Contacts of the helix formed by residues 167 - 180 (chain Q) in PDB entry 5L4K
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 VAL 167 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163Q LYS 4.6 7.3 + - - +
164Q ALA 3.4 19.6 + - - +
166Q LEU* 1.3 77.8 - - - +
168Q GLU* 1.3 71.7 + - + +
170Q GLN* 4.1 1.0 - - - +
171Q LEU* 3.0 25.8 + - + +
193Q ALA* 4.2 24.5 - - + +
196Q THR* 5.3 3.7 - - + +
197Q ALA* 4.7 17.5 - - + +
203Q PRO* 6.2 1.1 - - + -
206Q LEU* 3.7 34.3 - - + -
210Q LEU* 4.8 12.8 - - + -
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Residues in contact with GLU 168 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q ALA* 4.1 24.2 - - - +
132Q ARG* 5.5 5.2 + - - -
134Q VAL* 5.9 0.5 - - - +
135Q SER* 5.2 2.3 + - - -
165Q LEU* 3.5 18.5 + - + +
167Q VAL* 1.3 78.0 - - + +
169Q VAL* 1.3 60.7 + - + +
170Q GLN 2.6 4.3 + - - -
171Q LEU* 2.5 33.4 + - + -
172Q LEU* 2.8 16.8 + - - +
205Q LYS* 5.6 3.8 + - - -
206Q LEU* 3.5 29.3 - - + +
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Residues in contact with VAL 169 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q ALA* 4.4 24.5 - - + -
134Q VAL* 4.9 11.0 - - + -
150Q GLY* 4.3 20.4 - - - +
153Q LEU* 4.0 36.1 - - + +
154Q LEU* 5.9 2.2 - - + -
157Q LEU* 4.1 17.9 - - + -
165Q LEU* 3.7 16.5 + - + +
166Q LEU* 4.6 4.5 - - + -
168Q GLU* 1.3 74.6 - - + +
170Q GLN* 1.3 56.6 + - - +
172Q LEU* 3.4 12.1 - - + +
173Q GLU* 3.0 24.9 + - - +
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Residues in contact with GLN 170 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q LEU* 3.5 34.6 - - + +
158Q LYS* 5.5 3.2 - - - +
166Q LEU* 3.8 31.8 + - + +
167Q VAL 3.8 2.0 + - - +
168Q GLU 2.6 4.4 + - - -
169Q VAL* 1.3 72.1 - - - +
171Q LEU* 1.3 58.5 + - - +
172Q LEU 3.1 1.8 - - - -
173Q GLU* 2.7 28.7 + - + +
174Q SER* 2.9 12.0 + - - -
189Q ALA* 4.2 9.9 - - + +
192Q SER* 2.7 49.5 + - - +
193Q ALA* 3.2 8.7 + - + -
196Q THR* 4.5 2.1 + - - -
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Residues in contact with LEU 171 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Q VAL* 3.0 25.2 + - + +
168Q GLU* 2.5 12.2 + - + +
170Q GLN* 1.3 72.4 - - - +
172Q LEU* 1.3 62.2 + - - +
174Q SER* 3.4 16.9 - - - -
175Q LYS* 3.5 14.8 + - - +
190Q LEU* 4.4 7.2 - - + -
193Q ALA* 4.2 7.6 - - + +
206Q LEU* 4.8 9.6 - - + +
209Q THR* 3.9 20.4 - - + -
210Q LEU* 3.6 51.8 - - + +
213Q GLN* 3.7 31.1 - - + +
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Residues in contact with LEU 172 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Q VAL* 3.4 54.1 - - + +
135Q SER* 4.5 9.6 - - - +
138Q PHE* 4.6 15.5 - - + -
146Q ALA* 5.1 2.9 - - + +
168Q GLU* 2.8 14.5 + - - +
169Q VAL* 3.4 15.3 - - + +
171Q LEU* 1.3 73.8 - - - +
173Q GLU* 1.3 80.8 + - - +
174Q SER 3.0 1.0 + - - -
175Q LYS* 3.0 30.7 + - + +
176Q THR* 3.0 28.7 + - - +
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Residues in contact with GLU 173 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Q ALA 3.7 16.3 - - - +
147Q LEU* 3.8 25.5 - - + +
150Q GLY* 2.9 35.5 - - - +
151Q SER* 3.8 8.1 + - - -
154Q LEU* 4.4 8.1 - - + +
169Q VAL 3.0 14.0 + - - +
170Q GLN* 2.7 21.8 + - + +
172Q LEU* 1.3 80.2 - - - +
