Contacts of the helix formed by residues 186 - 200 (chain Q) 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 186 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39Q ALA* 4.4 2.5 - - + -
41Q ASP* 3.4 23.3 + - - +
42Q GLY* 4.5 20.4 - - - +
43Q VAL 5.1 2.5 - - - +
44Q LEU* 5.8 2.5 - - + +
185Q THR* 1.4 74.6 + - - +
187Q LYS* 1.3 60.5 + - - +
188Q SER 3.3 0.2 - - - -
189Q ALA* 3.1 13.6 + - + +
190Q LEU* 3.0 48.5 + - + +
215Q THR* 4.8 14.6 - - + -
216Q LEU 4.9 0.4 - - - +
217Q THR* 4.1 26.5 - - + -
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Residues in contact with LYS 187 (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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185Q THR* 3.0 14.7 + - + +
186Q LEU* 1.3 78.8 - - - +
188Q SER* 1.4 59.7 + - - +
190Q LEU* 3.3 14.3 + - + +
191Q ALA* 3.2 27.8 + - - +
236Q LEU* 5.5 1.6 - - - +
239Q LYS* 3.6 35.0 - - - +
243Q GLU* 5.7 0.2 + - - -
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Residues in contact with SER 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183Q GLU* 4.7 5.0 + - - -
184Q MET* 3.5 30.3 - - - -
185Q THR* 3.0 23.5 + - - +
187Q LYS* 1.4 78.4 - - - +
189Q ALA* 1.4 56.2 + - - +
191Q ALA* 3.7 7.1 - - - +
192Q LEU* 3.1 36.2 + - - +
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Residues in contact with ALA 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q ILE* 4.3 32.1 - - + +
39Q ALA* 4.4 14.4 - - + -
42Q GLY 5.8 0.4 - - - +
44Q LEU* 4.0 11.2 - - + +
184Q MET* 4.7 3.3 - - + +
185Q THR 3.5 2.4 + - - -
186Q LEU* 3.1 25.1 + - + +
188Q SER* 1.4 75.1 - - - +
190Q LEU* 1.3 58.9 + - - +
192Q LEU* 4.3 2.1 - - - +
193Q ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q LEU* 3.7 23.1 - - + -
186Q LEU* 3.0 37.4 + - + +
187Q LYS* 3.3 17.2 + - + +
189Q ALA* 1.3 75.3 - - - +
191Q ALA* 1.3 60.7 + - - +
194Q ILE* 3.1 32.1 + - + +
213Q ILE* 4.4 7.2 - - + -
215Q THR* 4.6 7.0 - - + -
228Q LEU* 4.6 7.9 - - + -
236Q LEU* 3.8 42.6 - - + -
239Q LYS* 5.1 1.1 + - - -
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Residues in contact with ALA 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Q LYS* 3.2 21.0 + - - +
188Q SER* 3.7 11.2 - - - +
189Q ALA 3.3 0.4 - - - -
190Q LEU* 1.3 77.3 - - - +
192Q LEU* 1.4 61.7 + - + +
194Q ILE* 3.5 2.4 + - - +
195Q LYS* 3.0 26.5 + - - +
239Q LYS* 4.8 7.0 - - - +
243Q GLU* 4.6 20.2 - - - +
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Residues in contact with LEU 192 (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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37Q ILE* 4.0 15.7 - - + +
175Q LEU* 4.4 4.7 - - + -
178Q ASP* 3.1 31.4 - - + +
179Q TYR* 4.0 18.4 - - + -
184Q MET* 3.7 27.6 - - + -
188Q SER* 3.1 18.2 + - - +
189Q ALA 4.3 0.7 - - - +
191Q ALA* 1.4 77.0 - - + +
193Q ALA* 1.3 65.1 + - - +
195Q LYS* 3.5 31.4 - - + +
196Q VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 193 (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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35Q LEU* 4.0 11.4 - - + +
37Q ILE* 3.9 8.7 - - + +
44Q LEU* 3.5 36.3 - - + -
46Q ALA* 4.8 0.4 - - + -
189Q ALA 3.0 20.1 + - - +
190Q LEU 3.7 3.4 - - - +
192Q LEU* 1.3 76.9 - - - +
194Q ILE* 1.4 62.0 - - + +
196Q VAL* 3.3 0.3 + - - -
197Q LEU* 3.0 39.3 + - + +
213Q ILE* 5.3 0.7 - - + -
