Contacts of the helix formed by residues 789 - 795 (chain A) in PDB entry 5ZR1
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 HIS 789 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A SER* 1.3 76.1 + - - +
790A VAL* 1.3 60.0 + - - +
791A ILE 3.1 2.7 - - - -
792A THR* 3.2 26.7 + - + +
793A PHE* 2.8 55.7 + + + +
796A ARG* 4.3 10.4 + - - -
254D LEU* 4.0 8.0 - - + +
274D TYR* 3.6 71.0 + + + +
275D MET 5.5 3.4 - - - -
277D GLN* 5.9 2.0 - - - -
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Residues in contact with VAL 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A SER* 3.3 18.8 - - - +
789A HIS* 1.3 77.2 - - - +
791A ILE* 1.3 64.3 + - + +
793A PHE* 4.0 0.9 - - - -
794A MET* 3.3 31.7 + - + +
878A ILE* 5.1 2.7 - - + -
896A ILE* 3.8 29.8 - - + -
900A GLU* 3.5 33.7 - - + +
254D LEU* 3.8 37.5 - - + -
255D ASN* 5.7 2.2 - - + +
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Residues in contact with ILE 791 (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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788A SER* 4.8 9.2 + - - +
789A HIS 3.1 1.2 - - - +
790A VAL* 1.3 78.6 - - + +
792A THR* 1.3 68.0 + - - +
794A MET* 3.3 2.9 + - - +
795A THR* 3.2 38.4 + - + +
900A GLU* 3.3 50.5 - - + +
903A ARG* 3.3 42.4 - - + +
904A ALA* 4.2 7.3 - - + +
907A GLU* 5.0 5.4 - - - +
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Residues in contact with THR 792 (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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788A SER 4.8 3.1 + - - -
789A HIS* 3.2 28.5 + - + +
791A ILE* 1.3 82.0 - - - +
793A PHE* 1.3 62.1 + - - +
795A THR* 3.3 16.7 + - - +
796A ARG* 3.3 48.6 + - - +
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Residues in contact with PHE 793 (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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789A HIS* 2.8 30.7 + + - +
790A VAL 4.2 2.2 - - - +
792A THR* 1.3 77.6 - - - +
794A MET* 1.3 61.1 + - + +
796A ARG 3.4 7.4 + - - -
797A LEU* 3.4 35.4 - - + +
872A GLN* 4.7 10.8 - - - -
873A LEU* 5.0 2.7 - - + -
876A ALA* 3.9 19.1 - - + -
878A ILE* 3.5 32.8 - - + -
102D GLY* 5.5 2.2 - - - -
103D PRO* 4.3 23.3 - - + -
252D THR 6.2 0.4 - - - -
254D LEU* 3.7 26.9 - - + -
277D GLN* 3.2 37.4 - - - +
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Residues in contact with MET 794 (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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790A VAL* 3.3 21.5 + - + +
791A ILE* 3.3 2.6 + - + -
793A PHE* 1.3 74.1 - - - +
795A THR* 1.3 64.4 + - - +
796A ARG 3.2 1.9 + - - -
797A LEU* 3.8 16.7 + - + +
802A LYS* 3.6 24.1 - - - +
805A ILE* 4.8 13.5 - - - -
878A ILE* 3.8 31.2 - - + -
896A ILE* 3.7 30.3 - - + -
900A GLU 3.4 24.9 - - - +
901A ALA* 3.8 5.6 - - - +
904A ALA* 3.7 17.2 - - + +
905A MET* 3.9 15.2 - - + +
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Residues in contact with THR 795 (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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791A ILE* 3.2 18.5 + - + +
792A THR* 3.3 18.4 + - - +
794A MET* 1.3 77.3 - - - +
796A ARG* 1.3 65.6 + - - +
797A LEU 3.5 0.9 - - - -
802A LYS* 3.6 20.1 + - - -
904A ALA* 3.7 26.7 - - + +
907A GLU* 3.3 34.9 + - + +
908A ASP* 5.7 2.3 - - - +
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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