Contacts of the helix formed by residues 718 - 733 (chain F) in PDB entry 5G04
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 LYS 718 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689F LEU* 4.2 13.5 - - - +
713F LEU* 3.4 33.1 + - + +
716F ASN* 3.2 24.0 - - - +
717F GLU* 1.3 71.7 - - - +
719F TYR* 1.3 63.1 + - - +
720F LYS 3.4 2.7 - - - -
721F SER* 3.4 16.7 + - - +
722F ALA* 3.1 22.2 + - - +
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Residues in contact with TYR 719 (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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714F PHE* 3.9 20.8 + + - -
717F GLU* 2.7 68.5 + - + -
718F LYS* 1.3 70.1 - - - +
720F LYS* 1.3 60.1 + - - +
722F ALA* 3.6 6.0 - - - +
723F LEU* 3.0 36.6 + - - +
746F VAL* 4.0 20.8 - - + +
749F LYS* 3.4 49.7 - - + +
750F LEU* 4.0 30.3 - - + -
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Residues in contact with LYS 720 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718F LYS 3.4 0.4 - - - -
719F TYR* 1.3 78.1 - - - +
721F SER* 1.3 61.4 + - - +
723F LEU* 3.6 8.8 + - + +
724F GLN* 3.2 43.9 + - - +
750F LEU* 5.7 1.0 - - - +
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Residues in contact with SER 721 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709F ARG* 5.4 2.9 + - - -
713F LEU* 3.8 21.2 - - - +
718F LYS* 3.4 25.4 + - - +
719F TYR 3.4 0.2 - - - -
720F LYS* 1.3 76.6 - - - +
722F ALA* 1.3 61.3 + - - +
724F GLN* 3.4 10.0 + - - +
725F GLU* 3.2 23.7 + - - +
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Residues in contact with ALA 722 (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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710F ALA* 4.0 24.0 - - - +
713F LEU* 4.3 11.2 - - + +
714F PHE* 4.4 8.3 - - - +
718F LYS 3.1 14.5 + - - +
719F TYR* 3.6 8.5 - - - +
720F LYS 3.3 0.2 - - - -
721F SER* 1.3 75.5 - - - +
723F LEU* 1.3 66.6 + - - +
725F GLU* 3.2 5.9 + - - +
726F LEU* 3.0 28.2 + - + +
746F VAL* 4.7 13.5 - - + -
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Residues in contact with LEU 723 (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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719F TYR 3.0 19.4 + - - +
720F LYS* 4.0 7.4 - - + +
722F ALA* 1.3 74.7 - - - +
724F GLN* 1.3 62.9 + - - +
726F LEU* 3.2 5.2 + - + +
727F GLU* 3.0 43.5 + - + +
743F ILE* 3.8 25.1 - - + -
746F VAL* 3.8 22.9 - - + -
747F TYR* 3.6 39.5 - - + +
750F LEU* 3.8 16.4 - - + -
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Residues in contact with GLN 724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720F LYS* 3.2 32.5 + - - +
721F SER* 3.4 13.0 - - - +
722F ALA 3.3 0.2 - - - -
723F LEU* 1.3 78.9 - - - +
725F GLU* 1.3 59.0 + - + +
727F GLU* 3.6 12.6 + - - +
728F GLU* 3.0 34.6 + - - +
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Residues in contact with GLU 725 (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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696F ILE* 3.4 17.0 - - - +
706F LYS* 4.3 15.8 - - + +
709F ARG* 3.2 60.7 + - - +
710F ALA* 3.6 8.4 + - + -
713F LEU* 3.5 16.3 - - + +
721F SER 3.2 9.3 + - - +
722F ALA 3.2 8.7 + - - +
724F GLN* 1.3 77.7 - - + +
726F LEU* 1.3 58.6 + - - +
727F GLU 3.3 0.4 - - - -
728F GLU* 3.3 16.8 + - - +
729F LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 726 (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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707F PHE* 4.5 10.8 - - + -
710F ALA* 3.7 14.8 - - + -
722F ALA* 3.0 24.0 + - + +
723F LEU* 3.2 7.8 + - - +