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Residues in contact with ILE 194 (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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190Q LEU* 3.1 19.1 + - - +
191Q ALA 3.9 2.7 - - - +
193Q ALA* 1.4 76.2 - - + +
195Q LYS* 1.3 64.2 + - - +
197Q LEU* 3.5 18.2 - - + +
198Q ASN* 2.8 48.0 + - - +
211Q VAL* 5.1 8.5 - - + -
213Q ILE* 4.0 25.4 - - + -
233Q VAL 5.8 0.2 - - - +
236Q LEU* 4.2 33.4 - - + +
237Q ILE* 5.3 4.9 - - + -
239Q LYS* 4.3 11.0 - - - +
240Q HIS* 3.9 19.7 - - + +
243Q GLU* 4.4 3.1 - - - +
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Residues in contact with LYS 195 (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 MET* 4.2 5.6 - - + -
178Q ASP* 3.7 32.6 + - + +
191Q ALA 3.0 15.6 + - - +
192Q LEU* 3.5 35.3 - - + +
194Q ILE* 1.3 75.7 - - - +
196Q VAL* 1.4 69.7 + - + +
198Q ASN* 3.0 7.9 + - - +
199Q LYS* 3.0 55.8 + - + +
243Q GLU* 5.0 5.5 + - - +
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Residues in contact with VAL 196 (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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35Q LEU* 3.6 19.1 - - + -
171Q ALA* 3.6 39.0 - - + +
174Q MET* 4.2 18.4 - - + -
175Q LEU* 3.6 26.9 - - + -
178Q ASP* 5.4 0.4 - - + +
192Q LEU 3.1 15.8 + - - +
195Q LYS* 1.4 86.8 - - + +
197Q LEU* 1.3 57.4 + - - +
199Q LYS* 3.1 6.7 + - - +
200Q THR* 3.0 27.3 + - - +
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Residues in contact with LEU 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q THR* 5.5 2.7 - - + -
35Q LEU* 3.9 11.4 - - + +
46Q ALA* 3.3 33.4 - - + -
47Q ALA 6.4 0.2 - - - -
193Q ALA* 3.0 29.5 + - + +
194Q ILE* 3.5 26.9 - - + +
196Q VAL* 1.3 75.9 - - - +
198Q ASN* 1.3 71.0 + - - +
200Q THR* 3.1 24.1 - - + +
201Q MET* 3.7 3.5 - - + +
206Q LEU* 3.1 30.3 - - + +
211Q VAL* 3.6 30.1 - - + -
213Q ILE* 5.1 0.4 - - + -
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Residues in contact with ASN 198 (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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194Q ILE* 2.8 31.4 + - - +
195Q LYS* 3.0 7.9 + - - +
197Q LEU* 1.3 88.8 - - - +
199Q LYS* 1.3 66.2 + - - +
201Q MET 3.6 2.8 - - - +
203Q VAL 3.4 21.0 - - - +
204Q SER* 3.4 8.9 - - - +
205Q LYS* 3.6 0.6 - - - +
206Q LEU* 3.4 25.2 - - - +
240Q HIS* 2.2 57.8 + - + +
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Residues in contact with LYS 199 (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 MET* 3.6 39.3 - - + -
195Q LYS* 3.0 50.9 + - - +
196Q VAL 3.1 4.2 + - - +
198Q ASN* 1.3 90.3 - - - +
200Q THR* 1.4 61.8 + - - +
201Q MET 3.4 6.8 - - - +
204Q SER 5.8 1.1 - - - +
240Q HIS* 4.6 7.3 - - - -
243Q GLU* 6.0 0.2 + - - -
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Residues in contact with THR 200 (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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33Q THR* 3.3 35.3 + - + +
166Q ASN 3.8 0.5 + - - -
167Q ASN* 3.4 37.5 + - - +
170Q ALA* 6.6 0.2 - - - -
171Q ALA* 4.8 10.1 - - - -
196Q VAL* 3.0 15.3 + - + +
197Q LEU* 3.1 27.6 - - - +
199Q LYS* 1.4 73.3 - - - +
201Q MET* 1.3 71.1 + - + +
202Q ASP 4.0 0.2 + - - -
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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