Contacts of the helix formed by residues 159 - 176 (chain X) 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 PRO 159 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LYS* 5.7 1.6 - - - -
18X CYS* 3.7 8.3 - - - -
158X ASP* 1.3 89.9 - - + +
160X ASP* 1.3 58.3 + - - +
162X LEU* 3.5 10.5 - - + -
163X PHE* 2.9 35.0 + - - +
188X ILE* 3.5 18.3 - - + +
190X GLU* 3.5 35.0 - - - +
193X LYS* 3.5 28.7 - - - +
195X THR* 5.4 1.3 - - - +
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Residues in contact with ASP 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206W LYS* 3.8 13.8 - - + +
207W GLY 5.1 0.3 + - - -
158X ASP* 3.0 23.1 + - - +
159X PRO* 1.3 87.1 - - - +
161X HIS* 1.3 58.4 + - - +
163X PHE* 4.2 4.4 - - - +
164X GLU* 3.1 24.8 + - - +
193X LYS* 4.2 12.3 + - - -
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Residues in contact with HIS 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203W ARG* 4.5 15.9 + - + -
204W CYS 3.7 22.6 + - - -
205W GLU* 5.1 1.1 - - - -
206W LYS* 4.1 22.0 - - + +
154X GLU* 2.2 40.0 + - - +
156X ASN 4.3 0.2 - - - -
157X MET* 2.2 49.9 - - + +
158X ASP* 2.7 24.8 + - - +
160X ASP* 1.3 71.4 - - - +
162X LEU* 1.3 58.1 + - - +
163X PHE 3.2 2.0 - - - -
164X GLU* 2.9 20.1 + - - +
165X THR* 3.0 19.4 + - - -
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Residues in contact with LEU 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X MET* 3.3 27.5 - - + +
15X GLY* 3.6 24.9 - - - +
18X CYS* 3.2 39.9 - - + +
20X ALA* 3.5 26.0 - - + +
157X MET* 3.7 24.4 - - + -
158X ASP 2.9 12.1 + - - +
159X PRO* 3.2 11.6 + - + +
161X HIS* 1.3 75.1 - - - +
163X PHE* 1.3 60.6 + - - +
166X ILE* 3.1 26.2 + - - +
188X ILE* 4.1 6.7 - - + -
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Residues in contact with PHE 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X PRO 2.9 12.8 + - - +
160X ASP* 4.2 7.4 - - - +
162X LEU* 1.3 75.8 - - - +
164X GLU* 1.3 71.9 + - - +
166X ILE* 3.4 4.7 - - - +
167X SER* 2.8 53.7 + - - -
186X VAL* 4.6 21.1 - - + -
188X ILE* 3.3 26.6 - - + +
195X THR* 4.8 11.7 - - - -
196X THR 5.1 13.7 - - - -
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Residues in contact with GLU 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204W CYS* 4.0 17.8 - - - +
205W GLU 4.4 4.6 - - - +
206W LYS* 3.6 15.9 - - + -
207W GLY* 2.9 30.7 + - - -
160X ASP 3.1 21.7 - - - +
161X HIS 2.9 10.5 + - - +
163X PHE* 1.3 87.8 - - + +
165X THR* 1.3 59.1 + - - +
167X SER* 3.9 3.7 - - - -
168X GLN* 3.0 39.3 + - - +
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Residues in contact with THR 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204W CYS* 4.4 15.2 + - - +
13X MET* 4.0 17.5 - - - -
149X CYS* 5.5 3.4 - - + +
152X LEU* 4.2 34.5 + - + +
153X TRP* 4.9 1.3 - - - +
154X GLU* 4.7 0.2 + - - -
157X MET* 3.4 34.1 - - + +
161X HIS* 3.0 17.3 + - - -
164X GLU* 1.3 74.0 - - - +
166X ILE* 1.4 59.6 + - - +
168X GLN* 3.2 3.5 + - - +
169X ALA* 2.9 29.0 + - + +
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Residues in contact with ILE 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X MET* 4.1 22.0 - - + -
13X MET* 3.9 21.0 - - + +
20X ALA* 3.5 24.7 - - + -
21X ILE* 3.6 28.9 - - - +
22X ALA* 3.7 13.2 - - + +
162X LEU 3.1 21.0 + - - +
163X PHE* 3.4 8.5 - - - +
165X THR* 1.4 76.2 - - - +
167X SER* 1.4 59.7 + - - +
169X ALA* 3.9 3.9 - - - +
170X MET* 2.9 28.3 + - - +
186X VAL* 3.8 21.8 - - + -
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Residues in contact with SER 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X PHE* 2.8 47.8 + - - -
164X GLU* 4.0 7.2 - - - -
166X ILE* 1.4 72.8 - - - +
168X GLN* 1.3 63.6 + - - +
170X MET* 3.7 5.3 - - - +
171X LEU* 2.9 46.3 + - - +
184X VAL* 5.5 2.7 - - - +
