Contacts of the helix formed by residues 760 - 771 (chain F) in PDB entry 5JLH
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 GLY 760 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738F PHE* 3.4 30.4 - - - +
739F GLN* 5.5 8.3 - - - -
742F ARG* 3.9 20.4 - - - +
758F MET* 2.9 9.1 + - - +
759F ASP* 1.3 75.2 - - - +
761F LYS* 1.3 61.0 + - - +
762F GLN 3.5 0.7 - - - -
763F ALA* 3.8 6.1 - - - +
764F CYS* 3.7 10.4 + - - -
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Residues in contact with LYS 761 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F PHE* 3.6 27.5 - - + -
759F ASP* 2.9 25.1 + - - +
760F GLY* 1.3 74.8 - - - +
762F GLN* 1.3 70.0 + - - +
763F ALA 3.1 1.3 - - - -
764F CYS* 3.0 6.9 + - - +
765F GLU* 2.9 38.6 + - + +
781F GLY 5.3 1.3 - - - -
782F GLN* 3.9 30.0 + - - +
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Residues in contact with GLN 762 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742F ARG* 6.0 0.2 - - - +
754F PRO* 5.8 2.0 - - + -
757F PHE* 4.9 22.8 - - + +
758F MET 3.4 12.4 + - - +
759F ASP* 3.3 35.8 + - - +
760F GLY 3.5 0.2 - - - -
761F LYS* 1.3 74.0 + - - +
763F ALA* 1.3 66.1 + - - +
765F GLU* 3.2 23.7 + - - +
766F LYS* 2.9 33.8 + - + +
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Residues in contact with ALA 763 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742F ARG* 3.3 58.5 - - + +
753F ILE* 4.8 3.3 - - + +
754F PRO* 5.1 7.4 - - - +
760F GLY 3.8 9.1 + - - +
761F LYS 3.1 0.4 - - - -
762F GLN* 1.3 78.6 - - - +
764F CYS* 1.3 59.1 + - - +
766F LYS* 3.1 8.7 + - - +
767F MET* 2.9 34.9 + - - +
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Residues in contact with CYS 764 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F PHE* 3.4 50.9 - - + -
741F PHE* 3.4 28.7 - - + -
742F ARG 4.9 0.7 - - - -
760F GLY 3.8 2.2 - - - -
761F LYS 3.0 8.5 + - - +
763F ALA* 1.3 78.8 - - - +
765F GLU* 1.3 66.6 + - - +
767F MET* 4.3 7.2 - - - -
768F ILE* 2.9 33.1 + - + +
785F ILE* 4.3 14.1 - - + -
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Residues in contact with GLU 765 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F PHE* 6.1 1.3 - - + -
761F LYS* 2.9 22.6 + - + +
762F GLN* 3.4 30.8 + - - +
764F CYS* 1.3 76.7 - - - +
766F LYS* 1.3 60.3 + - + +
768F ILE* 4.2 3.1 - - - +
769F GLN* 3.0 33.9 + - - +
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Residues in contact with LYS 766 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752F ALA* 3.3 39.7 + - + +
753F ILE* 4.5 0.9 - - - +
754F PRO* 3.9 34.2 - - + +
757F PHE* 4.0 15.0 - - - -
762F GLN* 2.9 21.9 + - + +
763F ALA 3.5 6.5 - - - +
765F GLU* 1.3 76.9 - - + +
767F MET* 1.3 65.1 + - - +
769F GLN* 3.2 7.1 + - + +
770F ALA* 2.9 22.0 + - - +
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Residues in contact with MET 767 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F PHE* 3.4 53.4 - - + +
742F ARG* 4.0 14.6 - - - -
745F TYR* 4.0 22.0 - - + +
748F LEU* 5.1 3.4 - - + -
749F THR* 3.8 17.7 - - + -
753F ILE* 3.5 39.5 - - + -
763F ALA* 2.9 25.6 + - - +
764F CYS* 3.8 1.1 - - - +
766F LYS* 1.3 77.3 - - - +
768F ILE* 1.3 63.9 + - - +
771F LEU* 3.0 35.6 + - + +
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Residues in contact with ILE 768 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F PHE* 4.0 18.2 - - + -
764F CYS* 2.9 24.9 + - + +
765F GLU* 4.2 2.2 - - - +
767F MET* 1.3 78.0 - - - +
769F GLN* 1.3 65.8 + - - +
771F LEU* 3.6 5.8 + - + +
772F GLU 3.4 12.8 + - - -
773F LEU* 3.9 17.7 + - + +
778F TYR* 3.4 49.8 - - + +
785F ILE* 5.4 4.5 - - + -
787F PHE* 3.8 34.5 - - + -
795F LEU* 4.9 6.3 - - + -
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Residues in contact with GLN 769 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765F GLU* 3.0 22.3 + - - +
766F LYS* 3.4 8.7 - - + +
768F ILE* 1.3 82.3 - - - +
770F ALA* 1.3 63.8 + - + +
772F GLU* 3.3 14.7 + - - +
778F TYR* 6.1 0.4 - - - -
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Residues in contact with ALA 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749F THR* 4.4 6.7 - - - +
751F ASN* 6.0 2.0 - - + -
752F ALA* 3.8 27.8 - - + +
766F LYS 2.9 10.5 + - - +
767F MET 4.5 0.2 - - - +
769F GLN* 1.3 69.4 - - - +
771F LEU* 1.3 62.2 + - + +
772F GLU* 3.0 11.7 + - - +
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Residues in contact with LEU 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F PHE* 4.8 2.9 - - + -
748F LEU* 4.3 17.9 - - + -
749F THR* 3.6 31.0 - - + +
767F MET* 3.0 35.8 + - + +
768F ILE* 4.0 7.9 - - + +
770F ALA* 1.3 76.5 - - + +
772F GLU* 1.3 73.8 + - - +
773F LEU* 4.6 4.3 - - + +
795F LEU* 3.4 42.8 - - + +
798F GLU* 6.3 2.5 - - + -
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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