Contacts of the helix formed by residues 725 - 737 (chain C) in PDB entry 1RR8
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 ASP 725 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444C TYR* 3.3 29.0 - - + +
595C SER* 3.2 12.2 + - - +
724C LEU* 1.3 70.0 - - - +
726C PRO* 1.3 70.7 - - - +
727C ARG* 2.7 68.5 + - - +
728C ILE* 3.2 34.0 + - + +
729C THR* 4.1 2.9 + - - -
763C TYR* 2.9 14.4 + - - -
765C PHE* 3.9 9.0 - - + -
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Residues in contact with PRO 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C TYR* 3.9 15.7 - - + -
724C LEU 3.0 8.2 - - - +
725C ASP* 1.3 84.7 - - - +
727C ARG* 1.3 59.0 + - - +
728C ILE 3.2 0.2 - - - -
729C THR* 3.1 7.4 + - - +
730C VAL* 3.0 28.7 + - + +
744C TYR* 3.6 19.6 - - + +
752C PHE* 3.6 39.3 - - + -
754C TRP* 3.7 13.7 - - + -
755C ALA* 3.6 23.8 - - + -
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Residues in contact with ARG 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 3.3 22.0 - - - +
444C TYR* 3.9 12.7 - - - +
445C GLU* 3.0 27.9 + - - -
448C ARG* 3.7 8.7 - - - +
725C ASP* 2.7 38.5 + - - +
726C PRO* 1.3 77.1 - - - +
728C ILE* 1.3 56.4 + - - +
730C VAL* 3.8 7.6 - - - +
731C ALA* 2.9 30.8 + - - +
754C TRP* 3.7 17.3 - - + -
755C ALA* 3.7 21.8 - - + -
758C MET* 4.7 14.4 - - - -
759C ALA* 4.4 11.2 - - + +
763C TYR* 3.3 40.0 + - + +
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Residues in contact with ILE 728 (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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595C SER* 3.3 41.5 - - - +
598C LEU* 4.0 18.2 - - + -
599C GLN* 3.9 37.5 - - + +
602C LEU* 4.1 7.2 - - + -
725C ASP* 3.4 21.5 - - + +
726C PRO 3.2 0.4 - - - -
727C ARG* 1.3 76.8 - - - +
729C THR* 1.3 57.0 + - - +
731C ALA* 3.7 4.8 - - - +
732C TRP* 3.1 25.8 + - - +
763C TYR* 4.0 19.3 - - + -
765C PHE* 4.0 11.0 - - + -
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Residues in contact with THR 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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598C LEU* 4.0 9.0 - - - +
602C LEU* 5.1 0.2 - - - -
619C TYR* 2.7 44.3 + - + +
724C LEU* 5.5 0.7 - - - +
725C ASP 4.5 2.6 + - - -
726C PRO 3.1 9.5 + - - -
728C ILE* 1.3 76.8 - - - +
730C VAL* 1.3 59.7 + - - +
731C ALA 3.2 0.2 - - - -
732C TRP* 3.3 6.1 + - - +
733C CYS* 2.9 38.1 + - - -
740C ILE* 5.3 1.3 - - + -
743C ILE* 3.7 19.3 - - + -
744C TYR* 3.3 22.9 + - + +
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Residues in contact with VAL 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C PRO 3.0 16.5 + - - +
727C ARG* 3.3 6.5 + - - +
729C THR* 1.3 74.0 - - - +
731C ALA* 1.3 64.5 - - - +
733C CYS* 3.5 5.9 + - - +
734C LYS* 3.1 48.3 + - + +
740C ILE* 4.5 12.3 - - + -
744C TYR* 5.0 4.9 - - + -
755C ALA* 3.8 19.3 - - + +
756C ILE* 3.9 39.5 - - + +
759C ALA* 4.0 9.4 - - + +
760C ASP 4.6 0.4 - - - -
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Residues in contact with ALA 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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727C ARG 2.9 17.7 + - - +
728C ILE* 3.7 6.7 - - - +
730C VAL* 1.3 77.7 - - - +
732C TRP* 1.3 61.2 + - - +
734C LYS 3.4 0.5 + - - -
735C LYS* 3.1 24.9 + - - +
760C ASP 3.5 18.3 + - - +
761C GLU* 3.7 22.2 - - - +
763C TYR* 3.9 21.3 - - + +
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Residues in contact with TRP 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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602C LEU* 3.7 40.2 - - + +
606C THR* 2.9 35.6 + - + -
615C LYS* 3.2 36.1 - - + -
616C ILE 4.5 0.4 - - - -
619C TYR* 3.8 19.3 - + + -
728C ILE 3.1 19.0 + - - +
729C THR 3.6 4.3 - - - +
731C ALA* 1.3 76.1 - - - +
733C CYS* 1.3 81.5 + - - +
735C LYS* 3.3 4.9 + - - +
736C TRP* 3.1 60.7 + + - +
738C VAL* 4.0 23.8 - - + -
743C ILE* 3.9 22.2 - - + -
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Residues in contact with CYS 733 (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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729C THR* 2.9 26.7 + - - +
730C VAL* 3.8 4.0 - - + +
732C TRP* 1.3 91.3 - - - +
734C LYS* 1.3 57.0 + - + +
737C GLY* 3.2 8.1 + - - -
738C VAL* 3.1 47.7 + - - +
740C ILE* 4.2 24.0 - - + +
743C ILE* 3.6 31.2 - - - -
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Residues in contact with LYS 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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730C VAL* 3.1 32.8 + - + +
731C ALA 4.1 1.6 - - - +
733C CYS* 1.3 75.3 - - + +
735C LYS* 1.3 62.6 + - - +
737C GLY* 4.2 4.9 + - - -
756C ILE 4.1 10.9 + - - -
757C ASP 4.8 2.2 + - - -
759C ALA 3.2 27.3 + - - -
760C ASP* 4.2 12.8 - - - +
761C GLU* 3.8 34.6 - - + +
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Residues in contact with LYS 735 (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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603C LYS* 5.5 8.9 - - - +
731C ALA 3.1 17.9 + - - +
732C TRP* 3.5 6.7 - - - +
733C CYS 3.3 0.2 - - - -
734C LYS* 1.3 79.1 - - - +
736C TRP* 1.3 97.9 + - + +
737C GLY 3.7 0.3 + - - -
761C GLU* 4.4 21.7 - - + +
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Residues in contact with TRP 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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602C LEU 5.3 0.6 + - - -
603C LYS* 5.9 3.1 - - - -
606C THR* 3.7 29.0 - - + +
607C ALA 4.1 0.9 - - - -
608C PRO* 3.6 46.7 - - + -
612C ILE* 3.9 6.6 - - - +
615C LYS* 3.3 47.0 + - + +
732C TRP* 3.1 59.1 + + + +
735C LYS* 1.3 114.3 - - + +
737C GLY* 1.3 62.1 + - - +
738C VAL* 3.3 10.1 + - + +
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Residues in contact with GLY 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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612C ILE* 3.5 14.2 - - - +
733C CYS 3.2 7.8 + - - -
734C LYS 4.2 4.8 + - - -
735C LYS 3.5 3.8 + - - -
736C TRP* 1.3 78.1 - - - +
738C VAL* 1.3 59.0 + - - +
739C PRO* 3.5 9.5 - - - +
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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
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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