Contacts of the helix formed by residues 787 - 792 (chain A) in PDB entry 1JQO
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 787 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A TRP* 3.1 15.3 + - - +
782A THR* 3.8 42.8 + - + -
785A ARG* 3.9 4.8 - - - -
786A PHE* 1.3 80.0 - - - +
788A LEU* 1.3 67.2 + - - +
789A PRO* 3.3 5.2 - - - -
790A VAL* 3.0 21.8 + - + +
791A TRP* 3.1 13.6 + - + +
832A VAL* 3.4 36.7 + - + +
833A PHE* 5.5 0.4 - + - -
835A LYS* 3.0 28.4 + - + -
836A GLY* 3.6 19.0 - - - -
864A TYR* 5.2 1.6 - + - -
966A MET* 4.6 4.7 - - - -
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Residues in contact with LEU 788 (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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732A VAL* 4.7 0.4 - - + -
738A PHE* 4.0 23.6 - - + -
777A TRP* 4.6 5.2 - - + -
781A TRP* 3.7 42.9 - - + +
786A PHE* 3.3 13.7 - - + -
787A HIS* 1.3 75.9 - - - +
789A PRO* 1.3 66.6 - - + +
791A TRP* 3.3 28.3 + - + -
792A LEU* 2.9 53.5 + - + +
860A LEU* 3.9 27.4 - - + -
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Residues in contact with PRO 789 (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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605A GLY 5.4 1.9 - - - +
610A ARG* 3.8 13.7 + - - +
646A GLY* 6.1 0.2 - - - -
728A TYR* 4.2 21.9 - - + +
777A TRP* 3.3 41.5 - - + +
778A ILE* 4.0 20.0 - - + -
781A TRP* 3.2 27.4 - - + -
787A HIS* 3.5 4.3 - - - -
788A LEU* 1.3 96.8 - - + +
790A VAL* 1.3 61.9 + - + +
791A TRP 3.3 0.5 + - - -
792A LEU* 4.1 4.5 + - + -
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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
----------------------------------------------------------
610A ARG* 3.5 27.3 - - + +
645A VAL* 3.7 25.6 - - + -
646A GLY* 4.2 21.8 - - - +
778A ILE* 5.1 6.5 - - + -
787A HIS* 3.0 24.3 + - + +
789A PRO* 1.3 80.0 - - + +
791A TRP* 1.3 57.8 + - + +
794A VAL* 4.5 0.7 - - - +
829A LEU* 3.9 24.0 - - + +
832A VAL* 3.7 22.9 - - + -
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Residues in contact with TRP 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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610A ARG* 6.0 0.2 - - - -
786A PHE* 3.1 29.1 + + - -
787A HIS* 3.1 21.4 + - + -
788A LEU* 3.8 29.8 - - + -
789A PRO 3.2 0.4 - - - -
790A VAL* 1.3 81.3 - - + +
792A LEU* 1.3 90.5 + - + +
793A GLY 2.9 4.6 + - - -
794A VAL* 3.2 23.4 + - - +
795A GLY 3.8 2.6 + - - -
829A LEU* 4.2 8.7 - - + -
832A VAL* 5.1 3.1 - - + -
833A PHE* 3.5 37.4 - + + -
860A LEU* 3.9 8.7 - - - -
863A LYS* 4.0 8.3 - - + -
864A TYR* 3.5 52.2 - + + -
867A THR* 4.1 14.7 - - + +
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Residues in contact with LEU 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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727A GLU* 3.4 15.3 - - + +
728A TYR* 4.0 25.8 - - + -
731A VAL* 3.2 34.8 - - + -
732A VAL* 3.8 17.7 - - + -
788A LEU* 2.9 38.9 + - + +
789A PRO* 4.1 1.8 + - + +
790A VAL 4.0 0.4 - - - -
791A TRP* 1.3 100.1 - - + +
793A GLY* 1.3 65.8 + - - +
795A GLY* 4.1 3.1 + - - -
860A LEU* 4.6 7.9 - - + -
863A LYS* 5.0 11.7 - - + +
867A THR* 5.3 0.2 + - - -
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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