Contacts of the helix formed by residues 216 - 221 (chain C) in PDB entry 3PI5
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 216 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C MET* 1.3 71.9 - - - +
217C CYS* 1.3 55.4 + - - +
218C LYS* 2.7 46.9 + - - +
219C GLU* 2.7 37.5 + - + +
220C TYR* 4.0 0.5 + - - -
239C LYS* 6.1 0.2 - - - +
381C ASP 4.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE 4.3 0.2 - - - +
204C VAL 3.9 12.8 - - - +
215C MET 3.0 5.6 + - - +
216C ASP* 1.3 72.5 + - - +
218C LYS* 1.3 61.0 + - - +
219C GLU 3.1 0.2 - - - -
220C TYR* 3.2 34.8 + - + +
221C ASN* 3.2 17.4 + - - -
377C LEU* 3.6 20.3 - - + +
381C ASP 3.3 16.8 - - - -
382C CYS* 2.0 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ASP* 2.7 24.1 + - + +
217C CYS* 1.3 76.3 - - - +
219C GLU* 1.3 62.7 + - - +
221C ASN* 3.2 11.3 + - - +
222C TYR* 3.2 15.3 + - - +
380C GLU 3.9 12.9 + - - -
381C ASP* 3.6 24.2 + - - +
382C CYS 3.7 14.6 - - - +
383C GLY 3.8 18.2 - - - +
384C TYR* 4.9 19.4 - - + +
385C ASN* 5.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C MET* 3.5 31.0 - - + -
216C ASP* 2.7 30.0 + - + +
218C LYS* 1.3 80.1 - - - +
220C TYR* 1.3 61.8 + - - +
221C ASN 3.2 0.7 + - - -
222C TYR* 3.3 26.1 + - - +
237C PRO* 3.5 11.1 - - - +
239C LYS* 3.2 35.7 - - - +
240C VAL* 3.5 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 4.0 27.0 - - + +
204C VAL 4.6 0.2 - - - -
205C ARG* 3.9 9.9 - - - -
206C VAL* 3.8 44.7 + - + -
212C ASP* 4.1 3.6 + - - -
213C LEU* 3.3 27.6 - - + +
214C LYS 4.1 1.6 + - - -
215C MET* 3.5 43.4 + - + -
217C CYS* 3.3 34.8 - - + +
218C LYS 3.2 0.6 - - - -
219C GLU* 1.3 78.3 - - + +
221C ASN* 1.3 57.6 + - - +
222C TYR 3.5 0.4 + - - -
225C SER* 3.1 4.7 + - - -
240C VAL* 3.8 18.4 - - + -
331C THR* 2.5 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ARG* 5.8 1.1 + - - +
200C GLU* 6.0 0.9 - - - +
201C VAL 4.7 2.0 - - - +
202C ILE* 3.7 9.1 - - + +
203C ILE* 2.8 48.4 + - - +
217C CYS 3.2 9.9 + - - -
218C LYS 3.2 6.0 + - - +
219C GLU 3.1 0.6 - - - -
220C TYR* 1.3 78.3 - - - +
222C TYR* 1.3 51.0 + - - +
223C ASP* 2.8 5.4 - - - +
224C LYS* 2.6 30.4 + - - -
225C SER* 2.8 29.9 + - - +
382C CYS* 3.0 32.7 + - - +
383C GLY* 5.2 1.3 - - - -
384C TYR* 3.6 11.7 - - - +
----------------------------------------------------------
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