725F GLU* 1.3 73.2 - - - +
727F GLU* 1.3 60.2 + - + +
729F LEU* 3.2 10.2 + - + +
730F LYS* 2.9 28.1 + - - +
739F VAL* 4.0 19.4 - - + +
742F LEU* 3.7 36.1 - - + -
743F ILE* 3.7 36.3 - - + +
746F VAL* 3.8 18.4 - - + -
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Residues in contact with GLU 727 (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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723F LEU* 3.0 39.7 + - + +
724F GLN* 3.6 11.7 - - - +
726F LEU* 1.3 78.6 - - + +
728F GLU* 1.3 59.3 + - - +
730F LYS* 3.3 38.2 - - - +
731F GLN* 3.3 13.9 + - - +
743F ILE* 5.7 3.6 - - + -
747F TYR* 4.4 11.4 + - - -
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Residues in contact with GLU 728 (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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706F LYS* 4.8 17.5 + - + +
724F GLN* 3.0 29.5 + - - +
725F GLU* 3.3 16.9 + - - +
727F GLU* 1.3 73.1 - - + +
729F LEU* 1.3 65.4 + - - +
731F GLN* 3.3 14.5 + - - +
732F ILE* 3.1 28.6 + - + +
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Residues in contact with LEU 729 (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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703F PRO* 3.4 33.4 - - + +
706F LYS* 4.0 11.8 - - + +
707F PHE* 3.4 42.8 - - + +
725F GLU 3.0 12.3 + - - +
726F LEU* 3.2 15.5 - - + +
728F GLU* 1.3 74.5 - - - +
730F LYS* 1.3 52.7 + - - +
732F ILE* 3.1 8.9 + - + +
733F VAL* 2.6 45.2 + - + +
739F VAL* 3.4 29.6 - - + -
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Residues in contact with LYS 730 (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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726F LEU 2.9 12.6 + - - +
727F GLU* 3.3 30.0 - - - +
729F LEU* 1.3 72.0 - - - +
731F GLN* 1.3 61.4 + - + +
733F VAL 4.2 5.6 - - - +
734F PRO* 3.1 30.4 - - + +
739F VAL* 4.3 7.8 - - + +
740F TYR* 3.5 38.2 - - + +
743F ILE* 3.8 25.5 - - - +
759F ASN* 5.7 1.6 + - - +
762F TRP* 4.8 11.1 - - + -
145J ASN* 5.4 1.4 - - - +
147J THR* 5.7 6.5 - - + -
365J LYS* 5.6 9.7 - - - +
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Residues in contact with GLN 731 (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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727F GLU 3.3 11.2 + - - +
728F GLU* 3.3 15.4 + - - +
730F LYS* 1.3 77.5 - - + +
732F ILE* 1.3 63.6 + - + +
734F PRO* 4.4 3.5 - - - +
143J LEU* 6.0 1.9 - - - +
145J ASN* 3.2 34.3 + - - +
147J THR* 3.3 28.7 + - - +
148J LEU* 3.8 32.1 - - + +
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Residues in contact with ILE 732 (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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701F LYS* 3.7 41.3 - - + +
703F PRO* 4.2 10.0 - - + +
706F LYS* 3.8 36.1 - - + +
728F GLU* 3.1 18.7 + - + +
729F LEU* 3.1 9.2 + - + +
731F GLN* 1.3 79.5 - - + +
733F VAL* 1.3 70.9 + - + +
734F PRO* 3.8 4.8 - - - +
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Residues in contact with VAL 733 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703F PRO* 3.4 38.1 - - + -
729F LEU* 2.6 25.0 + - + +
730F LYS* 3.3 7.8 - - - +
732F ILE* 1.3 81.2 - - + +
734F PRO* 1.3 67.7 - - + +
735F LYS 4.7 0.9 - - - +
736F GLU* 3.5 38.1 + - + +
739F VAL* 4.2 10.8 - - + +
740F TYR* 5.8 0.2 - - - -
492R SER* 5.3 13.0 - - - -
493R LEU* 6.0 2.0 - - + +
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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
------------------------------------------------------------
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