Contacts of the helix formed by residues 181 - 200 (chain B) in PDB entry 3TW4
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 THR 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASP* 6.1 0.4 - - - +
179B THR 4.8 2.9 - - - +
180B LEU* 1.3 82.5 - - - +
182B PRO* 1.3 62.5 - - - +
183B GLU* 3.6 6.2 + - - +
184B GLU* 2.7 50.4 + - + +
185B CYS* 2.4 37.6 + - - -
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU 4.7 1.1 - - - +
181B THR* 1.3 86.7 - - - +
183B GLU* 1.3 56.7 + - - +
185B CYS* 3.8 7.4 - - + +
186B GLN* 2.9 28.1 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR* 3.1 5.9 + - - +
182B PRO* 1.3 76.9 - - - +
184B GLU* 1.3 67.5 + - - +
186B GLN* 3.1 7.8 + - - +
187B GLN* 2.9 26.5 + - - +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GDP 2.2 55.8 + - - +
149B SER 5.4 0.7 - - - +
179B THR 4.9 0.9 - - - +
180B LEU* 3.2 30.0 - - + +
181B THR* 2.7 50.2 + - + +
183B GLU* 1.3 73.0 - - + +
185B CYS* 1.3 63.0 + - - +
187B GLN* 3.9 3.9 - - - +
188B PHE* 2.9 25.1 + - - +
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Residues in contact with CYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ALA* 6.4 2.0 - - + -
180B LEU* 3.3 19.4 - - + +
181B THR 2.4 31.6 + - - +
182B PRO* 3.8 7.9 - - + +
184B GLU* 1.3 68.2 - - - +
186B GLN* 1.3 62.6 + - - +
188B PHE* 3.0 5.0 - - - +
189B LYS* 2.9 36.7 + - + +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO 2.9 20.2 + - - +
183B GLU* 3.4 7.9 - - - +
185B CYS* 1.3 76.8 - - - +
187B GLN* 1.3 65.3 + - - +
189B LYS* 3.2 7.4 + - - +
190B LYS* 3.0 24.6 + - - +
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLU 2.9 16.7 + - - +
184B GLU* 4.2 3.8 - - - +
186B GLN* 1.3 73.9 - - - +
188B PHE* 1.3 61.3 + - - +
190B LYS* 4.1 5.6 - - - +
191B GLN* 2.9 26.0 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 4.9 9.0 - - + -
147B ALA 3.5 25.1 - - - -
148B PRO* 3.8 18.2 - - + -
150B GLY 4.2 22.7 - - - +
151B HIS 5.0 2.2 - - - -
152B GLY 3.5 28.3 - - - -
174B ILE* 4.3 21.8 - - + -
180B LEU* 3.8 19.5 - - + -
184B GLU 2.9 16.1 + - - +
185B CYS* 3.0 11.2 - - - +
186B GLN 3.0 0.2 - - - -
187B GLN* 1.3 72.6 - - - +
189B LYS* 1.3 67.6 + - + +
191B GLN* 2.9 9.4 + - + +
192B ILE* 2.9 42.5 + - + +
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ILE* 3.6 17.3 - - + -
185B CYS* 2.9 26.2 + - - +
186B GLN* 3.6 8.1 - - - +
188B PHE* 1.3 71.5 - - - +
190B LYS* 1.3 57.4 + - - +
192B ILE* 2.6 34.5 + - - +
193B MET* 2.9 14.1 + - - +
223B ASP 5.5 0.2 - - - +
224B ARG* 2.5 33.1 + - - +
225B LEU 3.8 5.4 - - - +
226B PRO* 2.9 35.7 + - + +
228B ALA* 4.6 11.0 - - - -
262B ASP* 3.5 19.7 + - - -
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLN 3.0 13.0 + - - +
187B GLN* 4.1 5.6 - - - +
189B LYS* 1.3 78.0 - - - +
191B GLN* 1.3 57.4 + - - +
193B MET* 3.9 13.2 - - + +
194B LYS* 2.9 31.5 + - - +
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Residues in contact with GLN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B HIS 4.1 20.2 - - - +
