Contacts of the helix formed by residues 168 - 185 (chain M) in PDB entry 5A0Q
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 LEU 168 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M PHE* 2.9 41.3 - - + -
22M ILE* 5.7 1.8 - - + -
166M LEU 3.0 4.0 + - - -
167M SER* 1.3 72.7 - - - +
169M ASP* 1.4 62.8 + - - +
171M ALA* 3.5 2.0 - - + +
172M MET* 2.9 41.6 + - + +
197M ILE* 5.6 0.4 - - + -
199M THR* 4.7 7.6 - - + -
204M ARG* 3.5 35.7 - - - +
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Residues in contact with ASP 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M SER* 3.6 0.8 - - - -
168M LEU* 1.4 80.3 - - + +
170M ARG* 1.3 63.3 + - - +
172M MET* 3.3 9.5 + - - +
173M ARG* 3.1 20.3 + - - +
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Residues in contact with ARG 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152M GLN* 3.3 44.5 + - - +
164M VAL* 3.4 30.9 - - - +
167M SER* 3.6 19.5 + - - +
169M ASP* 1.3 79.9 + - - +
171M ALA* 1.4 51.0 - - - +
173M ARG* 3.3 9.5 + - + +
174M LEU* 2.8 31.6 + - - +
202W TYR* 3.3 30.9 + - + +
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Residues in contact with ALA 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ILE* 4.8 5.8 - - + +
20M PHE* 4.7 5.8 - - + -
22M ILE* 4.4 14.8 - - + -
166M LEU 4.7 4.3 - - - +
167M SER* 2.7 26.2 + - - +
168M LEU* 3.5 6.3 - - - +
169M ASP 3.2 0.4 - - - -
170M ARG* 1.4 75.6 - - - +
172M MET* 1.3 59.1 + - - +
174M LEU* 3.6 11.1 - - + +
175M VAL* 2.9 34.7 + - - +
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Residues in contact with MET 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ILE* 4.7 10.3 - - + -
168M LEU* 2.9 32.6 + - + +
169M ASP* 3.5 11.7 - - - +
171M ALA* 1.3 74.6 - - - +
173M ARG* 1.3 65.5 + - - +
175M VAL* 3.3 5.0 + - - +
176M LYS* 2.9 59.9 + - - +
195M ILE* 4.7 11.7 - - + -
197M ILE* 3.8 37.2 - - + -
204M ARG* 4.4 9.6 - - - +
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Residues in contact with ARG 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M ASP 3.1 10.1 + - - +
170M ARG* 3.6 11.4 - - + +
171M ALA 3.3 0.2 - - - -
172M MET* 1.3 80.9 - - - +
174M LEU* 1.3 55.2 + - - +
176M LYS* 3.2 17.9 + - - +
177M ASP* 2.9 41.1 + - + +
180M ILE* 4.4 20.2 - - - +
202W TYR* 6.2 3.1 - - + -
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Residues in contact with LEU 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ILE* 5.9 1.8 - - + -
148M LEU* 4.7 7.0 - - + -
149M LEU* 5.2 5.5 - - + +
152M GLN* 3.6 13.5 - - + +
153M VAL* 3.2 34.3 - - + -
170M ARG* 2.8 12.6 + - - +
171M ALA* 3.6 11.0 - - + +
172M MET 3.2 0.4 - - - -
173M ARG* 1.3 74.8 - - - +
175M VAL* 1.4 62.1 + - + +
177M ASP* 4.8 3.3 - - + +
178M VAL* 3.3 31.3 + - + +
202W TYR* 2.4 70.2 - - + +
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Residues in contact with VAL 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 4.0 17.9 - - + -
15M ILE* 2.9 41.7 - - + -
22M ILE* 4.0 23.1 - - + +
24M ALA* 4.0 22.4 - - + -
149M LEU* 5.5 0.7 - - - -
171M ALA 2.9 16.9 + - - +
172M MET* 3.7 5.6 - - - +
174M LEU* 1.4 71.7 - - - +
176M LYS* 1.3 67.8 + - - +
178M VAL* 3.3 19.0 - - - +
179M PHE* 3.9 8.1 + - - +
193M LEU* 4.7 1.2 - - + +
195M ILE* 4.6 8.3 - - + -
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Residues in contact with LYS 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M MET* 2.9 53.7 + - - +
173M ARG* 3.2 23.1 + - - +
175M VAL* 1.3 77.5 - - - +
177M ASP* 1.4 62.1 + - - +
179M PHE* 3.3 15.1 + - - +
180M ILE* 3.4 16.5 + - + +
193M LEU* 4.4 12.1 - - + +
195M ILE* 3.8 29.8 - - + -
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Residues in contact with ASP 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M ARG* 2.9 31.8 + - + +
174M LEU* 4.8 4.5 - - + +
176M LYS* 1.4 74.2 - - - +
178M VAL* 1.3 64.3 + - + +
180M ILE* 3.1 27.1 + - + +
181M SER* 2.9 32.0 + - - -
202W TYR 5.8 1.7 + - - -
