Contacts of the helix formed by residues 181 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR 4.8 3.4 - - - +
180A LEU* 1.3 85.7 - - + +
182A PRO* 1.3 63.5 - - - +
183A GLU* 3.6 6.1 + - - +
184A GLU* 2.7 31.2 + - + +
185A CYS* 2.4 38.8 + - - -
501B GDP 5.4 9.6 - - + +
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 4.7 0.9 - - - +
181A THR* 1.3 87.6 - - - +
183A GLU* 1.3 57.7 + - - +
185A CYS* 3.8 6.8 - - + +
186A GLN* 2.9 27.9 + - - +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 3.1 5.6 + - - +
182A PRO* 1.3 76.1 - - - +
184A GLU* 1.3 68.0 + - - +
186A GLN* 3.1 7.4 + - - +
187A GLN* 2.9 26.7 + - - +
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.4 30.5 - - + +
181A THR* 2.7 29.4 + - + +
183A GLU* 1.3 73.4 - - - +
185A CYS* 1.3 62.6 + - - +
187A GLN* 3.9 4.0 - - - +
188A PHE* 2.9 25.5 + - - +
501B GDP 4.6 11.0 - - - +
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Residues in contact with CYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA* 6.4 2.0 - - + -
180A LEU* 3.3 20.3 - - + +
181A THR 2.4 32.1 + - - +
182A PRO* 3.8 7.2 - - + +
184A GLU* 1.3 66.7 - - - +
186A GLN* 1.3 64.5 + - - +
188A PHE* 3.0 4.8 - - - +
189A LYS* 2.9 37.0 + - + +
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO 2.9 18.8 + - - +
183A GLU* 3.1 7.8 + - - +
185A CYS* 1.3 78.4 - - - +
187A GLN* 1.3 65.4 + - - +
188A PHE 3.0 0.2 + - - -
189A LYS* 3.2 7.7 + - - +
190A LYS* 3.1 22.4 + - - +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU 2.9 17.3 + - - +
184A GLU* 4.2 3.4 - - - +
186A GLN* 1.3 72.5 - - - +
188A PHE* 1.3 63.8 + - - +
190A LYS* 4.1 5.8 - - - +
191A GLN* 2.9 27.5 + - + +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.9 8.5 - - + -
147A ALA 3.5 21.1 - - - -
148A PRO* 3.8 23.8 - - + -
150A GLY 4.1 20.6 - - - +
151A HIS 5.0 2.5 - - - -
152A GLY 3.5 29.2 - - - -
174A ILE* 4.3 20.9 - - + -
180A LEU* 3.8 18.6 - - + -
184A GLU 2.9 15.5 + - - +
185A CYS* 3.0 12.6 - - - +
187A GLN* 1.3 73.4 - - - +
189A LYS* 1.3 69.3 + - + +
191A GLN* 2.9 9.4 + - + +
192A ILE* 2.9 38.5 + - + -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.6 16.8 - - + -
185A CYS* 2.9 26.2 + - + +
186A GLN* 3.7 7.6 - - - +
188A PHE* 1.3 71.1 - - - +
190A LYS* 1.3 57.3 + - - +
192A ILE* 2.6 34.1 + - - +
193A MET* 2.9 14.7 + - - +
224A ARG* 2.5 33.3 + - - +
225A LEU 3.9 4.9 - - - +
226A PRO* 2.9 37.3 + - + +
228A ALA* 4.6 11.0 - - - -
262A ASP* 3.5 19.6 + - - -
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLN 3.1 13.2 + - - +
187A GLN* 4.1 5.8 - - - +
189A LYS* 1.3 77.8 - - - +
191A GLN* 1.3 57.0 + - - +
193A MET* 3.9 13.8 - - + +
194A LYS* 2.9 32.2 + - - +
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A HIS 2.7 28.7 - - - +
152A GLY* 3.0 17.5 - - - -
187A GLN* 2.9 20.1 + - + +