174Q SER* 1.3 61.1 + - - +
176Q THR* 3.0 6.3 + - - -
177Q TYR* 3.0 40.4 + - + +
189Q ALA* 4.4 7.4 - - + -
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Residues in contact with SER 174 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Q GLN 2.9 10.0 + - - -
171Q LEU* 3.4 14.6 - - - -
173Q GLU* 1.3 77.3 - - - +
175Q LYS* 1.3 65.4 + - - +
177Q TYR* 3.1 4.2 + - - +
178Q HIS* 2.9 19.9 + - - +
186Q ALA* 3.8 22.7 + - - +
189Q ALA* 4.0 16.5 - - - +
190Q LEU* 4.0 17.1 - - - +
213Q GLN* 3.9 18.1 + - - +
217Q ILE* 4.5 4.0 - - - +
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Residues in contact with LYS 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Q SER* 5.9 0.6 + - - -
138Q PHE* 3.8 36.9 - - + -
171Q LEU* 3.5 13.2 + - - +
172Q LEU* 3.0 27.1 + - + +
174Q SER* 1.3 76.4 - - - +
176Q THR* 1.3 56.5 + - - +
178Q HIS* 2.6 26.8 + - - +
179Q ALA* 3.0 10.4 + - - +
209Q THR* 5.1 15.8 - - - +
213Q GLN* 3.3 34.1 - - - +
246Q LYS* 6.3 0.8 - - - +
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Residues in contact with THR 176 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q PHE* 3.8 19.8 - - - -
143Q TYR* 3.8 23.6 - - + +
146Q ALA* 3.8 19.4 - - + +
147Q LEU* 3.4 38.4 - - + -
172Q LEU* 3.0 18.6 + - - +
173Q GLU* 3.0 10.7 + - - -
175Q LYS* 1.3 78.8 - - - +
177Q TYR* 1.3 63.7 + - - +
178Q HIS 3.1 0.2 + - - -
179Q ALA* 3.2 2.8 + - - +
180Q LEU* 3.1 19.4 + - - +
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Residues in contact with TYR 177 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Q LEU* 3.4 41.7 - - + +
173Q GLU* 3.0 34.4 + - + +
174Q SER 3.7 4.9 - - - +
176Q THR* 1.3 77.3 - - - +
178Q HIS* 1.3 58.2 + - - +
180Q LEU* 3.4 6.3 + - + +
181Q SER 3.2 7.3 + - - -
182Q ASN* 3.0 36.8 + - + +
185Q LYS* 3.6 63.1 + - + -
186Q ALA* 3.9 16.6 - - + +
189Q ALA* 4.5 6.5 - - + -
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Residues in contact with HIS 178 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174Q SER 2.9 12.0 + - - +
175Q LYS* 2.6 21.7 + - - +
177Q TYR* 1.3 72.3 - - - +
179Q ALA* 1.3 55.3 + - - -
181Q SER* 3.9 8.9 + - - -
182Q ASN 4.3 14.2 + - - -
183Q LEU* 5.6 2.7 - - + +
186Q ALA* 4.6 2.6 - - + +
213Q GLN* 4.7 5.6 - - - +
216Q ILE* 3.4 34.9 - - + +
217Q ILE* 4.2 21.0 - - + +
220Q ALA* 4.6 13.9 - - + -
318Q ILE* 3.8 20.5 - - + +
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Residues in contact with ALA 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q PHE* 4.6 8.7 - - + -
143Q TYR* 3.5 39.8 - - + +
175Q LYS 3.0 9.2 + - - +
176Q THR 4.2 1.8 - - - +
178Q HIS* 1.3 75.8 - - - +
180Q LEU* 1.3 56.9 + - - +
181Q SER* 2.9 16.0 + - - -
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Residues in contact with LEU 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Q TYR* 3.9 28.5 - - + -
144Q GLN* 3.3 28.7 - - + +
147Q LEU* 3.8 19.5 - - + -
176Q THR 3.1 16.0 + - - +
177Q TYR* 3.4 9.4 + - + +
179Q ALA* 1.3 73.1 - - - +
181Q SER* 1.3 68.2 + - - +
182Q ASN* 3.4 21.3 + - - +
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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
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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