151X SER* 4.5 15.6 + - - +
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Residues in contact with VAL 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LEU* 3.9 20.9 - - + -
145M LEU* 3.3 29.1 - - + +
148M LEU* 3.3 36.1 - - + -
149M LEU* 4.1 11.4 - - + -
174M LEU* 3.3 22.4 - - + +
175M VAL 3.3 19.5 - - - +
177M ASP* 1.3 79.9 - - + +
179M PHE* 1.4 57.1 + - + +
181M SER* 3.4 8.3 + - - -
182M ALA 2.9 21.5 + - - -
151X SER* 5.8 0.7 - - - +
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Residues in contact with PHE 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M THR* 3.7 25.4 - - + -
13M LEU* 3.6 33.2 - - + -
24M ALA* 4.1 16.8 - - + -
25M SER* 4.2 0.7 - - - -
26M ASP* 3.8 16.2 - - + -
145M LEU* 4.2 10.3 - - + -
175M VAL 3.9 12.1 - - - -
176M LYS 3.3 9.5 + - - +
177M ASP 3.2 0.4 - - - -
178M VAL* 1.4 78.1 - - + +
180M ILE* 1.3 60.5 + - + +
181M SER 3.3 0.4 - - - -
182M ALA* 3.9 4.8 - - + +
183M ALA* 3.1 29.1 + - - +
189M THR* 3.6 29.6 - - + -
190M GLY 6.1 0.2 - - - -
193M LEU* 3.3 39.5 - - + -
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Residues in contact with ILE 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M ARG* 4.4 15.9 - - - +
176M LYS* 3.5 13.9 - - + +
177M ASP* 3.1 29.3 + - - +
179M PHE* 1.3 74.6 - - - +
181M SER* 1.3 61.7 + - - +
183M ALA* 3.5 4.0 + - - +
184M GLU* 3.3 33.7 + - + +
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Residues in contact with SER 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145M LEU* 5.8 0.9 - - - -
148M LEU* 5.3 2.0 - - - -
177M ASP* 2.9 16.4 + - - -
178M VAL* 3.5 11.0 - - - -
180M ILE* 1.3 76.0 - - - +
182M ALA* 1.4 61.5 + - - +
184M GLU* 3.6 1.9 + - - -
185M ARG 3.2 10.6 + - - -
147X GLY 4.9 4.9 - - - -
150X GLU* 2.7 47.8 - - - +
151X SER* 3.3 26.9 + - - -
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Residues in contact with ALA 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141M ALA* 4.0 16.2 - - + -
144M MET* 5.0 6.7 - - + -
145M LEU* 4.0 18.4 - - + +
178M VAL 2.9 17.3 + - - +
179M PHE* 4.2 4.0 - - - +
181M SER* 1.4 72.5 - - - +
183M ALA* 1.3 60.7 + - - +
184M GLU 3.4 0.2 - - - -
185M ARG* 4.5 3.8 - - - +
186M ASP* 2.9 32.9 + - - +
189M THR* 3.8 19.6 - - + -
150X GLU* 4.7 0.7 - - - -
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Residues in contact with ALA 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ARG* 4.8 2.6 + - - -
179M PHE 3.1 21.2 + - - +
180M ILE* 3.8 3.8 - - - +
181M SER 3.3 0.4 - - - -
182M ALA* 1.3 77.7 - - - +
184M GLU* 1.4 72.6 + - - +
186M ASP 3.2 12.3 - - - +
187M VAL* 5.3 0.2 - - - -
189M THR* 3.4 24.0 - - + +
190M GLY* 3.9 15.7 - - - -
191M ASP 5.9 0.2 - - - +
19W ARG* 4.7 5.2 + - - -
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Residues in contact with GLU 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M ILE* 3.3 24.0 + - + +
181M SER* 3.6 3.3 + - - +
182M ALA 3.4 0.2 - - - -
183M ALA* 1.4 89.4 - - - +
185M ARG* 1.3 57.5 + - - +
19W ARG* 3.7 19.4 + - - +
26W VAL* 4.6 1.4 - - - +
29W LYS* 3.7 30.8 - - + +
150X GLU* 4.7 5.4 - - - +
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Residues in contact with ARG 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M MET* 3.6 27.1 - - + -
181M SER 3.2 6.2 + - - +
182M ALA 4.2 0.2 - - - +
184M GLU* 1.3 80.3 - - - +
186M ASP* 1.3 59.5 + - - +
25W VAL* 4.1 1.0 - - + -
26W VAL* 3.1 59.6 + - - +
27W ALA 5.7 1.6 - - - -
29W LYS* 3.4 46.4 - - - +
134X ASP* 4.8 1.0 + - - -
135X PHE* 3.8 15.0 - - - -
146X TYR* 3.2 32.6 + - + +
150X GLU* 3.0 56.0 + - - +
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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
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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) + - + + + + + -
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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