152B GLY* 5.1 3.6 - - - -
187B GLN 2.9 20.7 + - - +
188B PHE* 2.9 10.9 + - + +
190B LYS* 1.3 77.5 - - - +
192B ILE* 1.3 55.0 + - - +
194B LYS* 3.5 7.0 - - - +
195B GLU* 2.9 34.4 + - + +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 5.3 10.8 - - + -
152B GLY 5.3 1.3 - - - +
153B LEU* 3.3 30.3 - - + -
161B MET* 5.9 2.2 - - + -
172B PRO* 6.4 2.9 - - + -
174B ILE* 3.5 37.7 - - + -
188B PHE* 2.9 36.4 + - + +
189B LYS* 2.6 20.3 + - - +
191B GLN* 1.3 68.8 - - + +
193B MET* 1.3 58.7 + - - +
195B GLU* 2.5 29.0 + - - +
196B ILE* 2.8 26.5 + - + +
226B PRO* 4.0 11.9 - - + -
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LYS* 2.9 12.7 + - - +
190B LYS* 3.9 10.8 - - + +
192B ILE* 1.3 75.9 - - - +
194B LYS* 1.3 57.9 + - - +
196B ILE* 3.1 14.9 + - + +
197B GLN* 2.9 35.3 + - - +
222B LYS 5.6 3.8 - - - +
223B ASP* 4.8 6.7 - - - +
225B LEU 3.4 11.2 - - - +
226B PRO* 3.3 36.1 - - + -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS 2.9 19.2 + - - +
191B GLN* 3.5 8.1 - - - +
193B MET* 1.3 75.7 - - - +
195B GLU* 1.3 57.6 + - - +
197B GLN* 5.1 2.7 - - - -
198B GLU* 2.9 35.1 + - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLY* 5.2 4.1 - - - -
153B LEU* 3.7 36.5 - - + +
158B ILE* 3.6 10.4 - - + +
191B GLN* 2.9 27.2 + - + +
192B ILE* 2.5 21.0 + - - +
194B LYS* 1.3 73.1 - - - +
196B ILE* 1.3 53.3 + - - +
198B GLU* 4.3 8.9 - - - +
199B HIS* 2.2 63.1 + - - +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 4.8 4.0 - - + -
158B ILE* 6.5 0.2 - - - -
161B MET* 4.8 13.7 - - + -
172B PRO* 6.0 5.6 - - + -
192B ILE* 2.9 30.7 - - + +
193B MET* 3.4 26.2 - - + +
195B GLU* 1.3 71.6 - - - +
197B GLN* 1.3 50.4 + - - +
198B GLU 2.9 3.8 - - - -
199B HIS* 2.5 9.3 + - - -
200B LYS* 2.4 36.0 + - - -
201B ILE* 3.4 44.9 + - + +
203B ILE* 5.2 16.2 - - + -
226B PRO* 5.0 3.8 - - + -
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Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B MET 2.9 18.7 + - - +
194B LYS* 4.6 2.5 - - - +
196B ILE* 1.3 74.1 - - - +
198B GLU* 1.3 59.8 + - - +
200B LYS* 3.7 12.6 + - - +
201B ILE 5.2 0.9 - - - +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS 2.9 22.2 + - - +
195B GLU* 3.6 9.6 - - - +
196B ILE 2.9 0.6 - - - -
197B GLN* 1.3 80.2 - - - +
199B HIS* 1.3 84.9 + - + +
200B LYS* 3.1 7.0 + - - +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 3.3 34.2 - - + +
162B LYS* 4.2 12.0 - - + +
195B GLU* 2.2 57.1 + - - +
196B ILE* 2.5 10.5 + - - +
198B GLU* 1.3 92.6 + - + +
200B LYS* 1.3 68.1 - - - +
201B ILE* 3.5 20.1 + - + +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 4.9 1.7 - - - +
165B HIS* 4.2 9.2 - - - -
196B ILE 2.4 13.7 + - - -
197B GLN* 3.7 10.1 + - - +
198B GLU 3.1 7.5 - - - +
199B HIS* 1.3 77.1 - - - +
201B ILE* 1.3 58.9 + - - +
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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
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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