188A PHE* 2.9 11.2 + - + +
190A LYS* 1.3 78.2 - - - +
192A ILE* 1.3 54.2 + - - +
194A LYS* 3.5 9.2 - - - +
195A GLU* 2.9 56.4 + - - +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 5.3 11.0 - - + -
152A GLY* 5.3 1.8 - - - +
153A LEU* 3.3 31.4 - - + +
161A MET* 5.9 2.2 - - + -
172A PRO* 6.4 2.9 - - + -
174A ILE* 3.5 37.2 - - + -
188A PHE* 2.9 36.8 + - + +
189A LYS* 2.6 19.9 + - - +
191A GLN* 1.3 68.0 - - - +
193A MET* 1.3 59.0 + - - +
195A GLU* 2.5 26.2 + - - +
196A ILE* 2.8 27.6 + - + +
226A PRO* 4.0 11.9 - - + -
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS* 2.9 11.2 + - - +
190A LYS* 3.9 13.9 - - + +
192A ILE* 1.3 76.0 - - - +
194A LYS* 1.3 58.9 + - - +
196A ILE* 3.1 15.2 + - + +
197A GLN* 2.9 40.2 + - - +
222A LYS 5.5 4.5 - - - +
223A ASP* 4.8 6.3 - - - +
225A LEU 3.4 11.4 - - - +
226A PRO* 3.3 35.7 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LYS 2.9 19.9 + - - +
191A GLN* 3.5 12.1 - - - +
193A MET* 1.3 75.2 - - - +
195A GLU* 1.3 57.6 + - - +
197A GLN* 4.4 9.7 - - - +
198A GLU* 2.9 34.2 + - - +
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Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.7 38.2 - - + +
191A GLN* 2.9 50.8 + - - +
192A ILE* 2.5 16.3 + - - +
194A LYS* 1.3 72.4 - - - +
196A ILE* 1.3 54.8 + - - +
198A GLU* 3.6 8.8 - - - +
199A HIS* 2.2 61.8 + - + +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.8 4.3 - - + -
161A MET* 4.8 12.6 - - + -
172A PRO* 6.0 5.4 - - + -
192A ILE* 2.8 31.8 + - + +
193A MET* 3.4 25.1 - - + -
195A GLU* 1.3 71.0 - - - +
197A GLN* 1.3 51.3 + - - +
198A GLU 2.9 3.6 - - - -
199A HIS* 2.5 9.4 + - - -
200A LYS* 2.4 35.9 + - - -
201A ILE* 3.4 44.5 + - + +
203A ILE* 5.2 15.0 - - + -
226A PRO* 5.0 3.6 - - + -
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Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A MET* 2.9 22.9 + - - +
194A LYS* 4.4 8.0 - - - +
196A ILE* 1.3 72.4 - - - +
198A GLU* 1.3 62.7 + - + +
200A LYS* 3.7 12.5 + - - +
201A ILE 5.2 0.7 - - - +
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS 2.9 23.0 + - - +
195A GLU* 3.6 8.8 - - - +
196A ILE 2.9 0.4 - - - -
197A GLN* 1.3 80.2 - - - +
199A HIS* 1.3 83.6 + - + +
200A LYS* 3.1 7.5 + - - +
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ILE* 5.1 17.7 - - + +
162A LYS* 4.2 11.4 - - + +
195A GLU* 2.2 57.4 + - + +
196A ILE* 2.5 10.1 + - - +
198A GLU* 1.3 90.9 + - + +
200A LYS* 1.3 69.7 + - - +
201A ILE* 3.6 19.4 - - + +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LYS* 4.9 2.1 - - - +
165A HIS* 4.2 8.7 - - - -
196A ILE 2.4 13.7 + - - -
197A GLN* 4.1 9.9 - - - +
198A GLU 3.1 7.7 - - - +
199A HIS* 1.3 77.8 - - - +
201A ILE* 1.3 58.7 + - - +
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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