Contacts of the helix formed by residues 724 - 742 (chain C) in PDB entry 1P93
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 SER 724 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C TYR* 2.7 34.2 + - - -
720C LYS 3.7 12.0 + - - -
721C LEU* 2.8 22.2 + - - -
723C ASP* 1.3 76.8 - - - +
725C MET* 1.3 54.3 + - - +
726C HIS 3.1 6.4 + - - -
727C GLU* 3.2 18.7 + - - +
728C VAL* 3.1 29.1 + - - +
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Residues in contact with MET 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C SER* 3.5 35.2 - - - +
605C ALA* 4.0 17.5 - - + -
606C PHE* 4.5 13.7 - - + -
648C TYR* 5.4 0.2 - - - -
649C VAL* 4.2 17.9 - - + -
670C LEU* 3.4 25.8 - - + -
673C SER* 5.4 0.4 - - - +
721C LEU* 3.8 19.5 - - - +
722C LEU* 3.5 17.7 - - + +
723C ASP 3.2 0.6 - - - -
724C SER* 1.3 75.9 - - - +
726C HIS* 1.3 63.4 + - + +
728C VAL* 3.9 20.6 - - + -
729C VAL* 2.8 37.7 + - + +
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Residues in contact with HIS 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C TYR* 3.1 31.2 + + - -
602C SER* 5.8 1.1 - - - -
673C SER* 2.9 48.0 + - - -
674C SER* 3.2 8.9 + - - -
722C LEU 4.8 4.3 - - - -
723C ASP* 3.5 19.4 + - - +
724C SER 3.1 0.6 - - - -
725C MET* 1.3 80.3 - - + +
727C GLU* 1.3 64.2 + - + +
729C VAL* 5.9 0.2 - - + -
730C GLU* 3.3 20.6 + - - +
771C LYS* 3.5 34.9 + - + +
772C LEU 3.0 28.5 + - - -
773C LEU* 5.5 1.4 - - - +
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Residues in contact with GLU 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ASP 4.4 8.3 - - - +
724C SER* 3.2 20.7 + - - +
726C HIS* 1.3 73.7 - - + +
728C VAL* 1.3 65.3 + - + +
730C GLU* 2.7 37.9 - - - +
731C ASN* 3.3 10.8 + - - +
771C LYS* 5.0 4.0 - - - +
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Residues in contact with VAL 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C ALA* 5.1 0.4 - - + -
645C HIS* 4.4 16.4 - - + +
646C MET* 6.1 0.2 - - - -
648C TYR* 3.9 33.0 - - + -
649C VAL* 5.0 3.8 - - + -
724C SER* 3.1 20.6 + - - +
725C MET* 3.7 26.5 - - + +
727C GLU* 1.3 77.6 - - + +
729C VAL* 1.3 59.2 + - + +
730C GLU 2.6 12.6 + - - -
731C ASN* 2.7 23.7 + - - +
732C LEU* 3.3 28.3 + - + +
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Residues in contact with VAL 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C TYR* 4.3 24.2 - - + +
601C MET* 3.9 18.4 - - + +
602C SER* 3.5 39.3 - - - +
725C MET* 2.8 31.3 + - + +
726C HIS* 4.3 2.7 - - + +
728C VAL* 1.3 80.6 - - + +
730C GLU* 1.3 60.9 + - - +
732C LEU* 3.4 8.9 + - - +
733C LEU* 3.1 43.8 + - + +
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Residues in contact with GLU 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C TYR* 5.6 0.2 + - - -
726C HIS 3.3 12.8 + - - +
727C GLU* 2.7 28.9 + - - +
728C VAL 2.6 4.4 + - - -
729C VAL* 1.3 77.2 - - - +
731C ASN* 1.3 62.1 + - - +
733C LEU* 3.7 5.9 - - - +
734C ASN* 2.7 53.0 + - - +
764C TYR* 5.2 0.8 + - - -
771C LYS* 5.0 8.1 + - - +
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Residues in contact with ASN 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C HIS* 3.3 46.0 + - + +
727C GLU* 3.9 11.4 + - - +
728C VAL* 2.7 13.2 + - - +
730C GLU* 1.3 90.7 + - - +
732C LEU* 1.3 61.9 + - - +
734C ASN* 3.4 8.5 + - - +
735C TYR* 3.1 27.6 + - - +
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Residues in contact with LEU 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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601C MET* 4.1 20.2 - - + -
605C ALA* 4.3 19.7 - - + -
642C GLN 4.3 2.0 - - - +
645C HIS* 4.1 19.1 - - + +
646C MET* 3.9 25.1 - - + -
728C VAL* 3.3 28.3 + - + +
729C VAL* 3.9 8.5 - - - +
731C ASN* 1.3 75.3 - - - +
733C LEU* 1.3 52.0 + - - +
735C TYR* 4.5 3.6 - - - -
736C CYS* 2.6 37.3 + - - +
3999C DEX 3.5 42.6 - - + +
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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
----------------------------------------------------------
598C TYR* 5.1 11.7 - - + +
600C TRP* 4.6 13.9 - - + +
601C MET* 4.4 13.9 - - + -
729C VAL* 3.1 40.2 + - + +
730C GLU* 3.7 5.2 - - - +
731C ASN 3.1 0.2 - - - -
732C LEU* 1.3 76.7 - - - +
734C ASN* 1.3 56.2 + - - +
735C TYR 2.9 5.6 - - - -
736C CYS* 3.5 12.6 - - - -
