +
795N LEU* 1.3 79.5 - - - +
797N LEU* 1.3 85.3 + - + +
798N LEU* 3.3 2.6 - - + +
799N GLN* 2.8 22.4 + - - +
800N VAL* 3.8 3.4 + - - -
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Residues in contact with LEU 797 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249N GLU* 4.8 13.2 - - + +
250N GLY* 5.6 7.6 - - - -
251N ASP* 5.4 19.7 - - + +
252N GLU* 5.5 7.0 - - + -
795N LEU 4.1 0.4 + - - -
796N ALA* 1.3 85.2 - - + +
798N LEU* 1.3 80.0 + - + +
800N VAL* 2.8 23.7 + - - +
801N ARG* 3.0 14.3 + - - +
813N CYS* 5.2 22.2 - - + -
816N SER* 4.9 4.9 + - - -
817N ILE* 6.6 0.4 - - + -
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Residues in contact with LEU 798 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796N ALA* 3.0 4.2 + - + +
797N LEU* 1.3 88.8 - - + +
799N GLN* 1.3 70.4 + - + +
801N ARG* 3.9 15.2 - - - +
802N ALA* 2.9 29.8 + - + +
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Residues in contact with GLN 799 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795N LEU* 3.5 39.5 - - + -
796N ALA* 2.8 19.7 + - + +
798N LEU* 1.3 84.3 - - + +
800N VAL* 1.3 57.9 + - - +
802N ALA* 3.3 14.4 - - - +
803N ILE* 3.0 36.9 + - + +
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Residues in contact with VAL 800 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789N GLN 5.4 0.2 - - - +
790N ILE* 4.0 44.2 - - + +
795N LEU* 4.8 15.3 - - + +
796N ALA 4.5 6.5 - - - +
797N LEU* 2.8 16.8 + - - +
799N GLN* 1.3 69.5 - - - +
801N ARG* 1.3 61.4 + - - +
803N ILE* 3.1 11.4 + - + +
804N LEU* 2.9 37.7 + - + +
816N SER* 3.7 28.0 - - - +
820N LYS* 5.1 8.1 - - + -
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Residues in contact with ARG 801 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797N LEU 3.0 12.9 + - - +
798N LEU* 3.9 15.1 - - - +
800N VAL* 1.3 72.4 - - - +
802N ALA* 1.3 59.3 + - - +
804N LEU* 3.1 3.5 + - - +
805N GLN* 2.7 61.8 + - - +
811N SER* 2.6 34.6 + - - +
812N THR* 4.6 14.9 - - - +
813N CYS* 5.0 3.6 - - - +
816N SER* 3.5 16.2 + - - +
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Residues in contact with ALA 802 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798N LEU* 2.9 21.6 + - + +
799N GLN* 3.3 21.1 - - - +
801N ARG* 1.3 76.0 - - - +
803N ILE* 1.3 58.0 + - + +
805N GLN* 3.9 3.6 - - - +
806N GLN* 2.8 53.1 + - - +
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Residues in contact with ILE 803 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786N PHE* 3.9 29.6 - - + -
789N GLN* 3.7 41.3 - - + +
790N ILE* 4.4 14.8 - - + +
795N LEU* 4.5 8.7 - - + -
799N GLN* 3.0 21.5 + - + +
800N VAL* 3.5 9.4 - - - +
802N ALA* 1.3 75.4 - - + +
804N LEU* 1.3 59.1 + - - +
806N GLN* 3.1 12.8 + - - +
807N LEU* 2.9 42.3 + - + +
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Residues in contact with LEU 804 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782N PHE* 4.1 11.7 - - + -
790N ILE* 3.7 16.8 - - + -
800N VAL* 2.9 23.3 + - + +
801N ARG 3.8 0.9 - - - +
803N ILE* 1.3 71.2 - - - +
805N GLN* 1.3 59.9 + - - +
807N LEU* 3.4 9.3 + - + +
808N GLY 3.3 5.7 + - - -
809N LEU* 2.9 43.7 + - + +
811N SER* 3.3 25.4 - - - +
816N SER* 3.6 26.2 - - - +
819N VAL* 3.7 44.4 - - + -
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Residues in contact with GLN 805 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801N ARG* 2.7 58.1 + - - +
802N ALA* 3.9 4.7 - - - +
804N LEU* 1.3 72.0 - - - +
806N GLN* 1.3 62.2 + - + +
808N GLY* 3.1 16.1 + - - -
809N LEU 3.1 13.0 + - - +
810N ASN* 4.8 2.9 - - - +
811N SER* 3.4 18.0 + - - +
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Residues in contact with GLN 806 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802N ALA* 2.8 43.6 + - - +
803N ILE* 3.5 12.1 + - - +
805N GLN* 1.3 78.5 - - + +
807N LEU* 1.3 60.3 + - + +
808N GLY* 4.6 0.2 - - - -
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Residues in contact with LEU 807 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775N THR* 3.4 17.0 + - + +
781N ILE* 3.8 38.1 - - + +
782N PHE* 4.7 12.3 - - + -
783N GLU* 5.6 0.4 - - - +
786N PHE* 4.1 38.6 - - + -
790N ILE* 5.3 0.7 - - + -
803N ILE* 2.9 32.4 + - + +
804N LEU* 3.7 26.0 - - + +
805N GLN 3.2 0.2 - - - -
806N GLN* 1.3 78.1 - - - +
808N GLY* 1.3 58.1 + - - +
809N LEU* 4.9 4.5 - - + +
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Residues in contact with GLY 808 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773N SER* 3.8 9.9 + - - -
775N THR* 3.7 22.9 + - - -
805N GLN 3.1 10.2 + - - -
807N LEU* 1.3 80.7 - - - +
809N LEU* 1.3 65.8 + - - +
810N ASN 4.3 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