Contacts of the helix formed by residues 718 - 727 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695H THR* 5.2 7.7 + - - -
699H ILE* 5.7 0.2 - - - +
716H GLY 3.7 2.0 - - - -
717H CYS* 1.3 78.9 - - - +
719H LYS* 1.3 59.1 + - - +
721H SER* 3.7 18.2 - - - -
722H LEU* 2.9 31.3 + - - +
903H MET* 4.5 7.0 - - - +
906H GLY* 5.0 2.7 - - - -
2501H ADP 3.2 16.4 + - - -
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Residues in contact with LYS 719 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711H ILE* 3.9 18.5 - - + +
712H VAL* 4.0 21.1 - - - -
713H GLY* 3.4 23.6 + - - +
714H GLN 4.0 3.8 - - - -
717H CYS* 4.2 10.8 - - + +
718H GLY* 1.3 72.8 - - - +
720H SER* 1.3 61.1 + - - +
721H SER 3.1 0.4 - - - -
722H LEU* 3.3 6.4 + - - +
723H LEU* 2.9 29.8 + - - +
854H ASP* 5.2 0.2 - - - -
887H VAL* 3.6 34.3 - - + +
888H THR* 4.6 7.3 + - - +
889H HIS* 4.5 12.1 + - - -
903H MET* 4.4 7.0 - - + -
1513H ASP* 4.1 8.9 + - - -
2501H ADP 2.6 39.3 + - - +
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Residues in contact with SER 720 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719H LYS* 1.3 76.9 - - - +
721H SER* 1.3 57.3 + - - +
723H LEU* 3.2 5.7 + - - +
724H LEU* 2.9 37.5 + - - +
775H GLN* 2.9 8.2 + - - -
854H ASP* 3.0 28.1 + - - -
2501H ADP 3.2 12.4 + - - -
2503H MG 2.4 30.4 - - - -
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Residues in contact with SER 721 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688H TRP* 3.7 21.4 - - - -
695H THR* 5.7 4.3 - - - -
696H LEU* 6.1 3.4 - - - -
718H GLY* 3.7 14.5 - - - -
719H LYS 3.1 0.6 - - - -
720H SER* 1.3 76.1 - - - +
722H LEU* 1.3 59.8 + - - +
724H LEU* 3.2 4.3 + - - +
725H ALA* 2.9 30.3 + - - +
730H MET* 4.3 5.4 - - - +
2501H ADP 3.5 39.2 + - - -
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Residues in contact with LEU 722 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681H ILE* 4.2 13.2 - - + -
696H LEU* 6.0 4.5 - - + -
699H ILE* 4.3 27.6 - - + -
701H ILE* 4.9 12.6 - - + -
711H ILE* 4.0 30.3 - - + -
718H GLY 2.9 20.4 + - - +
719H LYS 3.6 3.4 - - - +
721H SER* 1.3 75.7 - - - +
723H LEU* 1.3 50.3 + - + +
725H ALA* 4.6 5.4 - - + -
726H THR* 2.7 59.5 + - + +
732H LYS* 5.6 1.6 - - - +
901H ILE* 4.9 7.2 - - + -
903H MET* 4.4 21.8 - - - -
908H ILE* 5.8 0.7 - - + -
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Residues in contact with LEU 723 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711H ILE* 4.3 6.3 - - + -
719H LYS 2.9 11.1 + - - +
720H SER* 3.3 10.3 - - - +
721H SER 3.2 0.4 - - - -
722H LEU* 1.3 78.1 - - + +
724H LEU* 1.3 60.2 + - + +
726H THR* 2.5 16.9 + - + -
727H LEU* 3.2 18.4 + - - +
772H TYR* 3.6 27.4 - - + -
852H PHE* 3.5 38.9 - - + -
853H LEU 4.5 1.6 - - - -
854H ASP* 3.7 30.3 - - + +
885H VAL* 4.2 9.4 - - + +
887H VAL* 3.7 26.2 - - + -
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Residues in contact with LEU 724 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404H THR* 5.8 2.2 - - + +
688H TRP* 4.5 16.2 - - + -
720H SER* 2.9 23.5 + - - +
721H SER* 3.2 5.3 + - - +
723H LEU* 1.3 77.2 - - + +
725H ALA* 1.3 65.8 + - - +
727H LEU* 3.0 30.7 + - + +
729H GLU* 3.4 22.4 + - + +
730H MET* 3.8 8.1 + - + -
772H TYR* 3.4 33.7 - - + +
854H ASP* 5.5 0.4 - - - +
1212H THR* 4.3 22.9 - - + -
1480H GLU* 4.3 17.9 - - - +
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Residues in contact with ALA 725 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696H LEU* 4.1 10.1 - - + -
721H SER 2.9 17.7 + - - +
722H LEU* 4.0 5.2 - - + +
724H LEU* 1.3 72.2 - - - +
726H THR* 1.3 65.8 + - - +
727H LEU 3.0 1.3 - - - -
728H GLY* 2.9 15.1 + - - -
730H MET* 3.7 35.5 - - + +
732H LYS* 3.9 26.7 - - - -
737H VAL* 4.9 4.9 - - - +
739H TRP* 4.8 2.1 - - - -
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Residues in contact with THR 726 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679H VAL* 4.9 12.6 - - + +
681H ILE* 3.5 31.4 - - + +
701H ILE* 5.5 1.6 - - + -
703H ILE* 5.5 5.8 - - + -
722H LEU* 2.7 29.9 + - + +
723H LEU* 2.5 28.1 + - - -
725H ALA* 1.3 74.7 - - - +
727H LEU* 1.3 54.6 + - - +
728H GLY 3.1 0.2 - - - -
737H VAL* 4.8 2.9 - - - -
739H TRP* 3.0 31.5 - - - -
852H PHE* 3.9 24.7 - - + -
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Residues in contact with LEU 727 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723H LEU 3.2 11.2 + - - +
724H LEU* 3.0 31.8 + - + +
725H ALA 3.0 1.4 - - - -
726H THR* 1.3 75.5 - - - +
728H GLY* 1.3 55.5 + - - +
729H GLU* 3.0 15.0 + - + +
739H TRP* 4.2 4.3 - - - -
770H VAL* 3.7 30.4 - - + +
772H TYR* 3.9 21.3 - - + -
852H PHE* 3.8 26.2 - - + -
1212H THR* 4.5 5.2 - - - +
1215H ARG 5.3 3.8 - - - +
1216H ALA* 3.6 28.4 - - + -
1218H ARG* 4.1 15.1 + - - -
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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