Contacts of the helix formed by residues 718 - 727 (chain F) in PDB entry 5YWB
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 718 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695F THR* 5.2 7.3 + - - -
699F ILE* 5.7 0.5 - - - +
716F GLY 3.7 1.8 - - - -
717F CYS* 1.3 79.5 - - - +
719F LYS* 1.3 60.5 + - - +
720F SER 3.7 0.2 - - - -
721F SER* 3.7 18.6 - - - -
722F LEU* 2.9 30.3 + - - +
903F MET* 4.5 7.0 - - - +
906F GLY* 5.0 3.3 - - - -
2501F ADP 3.2 16.0 + - - -
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Residues in contact with LYS 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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711F ILE* 3.9 17.3 - - + +
712F VAL* 4.0 21.3 - - - -
713F GLY* 3.4 24.0 + - - +
714F GLN 4.0 3.8 + - - -
717F CYS* 4.2 10.8 - - + +
718F GLY* 1.3 72.2 - - - +
720F SER* 1.3 60.0 + - - +
721F SER 3.1 0.9 - - - -
722F LEU* 3.3 6.0 + - - +
723F LEU* 2.9 30.1 + - - +
854F ASP* 5.2 0.2 - - - -
887F VAL* 3.6 34.6 - - + +
888F THR* 4.6 7.7 + - - +
889F HIS* 4.5 12.3 + - - -
903F MET* 4.4 7.0 - - + -
1513F ASP* 4.1 9.1 + - - -
2501F ADP 2.6 38.5 + - - +
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Residues in contact with SER 720 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719F LYS* 1.3 78.7 - - - +
721F SER* 1.3 57.0 + - - +
723F LEU* 3.2 5.7 + - - +
724F LEU* 2.9 36.8 + - - +
775F GLN* 2.9 7.9 + - - -
854F ASP* 3.0 29.1 + - - -
2501F ADP 3.2 12.9 + - - -
2503F MG 2.4 30.3 - - - -
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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
----------------------------------------------------------
688F TRP* 3.7 22.5 + - - -
695F THR* 5.7 4.7 - - - -
696F LEU* 6.1 3.1 - - - -
718F GLY* 3.7 13.9 - - - -
719F LYS 3.1 0.8 - - - -
720F SER* 1.3 75.3 - - - +
722F LEU* 1.3 60.1 + - - +
724F LEU* 3.2 4.4 + - - +
725F ALA* 2.9 32.0 + - - +
730F MET* 4.3 5.8 - - - +
2501F ADP 3.5 39.2 + - - -
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Residues in contact with LEU 722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681F ILE* 4.2 12.8 - - + -
696F LEU* 6.0 4.9 - - + +
699F ILE* 4.3 28.0 - - + -
701F ILE* 4.9 12.8 - - + -
711F ILE* 4.0 29.4 - - + -
718F GLY 2.9 19.8 + - - +
719F LYS 3.6 3.6 - - - +
721F SER* 1.3 75.0 - - - +
723F LEU* 1.3 51.1 + - + +
725F ALA* 4.6 5.2 - - + +
726F THR* 2.7 60.0 + - + +
732F LYS* 5.6 1.3 - - - +
901F ILE* 4.9 7.9 - - + -
903F MET* 4.4 21.5 - - - -
908F ILE* 5.8 0.7 - - + -
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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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711F ILE* 4.3 6.1 - - + -
719F LYS 2.9 10.9 + - - +
720F SER* 3.3 11.0 - - - +
721F SER 3.2 0.2 - - - -
722F LEU* 1.3 78.1 - - + +
724F LEU* 1.3 60.2 + - + +
726F THR* 2.5 17.5 + - - +
727F LEU* 3.2 18.0 + - - +
772F TYR* 3.6 26.9 - - + -
852F PHE* 3.5 39.1 - - + -
853F LEU 4.5 2.2 - - - -
854F ASP* 3.7 31.2 - - + +
885F VAL* 4.2 9.2 - - + +
887F VAL* 3.7 26.0 - - + -
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Residues in contact with LEU 724 (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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404F THR* 5.8 2.2 - - + +
688F TRP* 4.5 16.2 - - + -
720F SER* 2.9 23.8 + - - +
721F SER* 3.2 5.1 + - - +
723F LEU* 1.3 76.4 - - + +
725F ALA* 1.3 66.6 + - - +
727F LEU* 3.0 31.0 + - + +
729F GLU* 3.4 22.3 + - + +
730F MET* 3.8 7.6 + - + -
772F TYR* 3.4 34.3 - - + +
854F ASP* 5.5 0.2 - - - +
1212F THR* 4.3 21.8 - - + -
1480F GLU* 4.3 17.5 - - - +
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Residues in contact with ALA 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 LEU* 4.1 10.1 - - + -
721F SER 2.9 17.4 + - - +
722F LEU* 4.0 5.2 - - + +
724F LEU* 1.3 73.8 - - - +
726F THR* 1.3 66.2 + - + +
727F LEU 3.0 1.3 - - - -
728F GLY* 2.9 14.6 + - - -
730F MET* 3.7 36.2 - - + +
732F LYS* 3.9 25.8 - - - -
737F VAL* 4.9 5.2 - - - +
739F TRP* 4.8 2.4 - - - -
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Residues in contact with THR 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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679F VAL* 4.9 12.9 - - + +
681F ILE* 3.5 32.0 - - + +
701F ILE* 5.5 1.8 - - + -
703F ILE* 5.5 5.6 - - + -
722F LEU* 2.7 29.4 + - + +
723F LEU* 2.5 28.5 + - - -
725F ALA* 1.3 73.2 - - - +
727F LEU* 1.3 55.9 + - - +
728F GLY 3.1 0.2 - - - -
737F VAL* 4.8 2.7 - - - -
739F TRP* 3.0 32.2 - - - -
852F PHE* 3.9 25.7 - - + -
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Residues in contact with LEU 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 3.2 10.3 + - - +
724F LEU* 3.0 31.2 + - + +
725F ALA 3.0 1.2 - - - -
726F THR* 1.3 75.1 - - - +
728F GLY* 1.3 55.6 + - - +
729F GLU* 3.0 16.1 + - + +
739F TRP* 4.2 4.3 - - - -
770F VAL* 3.7 30.8 - - + +
772F TYR* 3.9 21.3 - - + -
852F PHE* 3.8 27.4 - - + -
1212F THR* 4.5 5.2 - - - +
1215F ARG 5.3 3.6 - - - +
1216F ALA* 3.6 28.1 - - + -
1218F ARG* 4.1 14.9 + - - -
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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