Contacts of the helix formed by residues 742 - 754 (chain C) in PDB entry 5FB0
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 CYS 742 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C CYS* 3.2 13.9 - - + +
720C CYS* 3.5 10.5 - - - -
724C PHE* 3.3 34.8 - - + -
729C HIS* 3.6 8.1 - - - +
740C TRP* 4.1 5.4 - - + -
741C SER* 1.3 76.6 - - - +
743C ILE* 1.3 65.4 + - - +
744C PHE* 3.3 24.2 + - - -
745C CYS* 3.4 2.0 + - - -
746C ARG* 3.2 22.4 + - - +
902C ZN 2.3 33.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 743 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C HIS* 3.0 22.9 + - + +
730C ILE 3.7 17.0 - - - +
731C PRO* 4.5 2.9 - - + -
742C CYS* 1.3 74.1 - - - +
744C PHE* 1.3 76.8 + - + +
746C ARG* 4.6 4.7 - - + +
747C ILE* 2.9 30.9 + - + +
777C LEU* 3.5 49.8 - - + +
780C GLU* 4.9 0.4 - - + -
781C PHE* 3.6 26.5 - - + +
784C LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 744 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C GLU* 4.4 10.1 - - + -
722C ARG* 3.6 52.5 - - - +
724C PHE* 4.0 19.5 - + - -
742C CYS* 3.2 3.9 - - - -
743C ILE* 1.3 89.5 - - + +
745C CYS* 1.3 56.3 + - - +
747C ILE* 3.5 7.5 + - - +
748C LYS* 3.0 26.5 + - - +
781C PHE* 3.6 26.0 - + - -
784C LEU* 3.8 31.2 - - + -
785C LYS* 4.6 14.6 - - + -
788C CYS* 5.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 745 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C THR* 2.8 28.0 - - + +
720C CYS* 3.6 15.5 - - - -
722C ARG* 5.2 1.1 - - - -
741C SER* 4.4 7.0 - - - -
742C CYS* 3.4 5.2 + - - +
744C PHE* 1.3 75.9 - - - +
746C ARG* 1.3 60.0 + - - +
748C LYS* 3.2 10.9 + - - +
749C THR* 2.9 32.6 + - - +
902C ZN 2.5 35.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 746 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C HIS* 5.4 4.0 - - - -
731C PRO* 4.5 17.4 - - - +
734C GLU* 5.4 8.9 + - - +
737C LYS* 5.9 6.4 - - - +
740C TRP* 5.4 4.8 - - - +
741C SER* 3.8 25.0 + - - +
742C CYS 3.2 18.3 + - - +
743C ILE* 4.0 6.3 - - - +
745C CYS* 1.3 76.2 - - - +
747C ILE* 1.3 57.2 + - - +
749C THR* 3.3 8.1 + - - -
750C ILE* 3.0 33.1 + - - +
777C LEU* 3.3 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 747 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C ILE* 2.9 29.7 + - + +
744C PHE* 3.7 6.7 - - - +
746C ARG* 1.3 73.9 - - - +
748C LYS* 1.3 60.3 + - - +
750C ILE* 3.9 6.5 - - + +
751C GLN* 2.8 50.8 + - - +
777C LEU* 4.0 17.9 - - + +
778C LYS* 4.2 18.8 - - + -
781C PHE* 3.6 50.9 - - + -
871C ILE* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 748 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C PHE 3.0 14.2 + - - +
745C CYS* 3.2 12.3 + - - +
747C ILE* 1.3 79.3 - - - +
749C THR* 1.3 63.4 + - - +
751C GLN* 3.6 9.6 - - + +
752C GLU* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 749 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C CYS 2.9 15.9 + - - -
746C ARG* 3.6 10.3 - - - -
747C ILE 3.3 0.2 - - - -
748C LYS* 1.3 78.8 - - - +
750C ILE* 1.3 64.5 + - + +
752C GLU* 3.9 3.7 - - - +
753C ARG* 2.9 66.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 750 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746C ARG 3.0 16.0 + - - +
747C ILE* 3.9 9.2 - - + +
749C THR* 1.3 77.0 - - + +
751C GLN* 1.3 57.1 + - - +
753C ARG* 3.0 4.9 + - - +
754C SER* 2.5 54.9 + - - +
773C PRO 5.0 0.9 - - - +
774C GLU* 3.5 37.5 - - + +
777C LEU* 3.5 38.6 - - + -
778C LYS* 4.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 751 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C ILE* 2.8 35.0 + - - +
748C LYS* 3.6 10.8 - - + +
749C THR 3.3 0.2 - - - -
750C ILE* 1.3 80.6 - - - +
752C GLU* 1.3 63.1 + - + +
754C SER* 3.6 17.4 - - - +
870C ASN 5.1 2.4 + - - -
871C ILE* 4.6 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 752 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748C LYS* 3.0 52.0 + - + +
749C THR* 4.1 3.1 - - - +
751C GLN* 1.3 78.3 - - + +
753C ARG* 1.3 62.8 + - + +
754C SER 3.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 753 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C THR* 2.9 46.2 + - + +
750C ILE* 3.7 4.9 - - - +
752C GLU* 1.3 77.9 - - + +
754C SER* 1.3 64.9 + - - +
774C GLU* 5.6 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 754 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750C ILE* 2.5 34.9 + - - +
751C GLN* 3.6 16.2 - - - +
752C GLU 3.4 4.9 - - - +
753C ARG* 1.3 78.2 - - - +
774C GLU* 3.2 27.5 + - - -
778C LYS* 5.1 7.0 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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