Contacts of the helix formed by residues 783 - 792 (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 GLU 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780A GLY 4.4 9.2 - - - +
781A ILE* 4.0 11.3 - - - +
782A PHE* 1.3 77.1 - - - +
784A THR* 1.3 61.8 + - - +
785A LYS* 3.1 37.0 + - + +
786A PHE* 2.9 48.4 + - + +
787A LEU* 4.0 1.2 + - - +
806A HIS* 4.9 5.9 + - - -
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Residues in contact with THR 784 (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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747A GLY 2.6 32.5 + - - +
748A MET* 3.5 8.0 + - - +
750A LEU* 3.7 11.6 - - + +
751A GLY 3.1 18.3 + - - +
782A PHE 3.7 0.8 + - - -
783A GLU* 1.3 72.4 - - - +
785A LYS* 1.3 62.1 + - - +
787A LEU* 3.1 27.3 + - + +
788A SER* 3.8 4.7 + - - -
864A LEU* 4.0 30.4 - - + +
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Residues in contact with LYS 785 (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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783A GLU* 3.1 31.6 + - + +
784A THR* 1.3 77.5 - - - +
786A PHE* 1.3 76.7 + - + +
788A SER* 3.1 10.5 + - - +
789A GLN* 3.1 45.4 + - + +
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Residues in contact with PHE 786 (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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781A ILE 3.8 12.8 - - - -
782A PHE* 3.2 41.7 - + + -
783A GLU* 2.9 33.1 + - - +
785A LYS* 1.3 100.0 - - + +
787A LEU* 1.3 51.2 + - - +
789A GLN* 3.7 20.9 - - - -
790A ILE* 2.7 46.3 + - + +
803A ILE* 3.8 26.9 - - + -
806A HIS* 3.9 25.8 - + - -
807A LEU* 4.7 3.6 - - + -
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Residues in contact with LEU 787 (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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750A LEU* 4.4 13.9 - - + -
751A GLY* 3.8 21.8 - - - +
754A VAL* 3.7 30.3 - - + -
782A PHE* 4.1 11.9 - - + -
784A THR* 3.1 19.6 + - + +
786A PHE* 1.3 77.2 - - - +
788A SER* 1.3 61.8 + - - +
790A ILE* 4.2 0.5 - - - +
791A GLU* 3.1 28.1 + - - +
823A CYS* 3.9 36.9 - - + +
826A VAL* 4.3 11.0 - - + -
827A ALA* 4.3 12.8 - - + -
864A LEU* 6.0 0.9 - - + -
868A HIS* 4.2 13.2 + - + +
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Residues in contact with SER 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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784A THR 4.4 5.0 + - - -
785A LYS* 3.1 12.9 + - - -
787A LEU* 1.3 76.3 - - - +
789A GLN* 1.3 63.3 + - - +
792A SER* 2.7 33.5 + - - -
864A LEU* 4.4 5.2 - - - +
867A LEU* 3.8 23.3 + - - +
868A HIS* 3.4 26.5 + - - +
869A PRO* 3.8 11.0 - - - +
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Residues in contact with GLN 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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785A LYS* 3.1 41.6 + - + +
786A PHE* 3.7 13.4 - - - +
788A SER* 1.3 79.9 - - - +
790A ILE* 1.3 61.9 + - - +
791A GLU 3.5 0.2 + - - -
792A SER* 3.5 7.8 + - - -
793A ASP* 3.5 18.2 + - - +
799A GLN* 3.9 26.1 + - + +
803A ILE* 3.4 26.1 - - + +
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Residues in contact with ILE 790 (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* 3.7 28.7 - - + -
786A PHE* 2.7 26.4 + - + +
787A LEU 4.2 1.8 - - - +
789A GLN* 1.3 73.2 - - - +
791A GLU* 1.3 60.8 + - - +
793A ASP* 3.5 14.9 + - - +
800A VAL* 3.8 28.7 - - + +
803A ILE* 3.7 28.7 - - + -
804A LEU* 5.8 0.7 - - + -
819A VAL* 4.0 13.2 - - + -
820A LYS* 3.6 42.6 - - - +
823A CYS* 4.1 12.6 - - + -
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Residues in contact with GLU 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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787A LEU 3.1 18.2 + - - +
790A ILE* 1.3 75.2 - - - +
792A SER* 1.3 58.4 + - - +
793A ASP 3.2 5.6 + - - +
820A LYS* 4.1 17.4 + - + +
823A CYS* 3.6 10.3 - - + +
824A THR* 3.2 44.5 + - - +
827A ALA* 4.1 1.2 - - - +
868A HIS* 3.4 22.3 + - - +
869A PRO* 4.0 9.1 - - + +
870A HIS* 2.9 47.9 + - + +
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Residues in contact with SER 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* 2.7 22.4 + - - -
789A GLN* 4.0 6.3 - - - -
790A ILE 3.4 0.6 - - - -
791A GLU* 1.3 76.0 - - - +
793A ASP* 1.3 58.8 + - - +
794A CYS* 4.2 6.8 + - - -
867A LEU 5.2 1.0 + - - -
869A PRO* 3.4 24.4 - - - +
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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