186X VAL* 4.1 15.1 - - - +
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Residues in contact with GLN 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M ASN* 3.7 18.4 + - - +
204W CYS* 3.7 31.6 - - + -
148X MET* 4.1 1.1 - - + -
164X GLU* 3.0 26.2 + - - +
165X THR 3.7 3.4 - - - +
167X SER* 1.3 81.5 - - - +
169X ALA* 1.3 56.0 + - - +
171X LEU* 4.9 9.0 - - - +
172X ASN* 2.9 64.7 + - - +
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Residues in contact with ALA 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X MET* 4.0 11.1 - - + +
13X MET* 6.2 0.7 - - - -
148X MET* 3.7 18.7 - - + +
149X CYS* 3.5 35.4 - - + -
152X LEU* 5.4 1.3 - - + +
165X THR* 2.9 19.1 + - + +
166X ILE* 3.9 4.7 - - - +
168X GLN* 1.3 74.2 - - - +
170X MET* 1.3 62.5 + - - +
173X ALA* 3.1 28.9 + - - +
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Residues in contact with MET 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ALA* 5.2 3.1 - - + -
11X MET* 3.7 26.9 - - + +
22X ALA* 4.6 5.8 - - + -
23X ALA* 3.6 11.2 - - - -
24X ASP* 3.3 42.8 - - + +
166X ILE 2.9 18.9 + - - +
167X SER* 3.7 7.6 - - - +
169X ALA* 1.3 78.4 - - - +
171X LEU* 1.3 63.6 + - + +
173X ALA* 5.1 0.2 - - - -
174X VAL* 3.1 53.3 + - + +
183X GLY 4.4 0.2 - - - +
184X VAL* 3.7 38.1 - - + -
186X VAL* 6.0 0.2 - - + -
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Residues in contact with LEU 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X SER* 2.9 29.3 + - - +
168X GLN* 4.1 11.7 - - - +
170X MET* 1.3 80.7 - - + +
172X ASN* 1.3 61.8 + - - +
174X VAL* 5.0 2.7 - - + -
175X ASP* 3.0 40.4 + - + +
184X VAL* 3.8 29.8 - - + -
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Residues in contact with ASN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M PRO* 3.6 24.6 + - + +
151M ASN* 3.7 19.3 + - - +
148X MET* 3.1 27.1 - - + +
168X GLN* 2.9 44.7 + - - +
171X LEU* 1.3 78.7 - - - +
173X ALA* 1.3 65.6 + - - +
175X ASP* 4.7 1.2 - - - +
176X ARG* 3.8 14.6 + - - +
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Residues in contact with ALA 173 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147M PRO* 4.3 2.4 - - - +
141X CYS* 5.0 0.2 - - - -
144X GLN* 3.2 48.3 + - + +
145X MET* 3.7 23.1 - - + -
148X MET* 4.9 2.0 - - + +
169X ALA 3.1 18.4 + - - +
170X MET* 4.2 1.3 - - - +
172X ASN* 1.3 79.1 - - - +
174X VAL* 1.3 61.2 + - + +
177X ASP* 3.4 21.7 + - - +
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Residues in contact with VAL 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ALA* 4.0 23.1 - - + -
141X CYS* 4.8 4.9 - - - -
145X MET* 5.1 2.5 - - - -
170X MET* 3.1 46.3 + - + +
171X LEU* 4.6 2.0 - - + +
173X ALA* 1.3 80.4 - - + +
175X ASP* 1.4 64.2 + - - +
176X ARG 3.2 1.8 - - - -
177X ASP* 2.9 23.3 + - - +
180X SER* 3.3 11.7 - - - +
181X GLY* 3.2 36.1 - - - +
184X VAL* 5.8 1.1 - - + -
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Residues in contact with ASP 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ARG* 3.4 23.4 + - - -
29L GLN* 5.0 2.7 + - - -
171X LEU* 3.0 26.5 + - + +
172X ASN* 4.8 1.8 - - - +
174X VAL* 1.4 77.6 - - - +
176X ARG* 1.3 62.5 + - - +
177X ASP 3.6 1.6 - - - +
180X SER 5.4 0.2 - - - -
181X GLY* 5.9 1.6 - - - -
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Residues in contact with ARG 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L TYR* 3.5 18.6 + - + -
26L ILE* 2.4 60.3 + - + +
27L ALA 4.7 3.8 + - - -
29L GLN* 3.3 29.6 + - - +
146M GLN* 2.7 71.3 + - - +
147M PRO* 3.2 7.3 - - + +
150M ASP* 3.9 16.8 + - - +
144X GLN* 3.6 25.1 - - - +
172X ASN 3.8 12.9 + - - +
173X ALA 3.9 0.2 - - - +
175X ASP* 1.3 77.4 - - - +
177X ASP* 1.3 53.9 + - - +
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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