Contacts of the helix formed by residues 738 - 746 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737G LEU* 1.3 73.4 - - - +
739G GLN* 1.3 57.2 + - - +
741G PHE* 3.2 3.3 + - - +
742G ARG* 2.9 32.0 + - - +
759G ASP 5.6 0.2 - - - +
760G GLY* 3.4 29.8 - - - +
761G LYS* 3.6 30.1 - - + -
764G CYS* 3.4 27.3 - - + -
765G GLU* 6.1 0.9 - - + -
780G VAL* 4.0 10.3 - - + -
781G GLY 3.2 28.3 - - - -
782G GLN 3.2 14.8 - - - -
783G SER* 3.2 31.7 + - - -
784G LYS* 3.6 5.1 - - - -
785G ILE* 3.4 26.0 - - + -
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Residues in contact with GLN 739 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737G LEU* 3.4 7.9 - - + +
738G PHE* 1.3 79.7 - - - +
740G GLU* 1.3 64.9 + - + +
742G ARG* 3.4 11.7 + - - +
743G GLN* 2.9 57.5 + - - +
760G GLY* 5.4 8.9 - - - -
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Residues in contact with GLU 740 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736G ILE* 3.8 29.7 - - + +
737G LEU* 3.6 32.0 + - + +
738G PHE 3.3 0.4 - - - -
739G GLN* 1.3 78.6 - - + +
741G PHE* 1.3 57.5 + - - +
743G GLN* 4.9 2.7 - - - -
744G ARG* 2.9 46.1 + - + +
745G TYR* 5.6 0.4 - - - -
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Residues in contact with PHE 741 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736G ILE* 3.8 12.1 - - + +
737G LEU 3.1 18.2 + - - +
738G PHE 3.2 3.8 + - - +
740G GLU* 1.3 79.0 - - - +
742G ARG* 1.3 61.5 + - - +
745G TYR* 3.1 53.1 + + + +
748G LEU* 5.4 0.4 - - + -
764G CYS* 3.4 25.6 - - - -
767G MET* 3.4 39.8 - - + +
768G ILE* 4.0 23.3 - - + -
771G LEU* 4.8 3.6 - - + -
785G ILE* 5.8 2.0 - - + -
787G PHE* 4.1 23.3 - + + -
792G LEU* 4.4 6.3 - - + -
795G LEU* 4.0 24.9 - - + -
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Residues in contact with ARG 742 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738G PHE 2.9 16.3 + - - +
739G GLN* 3.9 12.6 - - - +
741G PHE* 1.3 75.4 - - + +
743G GLN* 1.3 68.1 + - - +
746G GLU* 2.9 44.4 + - + +
753G ILE* 4.3 21.0 - - + +
754G PRO* 4.7 5.5 + - - +
756G GLY* 3.7 28.1 - - - -
757G PHE 4.5 0.8 - - - +
758G MET* 3.6 33.2 + - - +
760G GLY* 3.9 14.4 - - - +
762G GLN* 6.0 0.2 - - - +
763G ALA* 3.3 39.6 - - + +
764G CYS* 5.3 0.4 - - - -
767G MET* 4.0 14.8 - - - -
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Residues in contact with GLN 743 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739G GLN* 2.9 43.1 + - - +
740G GLU* 4.3 2.7 - - - +
742G ARG* 1.3 77.3 - - - +
744G ARG* 1.3 70.1 + - + +
746G GLU* 4.1 13.6 + - - +
747G ILE* 6.1 0.2 - - - +
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Residues in contact with ARG 744 (chain G).
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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103G LYS* 3.6 39.0 - - - +
740G GLU* 2.9 34.2 + - + +
743G GLN* 1.3 83.2 - - + +
745G TYR* 1.3 75.2 + - + +
746G GLU 3.6 0.5 + - - -
747G ILE* 4.6 8.7 + - - +
799G ARG* 4.2 26.3 + - - +
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Residues in contact with TYR 745 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G LYS* 3.2 28.6 + - - +
104G PHE* 4.7 11.3 - - - -
736G ILE* 5.6 8.1 - - + +
740G GLU 5.6 0.2 - - - -
741G PHE* 3.1 45.1 + + + +
742G ARG 3.8 0.4 - - - -
744G ARG* 1.3 80.2 - - + +
746G GLU* 1.3 53.2 + - - +
747G ILE* 3.0 4.3 - - - -
748G LEU* 2.7 57.3 + - + +
767G MET* 4.0 8.3 - - + +
792G LEU* 4.6 18.0 - - + +
795G LEU* 5.1 4.7 - - + -
796G GLU* 3.3 33.0 + - - +
799G ARG* 3.7 23.3 - - + +
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Residues in contact with GLU 746 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742G ARG* 2.9 31.1 + - + +
743G GLN* 4.2 13.2 - - - +
744G ARG 3.4 2.2 - - - -
745G TYR* 1.3 74.4 - - - +
747G ILE* 1.3 64.6 + - + +
748G LEU 3.1 0.9 + - - -
749G THR 3.4 13.3 + - - +
750G PRO* 4.3 2.6 - - - +
753G ILE* 3.6 43.6 - - + +
767G MET* 4.3 0.4 - - - -
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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