Contacts of the helix formed by residues 952 - 957 (chain C) in PDB entry 1ZYC
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 LYS 952 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948C ASP* 4.1 14.8 - - - +
949C ASN* 3.3 32.2 + - - +
950C LYS 3.5 1.0 + - - -
951C MET* 1.3 78.9 - - - +
953C VAL* 1.3 59.3 + - - +
955C LYS* 3.6 4.4 - - - +
956C LYS* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 953 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C ARG* 6.2 1.6 - - - +
813C TRP* 4.3 10.8 - - + +
950C LYS 5.6 2.0 - - - +
952C LYS* 1.3 77.5 - - - +
954C GLU* 1.3 75.9 + - + +
955C LYS 2.5 18.0 + - - -
956C LYS* 3.0 21.4 + - - +
957C ILE* 3.3 25.3 + - + +
980C TRP* 3.5 32.5 - - + +
982C PRO* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 954 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C ARG* 3.0 22.0 + - - +
812C TYR* 2.4 38.8 + - - -
813C TRP* 3.9 13.2 - - + +
915C PHE* 4.0 15.4 - - + -
919C ILE* 3.4 20.1 - - + +
950C LYS 3.2 16.6 - - - +
951C MET* 3.3 28.8 - - + +
952C LYS 3.5 0.4 - - - -
953C VAL* 1.3 83.1 - - + +
955C LYS* 1.3 56.5 + - - +
957C ILE* 4.6 1.6 - - - -
958C ILE* 2.9 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 955 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942C PHE* 3.6 48.7 - - + -
946C PHE* 3.2 29.8 - - + -
948C ASP* 3.6 31.5 + - - +
951C MET 3.1 15.9 - - - +
952C LYS* 3.6 4.5 - - - +
953C VAL 2.5 7.5 + - - -
954C GLU* 1.3 74.7 - - - +
956C LYS* 1.3 64.5 + - - +
957C ILE 2.9 2.3 + - - -
958C ILE* 4.0 5.8 - - - +
959C ARG* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 956 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952C LYS* 3.2 23.7 + - - +
953C VAL* 3.0 14.1 + - - +
955C LYS* 1.3 76.4 - - - +
957C ILE* 1.3 58.7 + - - +
959C ARG* 4.2 4.4 + - - +
960C LEU* 3.0 30.5 + - + +
980C TRP* 3.5 59.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 957 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C TRP* 3.9 28.7 - - + -
816C PHE* 4.7 10.1 - - + -
915C PHE* 5.0 5.6 - - + -
953C VAL* 3.6 26.2 - - + +
954C GLU* 4.9 3.8 - - - -
955C LYS 2.9 0.8 - - - -
956C LYS* 1.3 76.5 - - + +
958C ILE* 1.3 57.8 + - + +
959C ARG 3.1 1.3 - - - -
960C LEU* 2.3 44.2 + - + +
961C LEU* 3.0 26.9 + - + -
975C LEU* 4.2 20.9 - - + -
980C TRP* 4.5 29.2 - - + +
981C LEU* 5.2 3.4 - - + -
----------------------------------------------------------
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