Contacts of the helix formed by residues 212 - 224 (chain B) in PDB entry 1TW2
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 GLY 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 4.4 12.3 - - - -
156B ASP* 4.7 0.9 - - - -
210B MET 3.5 0.4 + - - -
211B ALA* 1.3 69.8 - - - +
213B THR* 1.3 64.8 + - - -
214B VAL* 3.1 7.0 - - - +
215B ASP* 3.1 27.9 + - - +
216B THR* 3.4 12.0 + - - -
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Residues in contact with THR 213 (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 ARG* 2.8 24.8 + - - +
156B ASP* 2.7 36.1 + - + +
188B GLY* 3.4 28.0 - - - +
189B LYS* 4.6 0.9 - - - +
209B GLU* 3.4 27.4 - - + +
210B MET 3.7 4.7 - - - -
211B ALA 3.2 3.1 + - - -
212B GLY* 1.3 73.1 - - - +
214B VAL* 1.3 58.4 + - - +
216B THR* 3.2 6.1 + - + -
217B ALA* 2.8 28.1 + - - +
1635B SAH 4.7 0.4 - - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU* 3.6 25.1 - - + +
210B MET 3.2 17.9 + - - +
212B GLY 4.1 9.6 - - - +
213B THR* 1.3 77.6 - - - +
215B ASP* 1.3 66.3 + - - +
217B ALA* 3.8 2.4 - - - +
218B ARG* 2.9 55.3 + - - +
232B VAL* 3.7 25.9 - - + +
233B VAL 4.1 0.4 - - - -
234B GLU* 3.7 31.4 - - + +
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Residues in contact with ASP 215 (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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212B GLY* 3.1 19.1 + - - +
214B VAL* 1.3 87.7 - - - +
216B THR* 1.3 57.4 + - - +
218B ARG* 3.5 17.2 + - - +
219B SER* 3.2 27.4 + - - -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 5.7 5.7 - - - +
156B ASP* 4.7 9.3 - - + +
189B LYS* 3.2 51.2 + - + +
212B GLY 3.4 8.0 + - - -
213B THR* 3.2 11.0 + - - +
215B ASP* 1.3 79.4 - - - +
217B ALA* 1.3 63.8 + - - +
219B SER* 3.6 6.4 + - - -
220B TYR* 3.2 23.6 + - - +
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Residues in contact with ALA 217 (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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188B GLY 3.7 9.0 - - - +
189B LYS 3.4 30.6 - - - +
190B GLY* 4.2 3.1 - - - +
207B VAL* 4.8 3.4 - - + -
209B GLU* 5.7 0.2 - - + -
213B THR 2.8 17.2 + - - +
214B VAL* 3.8 7.9 - - - +
216B THR* 1.3 78.1 - - - +
218B ARG* 1.3 57.5 + - - +
220B TYR 3.5 0.3 + - - -
221B LEU* 3.0 35.5 + - - +
232B VAL* 4.1 16.4 - - + -
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Residues in contact with ARG 218 (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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214B VAL* 2.9 47.6 + - - +
215B ASP* 3.6 17.6 + - - +
217B ALA* 1.3 77.1 - - - +
219B SER* 1.3 57.7 + - - +
221B LEU* 3.3 4.2 + - - +
222B LYS* 2.9 29.1 + - - +
227B SER* 5.4 1.6 - - - -
232B VAL* 2.9 49.2 + - + +
233B VAL* 4.2 5.7 - - - +
234B GLU* 4.4 6.3 + - - +
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Residues in contact with SER 219 (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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215B ASP 3.2 15.1 + - - -
216B THR* 3.7 7.3 + - - -
217B ALA 3.4 0.4 - - - -
218B ARG* 1.3 74.8 - - - +
220B TYR* 1.3 65.9 + - - +
222B LYS* 3.6 14.1 - - - +
223B ASP* 3.1 33.4 + - - -
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Residues in contact with TYR 220 (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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163B GLN* 3.1 45.6 + - + +
164B ASP* 3.8 19.4 + - - -
189B LYS* 3.3 26.2 - - + +
190B GLY 4.1 4.3 - - - -
191B GLY* 4.3 1.2 - - - -
194B ALA* 4.0 18.4 - - + +
198B ARG* 4.2 10.2 + - - -
216B THR 3.2 18.6 + - - +
217B ALA 3.8 0.2 - - - +
219B SER* 1.3 78.0 + - - +
221B LEU* 1.3 66.7 + - + +
223B ASP* 3.3 7.0 + - + +
224B GLU* 3.1 60.1 + - + +
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Residues in contact with LEU 221 (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 4.5 0.9 - - - +
190B GLY* 3.7 24.5 - - - +
194B ALA* 4.3 13.9 - - + +
207B VAL* 4.5 7.9 - - + -
217B ALA 3.0 22.6 + - - +
218B ARG* 3.8 3.8 - - - +
220B TYR* 1.3 79.5 - - + +
222B LYS* 1.3 63.1 + - - +
224B GLU* 3.4 7.3 + - - +
226B LEU* 3.0 33.3 + - + -
227B SER* 3.6 8.9 + - - +
230B VAL* 3.6 48.7 - - + +
232B VAL* 3.5 26.9 - - + -
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Residues in contact with LYS 222 (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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218B ARG 2.9 17.7 + - - +
219B SER* 3.6 13.0 - - - +
221B LEU* 1.3 75.6 - - - +
223B ASP* 1.3 68.3 + - - +
225B GLY* 2.9 21.8 + - - -
227B SER* 4.1 20.6 + - - +
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Residues in contact with ASP 223 (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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219B SER* 3.1 24.0 + - - +
220B TYR* 3.3 8.0 + - + +
222B LYS* 1.3 86.8 - - - +
224B GLU* 1.3 63.0 + - - +
225B GLY 3.2 5.8 + - - -
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Residues in contact with GLU 224 (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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164B ASP* 4.2 8.1 - - - +
198B ARG* 3.3 18.7 + - - +
220B TYR* 3.1 56.7 + - + +
221B LEU* 3.7 4.5 - - - +
222B LYS 3.2 0.4 - - - -
223B ASP* 1.3 81.1 - - - +
225B GLY* 1.3 60.4 + - - +
226B LEU* 3.3 29.6 + - + +
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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