737C PHE* 2.6 36.4 + - - +
760C GLN* 5.9 4.0 - - + -
761C ILE* 3.1 31.9 - - + -
764C TYR* 3.8 30.7 - - + +
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Residues in contact with ASN 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730C GLU* 2.7 47.5 + - - +
731C ASN* 3.4 9.1 + - - +
733C LEU* 1.3 76.1 - - - +
735C TYR* 1.3 57.0 + - - +
737C PHE* 4.4 3.1 - - - +
738C GLN* 2.9 27.8 + - - +
761C ILE* 5.7 2.1 - - - +
764C TYR* 4.2 12.2 + - - -
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Residues in contact with TYR 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C ASP* 3.8 19.2 + - - +
641C ASP* 3.3 44.9 - - + +
642C GLN* 3.6 38.4 - - + -
645C HIS* 5.3 7.6 - + + -
731C ASN 3.1 17.3 + - - +
732C LEU* 4.1 5.4 - - - +
733C LEU 2.9 0.4 - - - -
734C ASN* 1.3 78.9 - - - +
736C CYS* 1.3 59.8 + - - +
737C PHE 3.5 0.4 - - - -
738C GLN* 3.6 15.8 - - - +
739C THR* 3.2 31.9 + - + +
3999C DEX 3.2 5.6 - - + +
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Residues in contact with CYS 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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600C TRP* 4.8 1.6 - - - -
601C MET* 3.9 21.8 - - + -
732C LEU 2.6 24.6 + - - +
733C LEU* 3.2 13.2 + - - -
735C TYR* 1.3 77.5 - - - +
737C PHE* 1.3 64.5 + - - +
738C GLN 3.2 0.2 - - - -
739C THR* 3.0 16.3 + - - -
740C PHE* 3.3 9.7 + - - +
749C PHE* 3.9 1.8 - - - -
757C ILE* 3.7 27.6 - - - -
3999C DEX 3.2 26.2 - - + +
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Residues in contact with PHE 737 (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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733C LEU 2.6 16.6 + - - +
734C ASN* 5.0 2.2 - - - -
736C CYS* 1.3 73.0 - - - +
738C GLN* 1.3 64.7 + - - +
740C PHE* 3.2 20.6 + + - +
741C LEU* 2.9 53.9 + - + +
757C ILE* 2.9 39.9 - - + -
758C THR* 4.2 2.2 - - - -
761C ILE* 3.0 40.8 - - + -
762C PRO* 3.1 38.4 - - + -
765C SER* 5.8 0.2 - - - -
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Residues in contact with GLN 738 (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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734C ASN 2.9 25.7 + - - +
735C TYR* 3.6 23.7 - - - +
736C CYS 3.2 0.2 - - - -
737C PHE* 1.3 77.6 - - - +
739C THR* 1.3 56.4 + - + +
741C LEU* 2.8 35.2 + - + +
742C ASP* 2.9 18.5 + - - +
745C MET* 5.5 1.3 - - - -
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Residues in contact with THR 739 (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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560C MET* 5.6 0.9 - - + -
642C GLN* 5.2 0.7 - - - +
735C TYR* 3.2 31.2 - - + +
736C CYS 3.0 14.7 + - - -
738C GLN* 1.3 80.0 - - + +
740C PHE* 1.3 59.3 + - - +
742C ASP 3.5 12.9 - - - +
745C MET* 4.3 21.5 - - - +
747C ILE* 4.2 26.1 - - + +
749C PHE* 3.4 13.1 - - - -
3999C DEX 2.5 32.8 + - - +
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Residues in contact with PHE 740 (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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736C CYS 3.3 10.5 + - - +
737C PHE* 3.2 32.9 + + - +
738C GLN 3.0 0.6 - - - -
739C THR* 1.3 78.8 + - - +
741C LEU* 1.3 73.4 + - + +
742C ASP 4.9 0.9 - - - -
743C LYS* 5.7 0.5 - - - -
749C PHE* 3.4 36.9 - + + -
753C LEU 4.6 0.4 - - - -
754C ALA* 3.9 29.8 - - + -
757C ILE* 4.0 12.6 - - + -
758C THR* 3.7 24.5 - - - -
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Residues in contact with LEU 741 (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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737C PHE* 2.9 58.2 + - + +
738C GLN* 2.8 16.7 + - + +
740C PHE* 1.3 86.2 - - + +
742C ASP* 1.3 65.8 + - + +
743C LYS* 3.2 7.3 + - - +
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Residues in contact with ASP 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738C GLN 2.9 11.0 + - - +
739C THR 3.5 8.6 - - - +
740C PHE 4.9 0.4 - - - -
741C LEU* 1.3 74.6 - - + +
743C LYS* 1.3 58.3 + - - +
744C THR* 2.8 41.0 + - - +
745C MET* 2.7 56.8 - - + +
747C ILE 5.5 0.5 - - - +
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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
------------------------------------------------------------
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