Contacts of the helix formed by residues 872 - 876 (chain C) in PDB entry 1ZYR
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 ASN 872 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 4.2 6.5 - - - +
678C PRO* 4.8 1.5 - - - +
683C ASN* 3.0 39.0 + - + +
684C PHE 3.5 4.8 + - - -
685C GLU 5.2 5.4 + - - +
687C ALA 5.1 3.5 + - - +
845C ASN* 4.9 4.0 + - - -
870C ILE 4.0 0.2 + - - -
871C LEU* 1.3 75.5 - - - +
873C PRO* 1.3 94.5 - - - +
874C LEU* 2.6 23.5 + - - +
875C GLY* 3.6 11.1 + - - +
876C VAL* 4.6 2.3 - - - +
784D ASP* 2.5 44.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 873 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 4.0 14.4 - - + +
677C MET* 3.4 27.8 - - - +
678C PRO* 3.7 9.0 - - + -
872C ASN* 1.3 90.3 - - - +
874C LEU* 1.3 51.3 + - + +
875C GLY 2.3 21.7 + - - -
876C VAL* 2.5 21.1 + - - +
877C PRO* 3.1 7.4 - - - +
947D ILE* 3.7 32.1 - - + +
948D THR* 4.1 8.3 - - - -
949D ILE* 4.1 22.0 - - + -
1023D MET* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 874 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C PHE 5.6 0.9 - - - +
685C GLU 5.9 1.8 - - - +
872C ASN* 2.6 19.0 + - - +
873C PRO* 1.3 71.1 - - + +
875C GLY* 1.3 58.8 + - - -
876C VAL 3.3 0.7 - - - -
877C PRO* 3.5 12.2 - - - +
878C SER* 5.0 0.5 + - - -
783D ARG* 3.7 14.4 - - + +
784D ASP* 2.6 48.0 - - - +
787D LEU* 3.7 22.4 - - + -
1023D MET* 3.2 39.0 - - + -
1028D ALA* 4.9 4.0 - - + -
1029D ARG* 2.9 42.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 875 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C GLU 5.4 4.4 + - - -
686C ASP* 5.0 4.0 - - - -
845C ASN* 5.6 6.5 + - - -
872C ASN* 3.6 11.8 + - - -
873C PRO 2.3 16.7 + - - -
874C LEU* 1.3 71.1 - - - +
876C VAL* 1.3 59.5 + - - +
877C PRO* 3.8 0.2 - - - -
878C SER 5.2 0.4 - - - -
879C ARG* 3.4 45.0 + - - +
881C ASN* 4.9 0.5 + - - -
884C GLN* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 876 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 3.9 24.0 - - + -
845C ASN* 4.8 2.9 - - - +
872C ASN 4.6 2.5 - - - +
873C PRO* 2.5 25.9 + - + +
875C GLY* 1.3 75.3 - - - +
877C PRO* 1.3 64.0 - - + +
878C SER 3.4 1.8 - - - -
879C ARG 2.7 23.5 - - - +
880C MET* 4.5 1.0 - - - -
881C ASN* 3.7 17.0 + - - +
882C LEU* 4.3 15.8 - - + +
884C GLN* 3.0 33.0 - - - +
885C ILE* 4.2 15.7 - - + -
949D ILE* 4.0 9.6 - - + -
----------------------------------------------------------
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