Contacts of the helix formed by residues 797 - 807 (chain A) in PDB entry 5HG1
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 LEU 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLU* 3.7 27.1 - - + +
793A ASP* 3.4 31.9 - - - +
794A CYS* 3.0 12.2 + - - +
795A LEU 3.1 9.8 - - - +
796A ALA* 1.3 76.9 - - - +
798A LEU* 1.3 65.5 + - - +
799A GLN 3.3 2.7 - - - -
800A VAL* 3.5 11.2 + - + +
801A ARG* 3.3 19.4 + - - +
813A CYS* 4.5 2.5 - - + +
816A SER* 4.0 18.5 + - - +
817A ILE* 3.5 45.8 - - + +
820A LYS* 4.0 11.2 - - + -
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Residues in contact with LEU 798 (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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793A ASP* 3.5 3.0 + - - -
796A ALA* 3.7 29.2 - - + +
797A LEU* 1.3 78.8 - - - +
799A GLN* 1.3 59.5 + - - +
801A ARG* 3.3 36.7 + - - +
802A ALA* 2.9 27.8 + - - +
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Residues in contact with GLN 799 (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 GLN* 3.9 40.4 + - + +
793A ASP* 2.9 20.9 + - - +
798A LEU* 1.3 76.3 - - - +
800A VAL* 1.3 63.6 + - - +
802A ALA* 3.4 14.3 + - - +
803A ILE* 3.2 30.1 + - + +
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Residues in contact with VAL 800 (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 ILE* 3.8 50.5 - - + +
793A ASP* 2.9 18.0 + - + +
797A LEU* 3.7 18.6 - - + +
798A LEU 3.3 0.2 - - - -
799A GLN* 1.3 76.1 - - - +
801A ARG* 1.3 62.7 + - - +
803A ILE* 3.1 6.2 + - - +
804A LEU* 2.9 28.7 + - + +
816A SER* 3.6 35.9 - - - +
819A VAL* 4.4 6.7 - - + -
820A LYS* 5.0 0.7 - - + -
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Residues in contact with ARG 801 (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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401A LYS 4.9 10.3 + - - -
403A GLU* 5.8 2.4 + - - -
797A LEU 3.3 11.0 + - - +
798A LEU* 3.3 36.6 + - - +
800A VAL* 1.3 79.1 - - - +
802A ALA* 1.3 53.5 + - - +
804A LEU* 3.1 6.2 + - - +
805A GLN* 2.7 41.2 + - + +
811A SER* 4.1 21.8 - - - +
812A THR 6.1 1.8 - - - -
813A CYS* 6.2 2.2 - - - +
816A SER* 3.9 12.7 + - - +
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Residues in contact with ALA 802 (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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798A LEU 2.9 14.6 + - - +
799A GLN* 3.6 25.4 - - - +
800A VAL 3.3 0.2 - - - -
801A ARG* 1.3 74.6 - - - +
803A ILE* 1.3 61.9 + - + +
805A GLN* 3.4 11.4 + - - +
806A HIS* 3.1 21.7 + - - +
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Residues in contact with ILE 803 (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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782A PHE* 5.0 2.2 - - + -
786A PHE* 3.8 41.5 - - + -
789A GLN* 3.4 33.7 - - + +
790A ILE* 3.7 33.7 - - + +
799A GLN* 3.2 21.1 + - - +
800A VAL* 3.1 7.0 + - - +
802A ALA* 1.3 74.7 - - - +
804A LEU* 1.3 70.1 + - + +
806A HIS* 3.0 18.5 + - - +
807A LEU* 3.1 21.0 + - + +
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Residues in contact with LEU 804 (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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758A LEU* 5.1 5.2 - - + -
768A PHE* 3.9 15.9 - - + -
782A PHE* 5.4 1.8 - - + -
790A ILE* 5.8 0.4 - - + -
800A VAL* 2.9 21.6 + - + +
801A ARG* 3.7 5.4 - - - +
803A ILE* 1.3 80.6 - - + +
805A GLN* 1.3 57.1 + - - +
807A LEU* 2.7 33.5 - - + +
809A LEU* 3.0 33.6 + - + +
811A SER* 3.8 33.0 - - - +
816A SER* 4.0 21.1 - - - +
819A VAL* 4.0 27.8 - - + -
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Residues in contact with GLN 805 (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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801A ARG* 2.7 27.2 + - + +
802A ALA* 3.5 11.1 - - - +
804A LEU* 1.3 70.4 - - - +
806A HIS* 1.3 68.4 + - - +
808A GLY* 2.8 21.2 - - - -
809A LEU 4.4 8.7 + - - +
811A SER* 5.3 0.4 + - - -
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Residues in contact with HIS 806 (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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775A ARG* 2.8 50.4 + - - -
781A ILE* 5.2 7.4 + - + +
783A GLU* 4.9 6.1 + - - -
786A PHE* 3.9 28.8 - + - -
802A ALA 3.1 10.5 + - - +
803A ILE* 3.0 14.1 + - - +
805A GLN* 1.3 78.7 - - - +
807A LEU* 1.3 67.3 + - + +
808A GLY* 3.5 2.8 + - - -
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Residues in contact with LEU 807 (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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773A SER* 3.5 3.8 - - - -
775A ARG* 3.7 11.2 - - + -
776A LEU* 4.3 17.0 - - + +
781A ILE* 3.3 48.9 - - + +
782A PHE* 4.1 29.6 - - + -
786A PHE* 4.7 1.6 - - + -
803A ILE* 3.1 24.0 + - + +
804A LEU* 2.7 10.0 - - + +
805A GLN 3.1 0.6 - - - -
806A HIS* 1.3 86.3 - - + +
808A GLY* 1.3 69.3 + - - +
809A LEU* 2.6 25.2 + - + +
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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