Contacts of the helix formed by residues 783 - 791 (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 GLU 783 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747N GLY 5.3 2.7 - - - -
780N GLY 3.2 19.4 + - - +
781N ILE* 3.0 9.4 + - - +
782N PHE* 1.3 74.3 - - - +
784N THR* 1.3 70.3 + - + +
785N LYS* 4.2 8.7 - - + +
786N PHE* 2.8 45.7 + - + -
787N LEU* 3.1 8.5 + - - +
807N LEU* 5.6 0.7 - - - +
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Residues in contact with THR 784 (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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536N THR* 6.2 2.0 - - + -
747N GLY* 4.5 19.1 + - - +
782N PHE 3.8 0.6 + - - -
783N GLU* 1.3 72.1 - - + +
785N LYS* 1.3 67.2 + - + +
787N LEU* 3.9 6.0 - - - +
788N SER* 3.1 28.8 + - - -
863N THR* 3.7 28.0 - - + -
864N LEU* 3.4 38.3 - - - +
867N LEU* 4.0 7.7 - - + +
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Residues in contact with LYS 785 (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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783N GLU* 2.9 7.0 + - - +
784N THR* 1.3 83.7 - - + +
786N PHE* 1.3 93.5 + - + +
788N SER* 3.5 3.0 + - - -
789N GLN* 3.0 58.2 + - + +
867N LEU* 4.4 14.6 - - + -
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Residues in contact with PHE 786 (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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781N ILE 4.1 12.6 - - - +
782N PHE* 4.8 5.6 - - + -
783N GLU* 2.8 56.1 + - + +
785N LYS* 1.3 101.4 - - + +
787N LEU* 1.3 63.3 + - - +
789N GLN* 3.0 28.3 + - - +
790N ILE* 3.0 30.2 + - + +
803N ILE* 3.9 17.9 - - + -
807N LEU* 4.1 24.5 - - + -
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Residues in contact with LEU 787 (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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750N LEU* 4.9 10.5 - - + -
751N GLY* 3.9 13.5 - - - +
754N VAL* 4.2 11.4 - - + -
782N PHE* 3.4 48.4 - - + +
783N GLU 3.1 7.3 + - - +
784N THR* 3.9 9.4 - - - +
786N PHE* 1.3 75.1 - - - +
788N SER* 1.3 63.1 + - - +
790N ILE* 3.5 1.8 + - - +
791N GLU* 3.3 36.5 + - - +
823N CYS* 3.6 42.2 - - + +
826N VAL* 5.7 0.2 - - + -
827N SER* 4.9 5.4 - - - +
864N LEU* 5.9 2.9 - - + -
868N HIS* 4.5 8.3 - - + +
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Residues in contact with SER 788 (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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784N THR* 3.1 21.1 + - - -
785N LYS* 3.6 4.7 - - - -
787N LEU* 1.3 79.4 - - - +
789N GLN* 1.3 62.0 + - - +
791N GLU 3.4 1.9 + - - -
792N SER* 3.3 17.3 + - - -
864N LEU* 4.5 0.5 - - - +
867N LEU* 3.7 27.4 - - - +
868N HIS* 3.3 28.4 + - - +
869N PRO* 3.6 18.9 - - - +
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Residues in contact with GLN 789 (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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785N LYS* 3.0 53.3 + - + +
786N PHE* 3.0 32.9 + - - +
788N SER* 1.3 75.2 - - - +
790N ILE* 1.3 63.0 + - - +
792N SER* 3.1 22.4 + - - +
795N LEU* 3.6 15.5 - - + +
803N ILE* 3.7 26.6 - - + +
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Residues in contact with ILE 790 (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* 3.9 20.9 - - + -
786N PHE* 3.0 19.9 + - + +
787N LEU 4.0 3.8 - - - +
788N SER 3.4 0.2 - - - -
789N GLN* 1.3 76.0 - - - +
791N GLU* 1.3 59.3 + - - +
792N SER 3.5 2.3 + - - +
795N LEU* 5.7 0.2 - - - +
800N VAL* 4.0 33.0 - - + +
803N ILE* 4.4 21.3 - - + -
804N LEU* 3.7 29.8 - - + -
807N LEU* 5.3 1.3 - - + -
819N VAL* 4.0 3.6 - - + -
820N LYS* 3.7 42.4 - - - +
823N CYS* 4.1 14.4 - - + -
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Residues in contact with GLU 791 (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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787N LEU* 3.3 13.7 + - - +
788N SER 3.4 0.6 + - - -
789N GLN 3.3 0.8 - - - -
790N ILE* 1.3 76.3 - - - +
792N SER* 1.3 65.5 + - - +
793N ASP* 3.1 4.9 + - - +
820N LYS* 4.1 21.0 - - + +
823N CYS* 3.4 23.8 - - + +
824N GLY* 3.3 20.1 - - - +
827N SER* 2.6 29.0 + - - -
868N HIS* 2.8 16.0 + - - +
869N PRO* 3.9 15.2 - - + +
870N HIS* 3.3 33.7 + - + +
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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