Contacts of the helix formed by residues 915 - 922 (chain C) in PDB entry 3P23
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 PRO 915 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C ASP* 3.8 19.1 - - + +
913C GLU 4.3 2.9 - - - +
914C LEU* 1.3 94.5 - - + +
916C ALA* 1.3 67.8 + - - +
917C GLU* 3.4 6.5 - - + +
918C VAL* 3.1 29.8 + - + +
919C ARG* 3.1 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 916 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914C LEU 3.6 0.8 + - - -
915C PRO* 1.3 70.6 - - - +
917C GLU* 1.3 58.8 + - - +
919C ARG* 2.9 45.9 + - - +
920C GLU* 3.1 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 917 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C PRO* 3.7 38.2 - - + +
884C THR* 5.2 8.7 + - - +
915C PRO* 4.6 5.1 - - + +
916C ALA* 1.3 78.9 - - - +
918C VAL* 1.3 68.9 + - + +
920C GLU* 3.6 15.6 + - - +
921C THR* 3.6 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 918 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C PRO* 4.1 11.2 - - - +
882C LEU* 4.6 12.6 - - + -
885C ASP* 3.8 37.7 - - + +
907C LYS* 5.0 0.7 - - + -
914C LEU* 4.3 12.8 - - + -
915C PRO* 3.5 30.3 - - + +
916C ALA 3.0 0.8 - - - -
917C GLU* 1.3 81.1 - - + +
919C ARG* 1.3 64.4 + - - +
920C GLU 3.1 2.0 + - - -
921C THR* 3.5 8.8 + - - +
922C LEU* 3.3 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911C TYR* 3.1 64.2 + - + +
912C ARG 4.7 8.9 + - - -
913C GLU 5.2 0.2 - - - -
914C LEU* 2.6 42.3 + - + +
915C PRO* 3.1 13.9 + - - +
916C ALA* 2.9 29.7 + - - +
918C VAL* 1.3 77.1 - - - +
920C GLU* 1.3 61.7 + - - +
922C LEU 4.1 0.9 - - - -
923C GLY* 3.4 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916C ALA 3.1 10.6 + - - +
917C GLU* 3.7 17.4 - - - +
918C VAL 3.1 0.4 - - - -
919C ARG* 1.3 77.3 - - - +
921C THR* 1.3 68.6 + - + +
922C LEU 3.2 2.0 + - - -
923C GLY 4.0 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879C THR* 3.5 28.9 + - + +
881C PRO* 3.5 36.7 - - + +
882C LEU* 4.6 2.8 + - - +
917C GLU 3.6 7.5 + - - +
918C VAL* 3.5 10.0 + - - -
920C GLU* 1.3 80.2 - - + +
922C LEU* 1.3 65.6 + - - +
932C TYR* 2.8 24.0 - - - -
936C ARG* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882C LEU* 3.9 13.7 - - + -
907C LYS* 3.8 29.2 - - + -
911C TYR* 4.3 4.9 - - + -
914C LEU* 4.4 5.8 - - + -
918C VAL* 3.3 31.5 + - + +
920C GLU 3.2 1.4 - - - -
921C THR* 1.3 83.6 - - - +
923C GLY* 1.3 70.8 + - - +
928C ASP* 3.3 19.6 - - - +
929C PHE* 3.7 23.3 - - + -
932C TYR* 3.5 43.1 - - + +
933C PHE* 3.9 10.8 - - + -
----------------------------------------------------------
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