Contacts of the helix formed by residues 148 - 166 (chain V) 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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G GLU* 4.5 15.2 + - - +
146V ASP 4.8 3.8 - - - +
147V ALA* 1.3 73.3 - - - +
149V LEU* 1.3 64.8 + - - +
150V SER* 3.7 7.2 + - - -
151V GLU* 3.1 41.4 + - - +
152V ILE* 3.0 27.0 + - - +
178V ASN* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148V THR* 1.3 72.9 - - - +
150V SER* 1.3 57.1 + - - +
152V ILE* 3.2 16.6 + - + +
153V VAL* 2.8 36.3 + - - +
175V ILE* 5.8 1.6 - - + -
176V ILE 5.8 4.0 - - - +
178V ASN* 4.7 13.6 + - + +
181V VAL* 3.5 34.3 - - + -
185V GLU* 4.0 31.6 - - + +
186V ILE* 4.3 12.6 - - + -
189V TYR* 4.0 33.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G SER* 2.6 29.8 + - - -
154G GLU* 3.5 32.9 + - - +
157G LYS* 5.3 2.2 - - - -
192G GLU* 5.0 5.7 + - - -
148V THR* 3.2 4.4 + - - -
149V LEU* 1.3 77.7 - - - +
151V GLU* 1.3 58.5 + - - +
153V VAL* 3.4 8.1 + - - +
154V GLU* 2.8 35.1 + - - +
192V GLU* 5.1 8.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G GLU* 5.9 4.0 - - + -
143V VAL* 4.4 4.1 - - + +
146V ASP 4.5 0.9 - - - +
147V ALA* 3.4 16.4 - - + +
148V THR* 3.1 47.5 + - - +
150V SER* 1.3 77.8 - - - +
152V ILE* 1.3 58.5 + - - +
154V GLU* 3.4 8.0 + - - +
155V ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141V PRO* 4.2 11.9 - - + -
143V VAL* 4.4 10.1 - - + -
147V ALA* 3.9 27.1 - - + +
148V THR 3.0 20.8 + - - +
149V LEU* 3.5 21.3 - - + +
151V GLU* 1.3 75.1 - - - +
153V VAL* 1.3 65.2 + - - +
155V ALA* 3.1 9.2 + - - +
156V TYR* 2.9 33.8 + - + -
176V ILE* 4.0 29.4 - - + +
178V ASN* 5.8 2.0 - - + +
189V TYR* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V LEU 2.8 22.7 + - - +
150V SER* 3.6 5.8 - - - +
152V ILE* 1.3 75.4 - - - +
154V GLU* 1.3 60.6 + - - +
156V TYR* 2.9 18.8 + - - +
157V LYS* 3.2 27.6 + - - +
189V TYR* 3.5 27.1 - - + +
192V GLU* 3.4 45.3 - - + +
193V LEU* 4.2 22.8 - - + +
196V VAL* 4.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G THR* 4.4 15.7 + - - +
150G SER* 3.6 29.7 + - - +
151G GLU* 5.9 3.4 - - + +
150V SER* 2.8 22.2 + - - +
151V GLU* 3.6 8.5 - - - +
153V VAL* 1.3 79.8 - - - +
155V ALA* 1.3 61.6 + - - +
157V LYS* 2.8 52.4 + - - +
158V PRO* 3.4 10.7 - - - +
192V GLU* 4.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141V PRO* 3.8 11.2 - - + +
142V SER 4.5 4.9 - - - +
143V VAL* 3.2 35.4 - - + -
151V GLU 2.9 12.3 + - - +
152V ILE 3.5 4.3 - - - +
154V GLU* 1.3 78.2 - - - +
156V TYR* 1.3 59.5 + - - +
158V PRO* 3.5 15.5 - - - +
159V LEU* 4.2 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139V LEU* 2.6 49.5 + - + -
141V PRO* 3.6 23.5 - - + +
152V ILE* 2.9 28.7 + - + -
153V VAL 2.9 8.7 + - - +
155V ALA* 1.3 76.3 - - - +
157V LYS* 1.3 67.5 + - + +
158V PRO 3.4 0.4 - - - -
159V LEU* 2.9 13.5 + - + +
160V ILE* 2.9 37.5 + - + +
173V VAL* 3.8 21.3 - - + -
174V CYS* 2.9 25.5 + - - +
176V ILE* 6.1 0.4 - - + -
189V TYR* 3.6 20.4 - - - -
