Contacts of the helix formed by residues 148 - 166 (chain G) in PDB entry 3MQT
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 THR 148 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASP 4.6 4.9 - - - +
147G ALA* 1.3 73.9 - - - +
149G LEU* 1.3 66.4 + - - +
150G SER* 3.7 6.8 + - - -
151G GLU* 3.0 38.0 + - - +
152G ILE* 2.9 26.6 + - - +
178G ASN* 5.9 0.7 - - - -
154V GLU* 4.4 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G THR* 1.3 74.8 - - - +
150G SER* 1.3 58.5 + - - +
152G ILE* 3.3 19.2 + - + +
153G VAL* 3.0 31.3 + - - +
175G ILE* 5.8 2.5 - - + -
176G ILE 5.8 3.4 - - - +
178G ASN* 4.7 10.5 + - + +
181G VAL* 3.4 39.7 - - + -
185G GLU* 3.8 28.9 - - + +
186G ILE* 4.3 9.0 - - + -
189G TYR* 3.9 33.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G THR* 3.1 3.4 + - - -
149G LEU* 1.3 76.5 - - - +
151G GLU* 1.3 61.1 + - - +
153G VAL* 3.1 8.8 + - - +
154G GLU* 2.9 31.5 + - - +
192G GLU* 5.3 5.8 + - - -
150V SER* 2.6 29.8 + - - -
154V GLU* 3.6 34.3 + - - +
157V LYS* 5.3 1.8 - - - -
192V GLU* 5.4 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G VAL* 4.5 4.5 - - + +
146G ASP 4.6 0.7 - - - +
147G ALA* 3.5 15.3 - - + +
148G THR* 3.0 41.5 + - - +
150G SER* 1.3 78.1 - - - +
152G ILE* 1.3 58.5 + - - +
154G GLU* 3.3 8.8 + - - +
155G ALA* 2.9 28.6 + - - +
154V GLU* 6.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G PRO* 4.1 10.7 - - + +
143G VAL* 4.4 15.9 - - + -
147G ALA* 3.9 27.4 - - + +
148G THR 2.9 21.1 + - - +
149G LEU* 3.5 21.8 - - + +
151G GLU* 1.3 75.7 - - - +
153G VAL* 1.3 56.9 + - - +
155G ALA* 3.1 5.1 + - - +
156G TYR* 2.9 38.6 + - + -
176G ILE* 3.9 27.4 - - + -
178G ASN* 5.9 1.3 - - - +
189G TYR* 3.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G LEU 3.0 19.0 + - - +
150G SER* 3.1 8.3 + - - +
152G ILE* 1.3 74.5 - - - +
154G GLU* 1.3 70.5 + - - +
156G TYR* 3.0 18.5 + - - +
157G LYS* 3.2 22.1 + - - +
189G TYR* 3.6 26.2 - - + +
192G GLU* 3.4 45.3 - - + +
193G LEU* 4.1 18.6 - - + -
196G VAL* 4.6 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G SER* 2.9 20.6 + - - +
151G GLU* 3.5 7.9 - - - +
153G VAL* 1.3 82.1 - - - +
155G ALA* 1.3 60.7 + - - +
157G LYS* 3.0 41.9 + - - +
158G PRO* 3.4 17.3 - - - +
192G GLU* 4.5 1.7 - - - +
148V THR* 4.5 16.7 + - - +
150V SER* 3.5 29.9 + - - +
151V GLU* 5.8 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G PRO* 3.9 11.4 - - + -
142G SER 4.6 5.6 - - - +
143G VAL* 3.6 31.6 - - + -
151G GLU 2.9 9.2 + - - +
152G ILE 3.1 5.1 + - - +
154G GLU* 1.3 76.9 - - - +
156G TYR* 1.3 62.0 + - - +
158G PRO* 3.2 18.1 - - - +
159G LEU* 4.2 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G LEU* 2.7 48.8 + - + -
140G TYR* 4.0 0.2 - - - -
141G PRO* 3.5 28.0 - - + +
152G ILE* 2.9 23.6 + - + -
153G VAL* 3.0 8.5 + - - +
155G ALA* 1.3 78.2 - - - +
157G LYS* 1.3 63.5 + - + +
159G LEU* 3.1 13.9 + - + +
160G ILE* 2.9 41.8 + - + +
173G VAL* 3.8 17.5 - - + -
174G CYS* 3.0 21.8 + - - +
176G ILE* 6.1 0.2 - - + -
189G TYR* 3.6 20.9 - - - -
