Contacts of the helix formed by residues 215 - 222 (chain C) in PDB entry 5G04
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 215 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 3.4 10.1 - - - +
214C THR* 1.3 79.7 - - - +
216C LYS* 1.3 80.1 + - - +
217C GLU* 2.7 43.0 + - + +
218C MET* 3.2 42.3 + - + +
219C LEU 3.3 4.5 + - - -
241C LEU* 4.1 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ASP* 1.3 86.3 + - - +
217C GLU* 1.3 54.7 + - - +
219C LEU* 3.2 14.2 + - + +
220C LYS* 3.0 43.9 + - + +
238C TYR* 6.0 1.1 - - + -
241C LEU* 3.7 17.1 - - + +
243C LEU* 3.8 43.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN* 4.5 21.6 + - - +
215C ASP* 2.7 37.1 + - + +
216C LYS* 1.3 70.0 - - - +
218C MET* 1.3 73.7 + - + +
220C LYS* 3.3 23.3 + - + +
221C PHE* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ILE* 6.0 4.5 - - + -
212C LEU 5.3 0.7 - - - +
213C ILE* 4.1 12.8 - - + -
214C THR* 3.3 35.4 - - - +
215C ASP* 3.2 35.9 + - + +
217C GLU* 1.3 83.9 - - + +
219C LEU* 1.3 61.5 + - - +
221C PHE* 3.4 17.6 - - - +
222C LEU* 3.3 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 4.2 11.2 - - + +
215C ASP 3.3 5.5 + - - +
216C LYS* 3.2 20.4 + - + +
218C MET* 1.3 76.8 - - - +
220C LYS* 1.3 64.8 + - + +
222C LEU* 3.5 26.9 + - + +
224C LEU* 4.5 10.5 - - + +
233C PHE* 3.9 26.0 - - + -
234C LEU* 3.5 35.0 - - + -
237C ILE* 4.1 22.2 - - + -
238C TYR* 4.9 8.3 - - + -
241C LEU* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LYS* 3.0 33.8 + - - +
217C GLU* 3.5 20.0 - - + +
219C LEU* 1.3 75.7 - - + +
221C PHE* 1.3 63.5 + - - +
222C LEU 3.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU 3.1 9.3 + - - +
218C MET* 3.4 13.7 - - - +
219C LEU 3.3 0.2 - - - -
220C LYS* 1.3 78.7 - - - +
222C LEU* 1.3 74.2 + - + +
223C SER* 3.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ILE* 3.7 20.4 - - + -
190C ASP* 5.7 2.0 - - - +
193C VAL* 3.7 27.8 - - + -
209C LEU* 4.7 3.1 - - + -
213C ILE* 3.7 29.6 - - + -
218C MET* 3.3 17.0 + - + +
219C LEU* 3.5 17.9 + - + +
220C LYS 3.3 13.3 - - - +
221C PHE* 1.3 89.2 - - + +
223C SER* 1.3 60.0 + - - +
224C LEU* 4.3 17.9 + - + +
233C PHE* 5.9 1.6 - - + -
----------------------------------------------------------
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