Contacts of the helix formed by residues 181 - 196 (chain W) in PDB entry 2Q4G
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 ILE 181 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153W LEU* 4.1 4.3 - - + +
154W SER 3.8 16.6 - - - +
155W ALA* 3.1 28.8 - - - +
157W SER* 5.5 0.7 - - - -
158W CYS* 3.5 19.3 - - - -
176W VAL* 4.3 12.8 - - + -
179W ASN* 2.8 31.1 + - + +
180W ASP* 1.3 71.5 - - - +
182W ASN* 1.3 67.0 + - - +
185W GLY 3.2 7.1 + - - -
186W VAL* 3.6 30.7 - - + +
189W LEU* 3.4 31.9 - - + -
205W LEU* 4.9 4.3 - - + -
208W CYS* 3.6 10.7 + - + +
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Residues in contact with ASN 182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154W SER* 5.5 1.6 - - - -
155W ALA* 4.4 12.0 - - + +
180W ASP* 3.1 27.5 + - - +
181W ILE* 1.3 85.0 - - - +
183W GLU* 1.3 67.1 + - - +
184W ALA* 4.5 3.8 - - + +
186W VAL* 3.1 20.0 + - - +
208W CYS 3.4 6.0 + - - -
209W GLY* 3.8 19.7 - - - +
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Residues in contact with GLU 183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182W ASN* 1.3 78.1 - - - +
184W ALA* 1.3 56.6 + - - +
187W ARG* 3.1 31.9 + - - +
209W GLY 3.8 3.4 + - - -
211W THR* 3.0 30.9 + - + +
213W ASP* 2.8 41.1 - - - +
214W ASN* 2.8 37.4 + - - +
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Residues in contact with ALA 184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ALA* 5.2 6.1 - - + -
182W ASN* 3.4 2.7 - - + +
183W GLU* 1.3 75.9 - - - +
185W GLY* 1.3 57.3 + - - +
187W ARG* 2.8 15.2 + - - +
188W VAL* 2.7 43.3 + - + +
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Residues in contact with GLY 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ALA* 4.2 10.2 - - - +
158W CYS* 3.4 31.5 - - - -
181W ILE 3.2 19.2 + - - -
184W ALA* 1.3 77.1 - - - +
186W VAL* 1.3 63.1 + - - +
188W VAL* 2.9 5.9 + - - +
189W LEU* 2.8 21.3 + - - +
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Residues in contact with VAL 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181W ILE* 3.6 24.6 - - + +
182W ASN 3.1 20.3 + - - +
185W GLY* 1.3 75.3 - - - +
187W ARG* 1.3 63.8 + - - +
189W LEU* 3.4 4.3 + - - +
190W CYS* 3.1 36.3 + - - -
205W LEU* 4.6 12.1 - - + -
208W CYS* 4.5 2.0 - - + +
210W VAL* 4.0 30.3 - - + -
214W ASN* 3.7 31.0 - - + +
217W ASP* 5.2 0.9 - - + -
218W LEU* 4.8 3.8 - - + -
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Residues in contact with ARG 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W GLU* 3.1 39.8 + - - +
184W ALA* 2.8 20.3 + - - +
186W VAL* 1.3 73.8 - - - +
188W VAL* 1.3 56.2 + - + +
190W CYS* 3.9 2.4 + - - +
191W GLN* 3.2 32.2 + - - +
213W ASP* 4.9 6.9 + - - +
216W ARG* 5.8 4.8 - - - +
217W ASP* 3.4 38.2 + - - +
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Residues in contact with VAL 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ALA 6.1 0.2 - - - +
158W CYS* 3.6 11.0 - - + +
159W GLU* 3.1 61.2 - - + +
162W ALA* 3.7 6.6 - - + +
184W ALA* 2.7 26.1 + - + +
185W GLY* 2.9 8.7 + - - +
187W ARG* 1.3 76.1 - - + +
189W LEU* 1.3 63.2 + - - +
191W GLN* 3.2 20.6 + - + +
192W GLY 3.2 5.4 + - - -
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Residues in contact with LEU 189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158W CYS* 3.4 29.2 - - + +
