Contacts of the helix formed by residues 738 - 746 (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 PHE 738 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737F LEU* 1.3 73.6 - - - +
739F GLN* 1.3 58.2 + - - +
741F PHE* 3.2 3.3 + - - +
742F ARG* 2.9 31.2 + - - +
759F ASP 5.6 0.2 - - - +
760F GLY* 3.4 26.2 - - - +
761F LYS* 3.6 29.6 - - + -
764F CYS* 3.4 31.8 - - + -
765F GLU* 6.1 0.9 - - + -
780F VAL* 4.0 10.8 - - + -
781F GLY 3.2 28.3 - - - -
782F GLN 3.2 13.9 - - - -
783F SER* 3.2 32.1 + - - -
784F LYS* 3.6 4.5 - - - -
785F ILE* 3.4 26.7 - - + -
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Residues in contact with GLN 739 (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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737F LEU* 3.4 8.2 - - + +
738F PHE* 1.3 79.4 - - - +
740F GLU* 1.3 60.2 + - + +
742F ARG* 3.8 11.2 - - - +
743F GLN* 2.9 63.3 + - - +
760F GLY* 5.5 8.7 - - - -
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Residues in contact with GLU 740 (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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736F ILE* 3.8 29.7 - - + +
737F LEU* 3.6 32.5 + - + +
738F PHE 3.3 0.4 - - - -
739F GLN* 1.3 79.3 - - + +
741F PHE* 1.3 58.0 + - - +
743F GLN* 4.9 2.7 - - - -
744F ARG* 2.9 46.0 + - + +
745F TYR* 5.2 0.4 - - - -
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Residues in contact with PHE 741 (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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736F ILE* 3.7 12.1 - - + +
737F LEU 3.1 17.4 + - - +
738F PHE 3.4 4.3 - - - +
740F GLU* 1.3 78.4 - - - +
742F ARG* 1.3 62.3 + - - +
745F TYR* 3.1 53.9 + + + +
748F LEU* 5.4 0.4 - - + -
764F CYS* 3.4 26.9 - - - -
767F MET* 3.4 40.1 - - + +
768F ILE* 4.0 23.1 - - + -
771F LEU* 4.8 3.6 - - + -
785F ILE* 5.8 1.8 - - + -
787F PHE* 4.2 21.5 - + + -
792F LEU* 4.4 6.3 - - + -
795F LEU* 4.0 24.5 - - + -
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Residues in contact with ARG 742 (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 2.9 15.9 + - - +
739F GLN* 3.9 13.0 - - - +
741F PHE* 1.3 74.7 - - + +
743F GLN* 1.3 67.5 + - - +
746F GLU* 2.9 44.5 + - + +
753F ILE* 4.3 20.4 - - + +
754F PRO* 4.7 5.5 + - - +
756F GLY* 3.7 27.7 - - - +
757F PHE 4.5 0.6 - - - +
758F MET* 3.5 33.5 + - - +
760F GLY* 3.9 14.5 - - - +
763F ALA* 3.3 38.3 - - + +
764F CYS* 5.3 0.4 - - - -
767F MET* 4.0 15.3 - - - -
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Residues in contact with GLN 743 (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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739F GLN* 2.9 44.4 + - - +
740F GLU* 4.3 3.1 - - - +
742F ARG* 1.3 77.3 - - - +
744F ARG* 1.3 69.6 + - + +
746F GLU* 4.1 13.7 + - - +
747F ILE* 6.1 0.2 - - - +
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Residues in contact with ARG 744 (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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103F LYS* 3.6 40.2 - - - +
740F GLU* 2.9 34.5 + - + +
743F GLN* 1.3 82.8 - - + +
745F TYR* 1.3 74.4 + - + +
746F GLU 3.6 0.7 + - - -
747F ILE* 4.6 8.8 + - - +
799F ARG* 4.2 25.5 + - - +
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Residues in contact with TYR 745 (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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103F LYS* 3.2 29.0 + - - +
104F PHE* 4.7 11.3 - - - -
736F ILE* 5.6 8.1 - - + +
740F GLU 5.6 0.2 - - - -
741F PHE* 3.1 44.7 + + + +
744F ARG* 1.3 80.4 - - + +
746F GLU* 1.3 52.1 + - - +
747F ILE 3.0 3.6 - - - -
748F LEU* 2.7 57.3 + - + +
767F MET* 4.0 9.5 - - + +
792F LEU* 4.6 19.0 - - + +
795F LEU* 5.0 4.0 - - + -
796F GLU* 3.3 34.1 + - - +
799F ARG* 3.7 23.6 - - + +
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Residues in contact with GLU 746 (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* 2.9 32.4 + - + +
743F GLN* 4.2 12.6 - - - +
744F ARG 3.4 2.2 + - - -
745F TYR* 1.3 74.4 - - - +
747F ILE* 1.3 64.6 + - + +
748F LEU 3.1 0.9 + - - -
749F THR 3.4 13.3 + - - +
750F PRO* 4.3 3.4 - - + +
753F ILE* 3.6 44.0 - - + +
767F MET* 4.3 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