Contacts of the helix formed by residues 215 - 222 (chain M) in PDB entry 3HOU
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 SER 215 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M GLY 4.1 1.6 + - - -
213M HIS 3.2 5.5 + - - -
214M ILE* 1.3 78.6 - - - +
216M VAL* 1.3 54.1 + - - +
217M LYS* 3.6 6.1 + - - +
218M ASP* 2.6 39.4 + - - +
219M PHE* 2.8 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M ILE 3.9 1.0 + - - +
215M SER* 1.3 73.0 - - - +
217M LYS* 1.3 59.4 + - + +
219M PHE* 2.9 43.1 - - + +
220M THR* 2.9 12.0 + - - +
226M GLU* 3.7 31.9 - - + +
230M ARG* 4.8 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215M SER* 3.2 5.4 + - - +
216M VAL* 1.3 76.6 - - + +
218M ASP* 1.3 59.8 + - - +
219M PHE 3.3 0.2 + - - -
220M THR* 3.5 6.5 + - - -
221M SER* 2.4 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M VAL* 5.7 0.2 - - + -
111M GLY 4.2 0.2 - - - +
112M LYS* 3.9 13.7 + - - +
113M LEU* 2.9 52.4 + - + +
214M ILE* 3.6 15.7 - - + -
215M SER* 2.6 38.1 + - - +
217M LYS* 1.3 76.6 - - - +
219M PHE* 1.3 70.8 + - - +
221M SER* 3.0 7.3 + - - -
222M LEU* 3.0 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211M PHE 4.6 2.9 - - - -
212M LYS 5.8 1.3 - - - -
214M ILE* 3.9 24.8 - - + +
215M SER 2.8 13.6 + - - -
216M VAL* 2.9 31.6 - - + +
218M ASP* 1.3 80.0 - - - +
220M THR* 1.3 59.8 + - - +
222M LEU* 2.7 32.7 + - - +
224M PHE* 3.5 13.4 + - + +
225M ASN 4.7 1.8 - - - +
226M GLU* 4.1 16.8 - - - -
230M ARG* 3.1 57.2 - - + -
231M PRO* 3.1 33.7 - - + -
232M GLU* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ARG* 2.8 19.0 + - - +
216M VAL* 2.9 16.2 + - - +
217M LYS* 3.7 8.2 - - - -
219M PHE* 1.3 78.1 - - - +
221M SER* 1.3 64.4 + - - -
222M LEU 2.8 4.5 - - - -
223M GLY* 2.6 16.1 + - - -
224M PHE 3.9 20.4 + - - +
225M ASN* 5.8 0.4 - - - -
226M GLU* 5.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 221 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M LEU* 4.1 9.1 - - - +
126M LEU* 3.7 27.6 - - - -
134M ARG* 2.6 37.1 - - - +
135M PHE 4.5 0.2 + - - -
138M ILE* 2.9 13.0 - - - +
217M LYS* 2.4 32.6 + - - +
218M ASP* 3.0 14.3 + - - -
220M THR* 1.3 72.8 - - - +
222M LEU* 1.3 55.4 + - - +
223M GLY 3.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M LYS* 5.2 0.5 + - - -
102M VAL* 4.1 16.8 - - + -
105M CYS* 3.9 13.2 - - + -
106M VAL* 4.1 17.7 - - + -
113M LEU* 3.9 21.8 - - + -
135M PHE* 3.5 39.4 - - + -
138M ILE* 3.6 28.3 - - + -
214M ILE* 4.9 5.8 - - + -
218M ASP 3.0 15.2 + - - +
219M PHE* 2.7 14.8 + - - +
221M SER* 1.3 74.9 - - - +
223M GLY* 1.3 51.4 + - - +
224M PHE* 2.8 31.5 - - + -
231M PRO* 6.2 1.1 - - + -
----------------------------------------------------------
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