Contacts of the helix formed by residues 168 - 176 (chain M) in PDB entry 2I2X
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 GLY 168 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M MET 3.0 1.0 + - - -
167M GLY* 1.3 70.1 - - - -
169M LYS* 1.3 63.6 + - - +
170M GLU* 3.0 16.4 + - - +
171M VAL 3.4 0.2 + - - -
172M PHE 3.0 19.4 + - - -
187M SER* 3.6 13.3 - - - -
191M LEU* 3.9 9.6 - - - -
222M GLN* 3.1 17.3 + - - -
459M TYR* 2.8 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M GLU* 3.6 25.3 + - - -
136M LEU* 4.3 6.3 - - + -
166M MET* 2.9 47.4 + - + +
167M GLY 3.3 2.0 + - - -
168M GLY* 1.3 76.3 - - - +
170M GLU* 1.3 57.2 + - - +
172M PHE* 3.5 7.1 - - - +
173M ASP* 2.9 49.3 + - - +
221M ALA* 3.9 19.5 - - + +
222M GLN* 3.6 6.7 - - + +
135N VAL* 3.9 14.1 - - - +
159N ARG* 5.1 0.2 - - - +
500N B13 3.4 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M LEU* 3.4 23.5 - - + +
168M GLY* 3.1 15.1 - - - -
169M LYS* 1.3 76.4 - - - +
171M VAL* 1.3 82.6 + - + +
173M ASP* 3.3 14.5 + - - +
174M TYR* 3.4 12.6 + - - +
191M LEU* 4.3 0.5 - - - +
451M VAL* 4.4 6.1 - - + +
453M VAL* 4.3 19.7 - - + +
454M PHE* 3.7 39.1 - - + +
455M LYS 4.8 2.1 + - - -
458M ASN* 4.9 2.1 + - - -
459M TYR* 2.5 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M GLU* 1.3 91.3 + - + +
172M PHE* 1.3 65.5 + - - +
174M TYR* 3.2 7.5 + - - +
175M ALA* 2.9 21.0 + - + +
183M GLY* 3.9 10.1 - - - +
186M TYR* 4.4 4.7 - - + -
187M SER* 3.7 20.0 - - - -
191M LEU* 3.8 15.7 - - + -
447M TYR* 4.0 43.3 - - + -
451M VAL* 4.9 4.7 - - + -
454M PHE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M GLY 3.0 18.4 + - - +
169M LYS 3.5 3.8 - - - +
171M VAL* 1.3 78.1 - - - +
173M ASP* 1.3 70.6 + - - +
175M ALA* 3.1 3.3 + - - +
176M VAL* 2.9 60.6 + - + +
184M LEU* 4.2 9.9 - - + -
187M SER* 3.4 14.9 - - - +
188M ILE* 3.9 20.2 - - + -
221M ALA 3.8 10.3 - - - -
222M GLN* 2.8 52.9 - - + +
225M THR* 3.7 21.5 - - + -
226M ALA* 3.9 10.3 - - + -
246M ALA* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M LYS* 2.9 40.4 + - - +
170M GLU* 3.8 6.6 - - - +
171M VAL 3.3 0.4 - - - -
172M PHE* 1.3 91.4 - - - +
174M TYR* 1.3 60.4 + - - +
176M VAL* 3.7 10.8 - - - +
177M LEU* 3.4 25.0 - - + +
221M ALA 4.7 1.0 - - - +
225M THR* 4.4 4.7 - - - +
137N ASP* 5.0 4.5 - - + +
138N ILE* 4.8 6.0 - - + +
141N ASN* 5.9 4.3 - - - +
500N B13 3.7 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M GLU 3.4 7.4 + - - +
171M VAL 3.2 7.8 + - - +
172M PHE 3.1 0.2 - - - -
173M ASP* 1.3 81.1 - - - +
175M ALA* 1.3 69.4 + - - +
177M LEU* 3.6 4.0 + - - -
178M ARG* 2.9 73.2 + - - +
180M ASP* 4.4 6.5 - - - -
447M TYR* 4.1 17.3 - + - -
450M GLU* 2.6 50.2 + - + +
451M VAL* 3.6 31.2 - - + -
103N ASP* 4.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171M VAL* 2.9 17.7 + - + +
172M PHE* 3.8 2.2 - - - +
174M TYR* 1.3 78.8 - - + +
176M VAL* 1.3 55.0 + - - +
177M LEU 3.1 4.9 - - - -
178M ARG* 2.9 18.8 + - - -
179M ASN 3.4 0.3 + - - -
180M ASP* 3.2 49.0 + - + +
183M GLY* 3.9 15.9 - - - -
184M LEU* 3.7 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M PHE* 2.9 52.8 + - + +
173M ASP* 3.7 12.8 - - - +
175M ALA* 1.3 77.0 - - - +
177M LEU* 1.3 74.7 + - + +
178M ARG 3.2 1.7 + - - -
179M ASN* 4.4 2.9 + - - +
184M LEU* 3.9 12.1 - - + -
225M THR* 5.2 0.2 - - + -
226M ALA* 4.1 18.2 - - + -
229M ILE* 4.0 16.5 - - + +
237M ASN 5.5 0.5 - - - +
238M LEU* 3.7 31.7 - - + +
242M ILE* 5.9 1.3 - - + -
96N PRO* 4.2 3.3 - - - +
138N ILE* 5.8 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