193V LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G SER* 5.3 1.8 - - - -
153V VAL* 3.2 17.9 + - - +
154V GLU* 2.8 41.5 + - - +
155V ALA 3.3 0.2 - - - -
156V TYR* 1.3 76.0 - - - +
158V PRO* 1.4 63.9 - - + +
160V ILE* 3.4 1.7 + - - +
161V ALA* 2.9 30.9 + - - +
192V GLU* 4.6 6.4 + - - -
196V VAL* 3.9 41.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154V GLU 3.4 14.6 - - - +
155V ALA* 3.5 13.0 - - - +
157V LYS* 1.4 93.9 - - + +
159V LEU* 1.3 58.2 + - + +
161V ALA* 3.9 6.9 - - + +
162V LYS* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139V LEU* 4.4 13.8 - - + +
140V TYR 3.7 30.5 - - - +
141V PRO* 3.7 21.1 - - + -
142V SER 5.2 0.2 - - - +
155V ALA 4.2 8.7 - - - +
156V TYR* 2.9 14.4 + - + +
158V PRO* 1.3 77.2 - - + +
160V ILE* 1.3 66.3 + - - +
162V LYS* 3.2 7.7 + - + +
163V ALA* 3.0 21.7 + - - +
339V ASP 4.8 2.2 - - - +
340V PHE* 3.6 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139V LEU* 3.7 23.3 - - + -
156V TYR* 2.9 38.5 + - + +
157V LYS 4.0 2.7 - - - +
159V LEU* 1.3 74.8 - - - +
161V ALA* 1.3 61.7 + - - +
163V ALA* 3.2 3.3 + - - +
164V LYS* 3.0 34.8 + - - +
173V VAL* 4.9 1.6 - - + -
193V LEU* 4.4 5.8 - - + -
196V VAL* 3.8 27.4 - - + +
197V ILE* 3.8 46.4 - - + -
201V MET* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157V LYS 2.9 18.9 + - - +
158V PRO* 3.9 7.6 - - + +
160V ILE* 1.3 77.1 - - - +
162V LYS* 1.3 62.8 + - - +
164V LYS* 3.4 13.5 + - + +
165V GLU* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158V PRO 3.0 19.2 + - - +
159V LEU* 3.2 10.1 + - + +
161V ALA* 1.3 77.7 - - - +
163V ALA* 1.3 60.9 + - - +
165V GLU* 3.2 8.1 + - + +
166V ARG* 3.1 56.6 + - - +
339V ASP* 3.7 24.2 + - + +
340V PHE* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139V LEU* 4.7 2.5 - - + -
159V LEU 3.0 11.7 + - - +
160V ILE* 3.2 11.9 + - - +
162V LYS* 1.3 74.5 - - - +
164V LYS* 1.3 65.2 + - - +
166V ARG* 3.1 8.8 + - - +
168V ALA* 3.0 30.5 + - + +
171V VAL* 3.8 28.7 - - + -
201V MET* 4.5 2.2 - - + -
340V PHE* 3.8 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160V ILE* 3.0 26.0 + - - +
161V ALA* 3.6 13.7 - - + +
163V ALA* 1.3 74.4 - - - +
165V GLU* 1.3 58.1 + - - +
167V GLY* 3.0 19.0 + - - +
168V ALA 4.7 0.9 - - - +
196V VAL 2.9 25.4 + - - -
197V ILE 3.2 24.8 + - - -
198V GLY* 4.5 2.0 - - - +
201V MET* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161V ALA 3.1 14.1 + - - +
162V LYS* 3.3 14.4 - - + +
163V ALA 3.1 0.2 - - - -
164V LYS* 1.3 76.8 - - - +
166V ARG* 1.3 82.0 + - - +
167V GLY 3.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162V LYS* 3.2 43.1 - - - +
163V ALA* 3.1 7.9 + - - +
165V GLU* 1.3 105.9 + - - +
167V GLY* 1.3 58.6 + - - +
168V ALA* 3.6 1.5 + - + +
339V ASP* 2.6 36.3 + - - +
340V PHE* 4.5 5.2 - - + -
355V LYS* 3.2 32.5 - - - +
356V ILE* 3.7 32.5 - - + +
358V ASP* 3.2 10.6 + - - -
359V GLY 2.9 21.0 + - - -
----------------------------------------------------------
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