193G LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G VAL* 3.2 17.5 + - - +
154G GLU* 3.0 40.2 + - - +
155G ALA 3.4 0.2 - - - -
156G TYR* 1.3 73.9 - - - +
158G PRO* 1.3 65.0 - - + +
160G ILE* 3.4 1.9 + - - +
161G ALA* 3.0 30.2 + - - +
192G GLU* 4.6 6.5 + - - -
196G VAL* 3.9 42.5 - - + +
150V SER* 5.3 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G GLU 3.4 14.8 - - - +
155G ALA* 3.2 16.8 - - - +
157G LYS* 1.3 93.3 - - + +
159G LEU* 1.3 56.4 + - + +
161G ALA* 3.3 6.6 + - + +
162G LYS* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G LEU* 4.4 14.5 - - + +
140G TYR 3.6 31.0 - - - +
141G PRO* 3.9 16.8 - - + -
142G SER 5.3 0.7 - - - +
155G ALA 4.4 6.7 - - - +
156G TYR* 3.1 20.1 + - + +
158G PRO* 1.3 78.8 - - + +
160G ILE* 1.3 59.0 + - - +
162G LYS* 3.2 13.0 + - - +
163G ALA* 3.0 26.3 + - - +
339G ASP 4.8 2.0 - - - +
340G PHE* 3.5 46.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G LEU* 3.8 22.9 - - + -
156G TYR* 2.9 42.6 + - + +
157G LYS 4.0 2.9 - - - +
159G LEU* 1.3 72.8 - - - +
161G ALA* 1.3 62.8 + - - +
163G ALA* 3.1 4.7 + - - +
164G LYS* 3.0 30.4 + - - +
171G VAL* 5.1 0.2 - - + -
173G VAL* 4.9 2.5 - - + -
193G LEU* 4.4 8.1 - - + -
196G VAL* 3.8 43.3 - - + +
197G ILE* 3.9 32.5 - - + -
201G MET* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G LYS 3.0 17.7 + - - +
158G PRO* 3.7 7.9 - - + +
159G LEU 3.2 0.4 - - - -
160G ILE* 1.3 77.1 - - - +
162G LYS* 1.3 58.3 + - - +
164G LYS* 3.4 12.9 + - - +
165G GLU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G PRO* 2.9 18.8 + - - +
159G LEU* 3.5 12.9 - - + +
161G ALA* 1.3 74.5 - - - +
163G ALA* 1.3 64.1 + - - +
165G GLU* 3.1 15.1 + - + +
166G ARG* 3.1 56.7 + - - +
339G ASP* 3.3 30.2 + - + +
340G PHE* 4.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G LEU* 4.7 2.9 - - + -
159G LEU 3.0 13.5 + - - +
160G ILE* 3.1 10.0 + - - +
162G LYS* 1.3 75.8 - - - +
164G LYS* 1.3 62.5 + - - +
166G ARG* 3.2 7.2 + - - +
168G ALA* 3.0 30.7 + - + +
171G VAL* 3.8 28.9 - - + -
201G MET* 4.5 2.7 - - - -
340G PHE* 3.7 23.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G ILE* 3.0 23.3 + - - +
161G ALA* 3.6 12.6 - - - +
163G ALA* 1.3 76.0 - - - +
165G GLU* 1.3 64.0 + - - +
167G GLY* 3.0 14.3 + - - -
168G ALA 4.8 1.1 - - - +
195G GLU 5.5 0.2 + - - -
196G VAL 3.0 24.6 + - - -
197G ILE 3.2 25.6 + - - -
198G GLY* 4.6 2.2 - - - +
201G MET* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G ALA 3.0 15.0 + - - +
162G LYS* 3.1 14.6 + - + +
164G LYS* 1.3 77.2 - - - +
166G ARG* 1.3 81.9 + - - +
167G GLY 3.3 0.8 + - - -
355G LYS* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G LYS* 3.1 51.2 + - - +
163G ALA* 3.2 6.5 + - - +
164G LYS 3.1 0.4 - - - -
165G GLU* 1.3 107.0 + - - +
167G GLY* 1.3 58.2 + - - +
168G ALA* 3.4 1.3 - - + +
339G ASP* 2.5 31.2 + - - +
340G PHE* 4.4 5.2 - - + -
355G LYS* 2.9 31.8 - - - +
356G ILE* 3.6 33.4 - - + +
358G ASP 3.2 12.0 + - - -
359G GLY 3.1 18.2 + - - -
----------------------------------------------------------
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