161W LEU* 3.6 35.0 - - + -
162W ALA* 4.4 5.4 - - - +
165W LEU* 3.8 12.2 - - + +
174W LEU* 4.6 10.1 - - + -
176W VAL* 4.1 22.9 - - + -
181W ILE* 3.4 29.4 - - + -
185W GLY 2.8 11.2 + - - +
186W VAL* 3.9 4.9 - - - +
188W VAL* 1.3 73.3 - - - +
190W CYS* 1.3 64.7 + - - +
192W GLY* 3.1 12.0 + - - -
193W LEU* 3.2 12.7 + - - +
203W LEU* 6.2 1.8 - - + -
205W LEU* 4.1 13.2 - - + -
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Residues in contact with CYS 190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W VAL* 3.1 24.9 + - - +
187W ARG 4.1 4.0 - - - +
189W LEU* 1.3 76.5 - - - +
191W GLN* 1.3 65.7 + - - +
193W LEU* 3.4 4.7 + - - -
194W LYS* 3.0 23.5 + - - +
203W LEU* 4.9 8.3 - - - -
205W LEU* 4.9 3.8 - - - -
217W ASP* 4.4 18.6 - - + +
218W LEU* 3.7 29.4 - - - -
221W ILE* 3.3 29.9 - - + +
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Residues in contact with GLN 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162W ALA* 5.8 0.2 - - + -
166W ARG* 5.1 4.7 - - - +
187W ARG* 3.2 25.2 + - - +
188W VAL* 3.2 15.8 + - + +
189W LEU 3.1 0.2 - - - -
190W CYS* 1.3 76.7 - - - +
192W GLY* 1.3 65.9 + - - +
194W LYS* 3.3 21.0 + - - +
195W ASP* 3.1 36.0 + - - +
217W ASP* 5.5 2.0 + - - -
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Residues in contact with GLY 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162W ALA* 4.1 27.3 - - - +
165W LEU* 4.5 3.4 - - - -
166W ARG* 4.6 5.3 - - - +
188W VAL 3.2 3.8 + - - -
189W LEU 3.1 7.8 + - - -
191W GLN* 1.3 78.6 - - - +
193W LEU* 1.3 63.3 + - - +
195W ASP* 3.0 10.7 + - - +
196W SER* 2.8 29.1 + - - -
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Residues in contact with LEU 193 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165W LEU* 3.7 29.0 - - + +
174W LEU* 6.2 0.7 - - + -
189W LEU* 3.2 12.2 + - + +
190W CYS* 3.7 10.3 - - - +
191W GLN 3.4 0.2 - - - -
192W GLY* 1.3 72.2 - - - +
194W LYS* 1.3 62.2 + - - +
196W SER* 2.7 18.3 + - - -
198W CYS* 4.1 9.9 - - - -
200W LEU* 3.4 51.1 - - + -
203W LEU* 3.7 25.8 - - + -
221W ILE* 3.7 21.5 - - + -
225W LYS* 2.8 22.2 + - - -
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Residues in contact with LYS 194 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190W CYS 3.0 14.3 + - - +
191W GLN* 3.4 25.9 - - - +
193W LEU* 1.3 79.3 - - - +
195W ASP* 1.3 73.0 + - - +
196W SER 3.5 2.8 - - - +
217W ASP 5.6 2.1 + - - -
220W GLY* 4.9 23.6 - - - -
221W ILE* 4.0 7.6 - - + +
224W SER* 5.0 14.9 + - - +
225W LYS* 4.2 5.6 + - - +
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Residues in contact with ASP 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166W ARG* 2.6 50.2 + - - +
191W GLN* 3.1 24.7 - - - +
192W GLY* 3.0 3.1 + - - +
194W LYS* 1.3 82.4 - - - +
196W SER* 1.3 70.4 + - - +
197W PRO* 3.4 4.6 - - - +
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Residues in contact with SER 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165W LEU 3.1 33.2 - - - -
166W ARG* 4.0 5.8 - - - +
192W GLY 2.8 19.3 + - - -
193W LEU* 2.7 16.9 + - - +
194W LYS 3.5 1.6 - - - +
195W ASP* 1.3 78.8 - - - +
197W PRO* 1.3 65.0 - - - +
198W CYS* 3.2 21.2 - - - -
225W LYS* 2.9 17.8 + - - -
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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