Contacts of the helix formed by residues 725 - 736 (chain C) in PDB entry 5Y3R
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 LEU 725 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C MET* 3.4 34.8 - - + -
654C ILE* 6.0 1.3 - - + -
723C ASP* 3.0 14.3 + - + +
724C GLU* 1.3 84.9 - - + +
726C LEU* 1.3 71.6 + - + +
729C CYS* 3.2 16.3 + - - +
975C ASP* 3.9 24.5 - - - +
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Residues in contact with LEU 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C GLY* 5.2 1.3 - - - -
600C VAL* 3.9 31.6 - - + +
602C MET* 4.8 7.9 - - + -
652C GLU 5.4 3.6 - - - +
654C ILE* 3.7 32.1 - - + -
721C TYR* 4.7 2.0 - - + -
722C LYS* 3.6 31.0 - - + +
723C ASP* 3.0 23.3 + - + +
725C LEU* 1.3 87.6 - - + +
727C ALA* 1.3 72.1 + - - +
729C CYS* 2.8 17.8 - - - -
730C LEU* 2.9 18.1 + - + +
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Residues in contact with ALA 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C MET* 3.7 5.4 - - + +
719C LYS* 5.5 0.9 - - - -
722C LYS* 3.1 35.9 - - + +
723C ASP 2.2 25.3 + - - +
726C LEU* 1.3 65.7 - - - +
728C SER* 1.3 57.4 + - - +
730C LEU* 2.2 34.4 + - - -
731C THR* 2.6 31.8 + - + -
758C LEU* 5.4 3.1 - - + -
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Residues in contact with SER 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ASP 2.6 9.3 + - - -
724C GLU* 2.8 44.5 + - - +
726C LEU 3.0 0.4 + - - -
727C ALA* 1.3 69.5 - - - +
729C CYS* 1.3 61.2 + - - +
731C THR* 2.5 22.1 + - - -
732C PHE* 2.9 26.6 + - - -
758C LEU* 3.1 26.3 - - - +
763C THR* 6.5 1.3 - - - -
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Residues in contact with CYS 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C ILE* 3.4 34.1 - - + -
725C LEU 3.2 12.5 + - - +
726C LEU* 2.8 31.2 + - - -
727C ALA 2.8 0.4 + - - -
728C SER* 1.3 77.4 - - - +
730C LEU* 1.3 68.0 + - - +
732C PHE* 3.8 4.2 - - - +
733C LEU* 2.9 33.5 + - + +
768C VAL* 6.1 5.2 - - + -
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Residues in contact with LEU 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C PHE* 5.9 4.5 - - + -
652C GLU* 5.1 4.0 - - - +
653C LEU 3.5 8.5 - - - +
654C ILE* 3.2 42.8 - - + +
656C GLN* 5.6 1.8 - - + -
718C MET* 3.4 14.1 - - + -
722C LYS* 3.9 21.3 - - + -
726C LEU* 3.0 39.3 - - + +
727C ALA* 2.2 21.1 + - - +
729C CYS* 1.3 68.8 - - - +
731C THR* 1.3 56.7 + - - +
733C LEU* 2.7 38.2 + - + +
734C LEU* 2.9 14.5 + - + +
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Residues in contact with THR 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715C ALA 5.3 0.4 - - - +
718C MET* 3.1 34.7 - - + -
719C LYS* 4.9 4.3 - - + +
727C ALA* 2.6 36.2 + - + +
728C SER* 2.5 19.1 + - - -
730C LEU* 1.3 70.7 - - - +
732C PHE* 1.3 78.6 + - - -
734C LEU* 2.2 32.0 + - - -
735C SER* 2.7 7.9 + - - -
755C ALA* 6.0 5.4 - - - -
758C LEU* 4.5 3.5 - - + +
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Residues in contact with PHE 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728C SER* 2.9 26.3 + - - +
729C CYS* 3.8 3.6 - - - +
731C THR* 1.3 95.4 + - - +
733C LEU* 1.3 64.3 + - - +
735C SER* 2.8 27.4 + - - +
736C LEU* 4.1 6.6 + - - +
755C ALA* 3.6 26.9 - - + -
758C LEU* 3.5 32.3 - - + -
759C GLY* 3.6 21.1 - - - -
763C THR* 4.8 7.6 - - - -
768C VAL* 5.1 7.9 - - + -
769C GLY* 3.4 37.9 - - - -
770C LEU* 4.9 0.2 - - + -
772C ALA* 5.1 4.1 - - + +
773C LEU* 4.4 9.6 - - + -
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Residues in contact with LEU 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C ILE* 3.5 16.6 - - + +
657C SER* 3.2 20.2 + - - +
658C THR* 3.2 60.6 - - + +
661C PRO* 3.1 18.5 - - + +
662C LEU* 4.5 11.7 - - + -
729C CYS* 2.9 28.3 + - + +
730C LEU* 2.7 19.8 + - + +
732C PHE* 1.3 72.7 - - - +
734C LEU* 1.3 55.4 + - - +
736C LEU* 4.2 1.6 + - - +
737C PRO* 2.9 18.4 - - - +
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Residues in contact with LEU 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C PHE* 6.3 3.1 - - + -
657C SER* 3.2 31.9 - - - +
710C PHE* 6.2 1.3 - - + -
714C VAL* 3.5 32.5 - - + +
715C ALA* 6.0 0.2 - - - -
718C MET* 3.5 24.0 - - + -
730C LEU* 3.1 19.5 - - + +
731C THR* 2.2 31.2 + - - +
733C LEU* 1.3 65.1 - - - +
735C SER* 1.3 59.8 + - - +
737C PRO* 3.0 31.6 - - + +
738C HIS* 4.5 2.3 + - - -
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Residues in contact with SER 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C THR 2.7 9.3 + - - -
732C PHE* 2.8 24.3 + - - -
734C LEU* 1.3 71.9 - - - +
736C LEU* 1.3 57.6 + - - +
737C PRO 3.0 1.1 - - - -
738C HIS* 2.3 44.3 + - - +
755C ALA* 5.5 3.6 - - - -
756C PHE* 4.4 24.9 - - - -
772C ALA* 4.2 17.7 - - - +
773C LEU* 5.9 1.3 - - - +
776C TRP* 5.1 7.2 - - - -
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Residues in contact with LEU 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661C PRO* 4.0 9.2 - - + -
662C LEU* 3.5 36.1 - - + -
732C PHE 4.1 5.8 + - - +
733C LEU 4.4 1.8 - - - +
735C SER* 1.3 78.6 + - - +
737C PRO* 1.3 63.3 - - + +
738C HIS 2.8 5.1 - - - -
739C ASN* 2.1 67.2 + - + +
740C ILE* 3.0 8.2 + - + +
772C ALA* 4.7 10.8 - - + -
775C GLU* 3.7 30.1 - - + +
776C TRP* 5.4 6.3 - - + +
779C TYR* 6.5 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