Contacts of the helix formed by residues 196 - 211 (chain A) in PDB entry 1TJY
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 ASP 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY 3.1 9.3 + - - +
194A TYR* 3.1 6.3 - - + +
195A ASN* 1.3 77.3 - - - +
197A ALA* 1.3 59.8 + - - +
198A THR* 3.1 13.5 + - - -
199A LYS* 3.0 51.7 + - + +
200A SER* 2.8 33.8 + - - -
223A ASN* 5.1 0.7 - - - -
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Residues in contact with ALA 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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195A ASN 4.2 1.4 + - - -
196A ASP* 1.3 73.1 + - - +
198A THR* 1.3 58.6 + - - +
200A SER* 3.8 5.0 - - - -
201A LEU* 3.0 29.6 + - - +
223A ASN* 4.7 14.0 + - - +
227A ALA* 4.9 2.1 - - - +
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Residues in contact with THR 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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196A ASP* 3.1 9.2 + - - -
197A ALA* 1.3 75.4 - - - +
199A LYS* 1.3 68.6 + - + +
201A LEU* 3.4 6.0 + - - +
202A GLN* 3.1 45.0 + - - +
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Residues in contact with LYS 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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192A PHE 5.7 0.2 - - - +
193A GLY* 3.8 14.1 - - - +
194A TYR* 4.6 23.3 - - + +
196A ASP* 3.0 31.7 + - + +
198A THR* 1.3 78.0 - - + +
200A SER* 1.3 57.6 - - - +
202A GLN* 3.4 11.6 + - - +
203A THR* 2.9 35.4 + - - +
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Residues in contact with SER 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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158A PHE* 3.3 20.6 - - - -
193A GLY* 3.1 22.3 + - - -
195A ASN 4.6 0.2 + - - -
196A ASP 2.8 26.3 + - - -
197A ALA* 3.8 4.3 - - - -
198A THR 3.2 0.2 - - - -
199A LYS* 1.3 76.7 - - - +
201A LEU* 1.3 56.6 + - - +
203A THR 3.3 0.3 + - - -
204A ALA* 2.9 26.7 + - - +
221A ASP* 5.3 0.5 + - - -
223A ASN* 4.2 16.2 + - - +
224A ALA* 4.5 1.4 + - - +
227A ALA* 3.5 19.5 - - - -
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Residues in contact with LEU 201 (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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197A ALA 3.0 18.0 + - - +
198A THR* 3.9 5.2 - - - +
199A LYS 3.3 0.2 - - - -
200A SER* 1.3 76.0 - - - +
202A GLN* 1.3 58.6 + - + +
204A ALA* 3.3 1.3 + - - +
205A GLU* 2.9 40.0 + - - +
227A ALA* 3.7 26.4 - - + +
230A GLN* 3.9 18.6 - - + -
231A ALA* 3.7 20.0 - - - +
234A ASN* 4.0 14.1 - - - +
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Residues in contact with GLN 202 (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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198A THR* 3.1 37.7 + - - +
199A LYS* 3.8 9.0 - - - +
201A LEU* 1.3 79.4 - - + +
203A THR* 1.3 61.9 + - - +
205A GLU* 3.8 7.6 - - - +
206A GLY* 3.0 20.6 + - - -
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Residues in contact with THR 203 (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 PHE* 3.5 25.6 - - + -
191A GLN* 3.7 35.9 - - + +
192A PHE 3.2 17.0 + - - +
199A LYS* 2.9 20.3 + - - +
200A SER 3.7 3.6 - - - -
201A LEU 3.3 0.2 - - - -
202A GLN* 1.3 76.1 - - - +
204A ALA* 1.3 58.7 + - - +
206A GLY* 3.2 2.9 + - - -
207A ILE* 3.0 28.9 + - + +
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Residues in contact with ALA 204 (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 PHE* 3.8 19.7 - - + -
200A SER 2.9 17.2 + - - +
201A LEU 3.7 1.3 - - - +
203A THR* 1.3 74.3 - - - +
205A GLU* 1.3 65.9 + - - +
207A ILE* 3.2 10.3 + - - +
208A ILE* 3.1 28.2 + - + +
217A ILE* 5.7 1.8 - - + -
227A ALA 3.7 11.0 - - - +
228A ALA* 3.8 7.9 - - + -
231A ALA* 3.5 20.2 - - + -
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Residues in contact with GLU 205 (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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201A LEU* 2.9 30.9 + - + +
202A GLN* 3.8 6.8 - - - +
204A ALA* 1.3 75.2 - - - +
206A GLY* 1.3 57.2 + - - +
208A ILE 3.4 0.5 + - - -
209A LYS* 3.0 49.2 + - - +
231A ALA* 3.6 17.7 - - + -
234A ASN* 3.0 32.4 - - - +
235A LEU* 3.7 22.9 - - + +
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Residues in contact with GLY 206 (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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191A GLN* 5.5 2.9 - - - -
202A GLN 3.0 15.1 + - - -
203A THR* 3.5 4.7 - - - -
205A GLU* 1.3 78.0 - - - +
207A ILE* 1.3 56.4 + - - +
209A LYS* 3.5 6.8 + - - +
210A ALA* 3.0 32.4 + - - +
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Residues in contact with ILE 207 (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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156A ALA* 4.0 15.3 - - + -
157A PHE 4.8 2.0 - - - +
158A PHE* 4.2 26.5 - - + -
189A THR* 4.2 11.2 - - + -
191A GLN* 3.7 31.2 - - + +
203A THR* 3.0 31.1 + - + +
204A ALA* 3.2 10.5 + - - +
206A GLY* 1.3 76.8 - - - +
208A ILE* 1.3 63.1 + - + +
210A ALA* 3.3 0.6 + - - -
211A TYR* 3.0 34.2 + - + +
214A LEU* 3.8 24.2 - - + -
217A ILE* 4.5 9.4 - - + -
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Residues in contact with ILE 208 (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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204A ALA* 3.1 17.9 + - + +
207A ILE* 1.3 79.5 - - + +
209A LYS* 1.3 61.5 + - - +
211A TYR 3.8 16.4 + - - +
212A PRO* 4.0 5.7 - - - +
214A LEU* 4.9 3.6 - - + -
217A ILE* 4.1 18.8 - - + -
228A ALA 4.2 3.8 - - - +
231A ALA* 3.9 8.5 - - + -
232A ALA* 3.6 34.5 - - + +
235A LEU* 3.7 21.3 - - + -
237A ARG* 4.0 30.4 + - + +
240A LEU* 4.0 17.5 - - + -
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Residues in contact with LYS 209 (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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205A GLU* 3.0 33.4 + - + +
206A GLY* 3.9 6.7 - - - +
208A ILE* 1.3 79.0 - - - +
210A ALA* 1.3 60.1 + - - +
211A TYR 3.5 0.3 + - - -
212A PRO* 3.9 9.9 - - - +
235A LEU* 3.6 34.7 - - + +
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Residues in contact with ALA 210 (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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191A GLN* 6.1 0.2 - - - +
206A GLY 3.0 19.3 + - - +
209A LYS* 1.3 76.8 - - - +
211A TYR* 1.3 86.1 + - + +
212A PRO* 3.4 7.8 - - - +
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Residues in contact with TYR 211 (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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188A VAL* 3.6 45.6 + - + -
189A THR* 3.8 30.6 + - + -
191A GLN* 4.4 7.5 + - - -
207A ILE* 3.0 23.1 + - + +
208A ILE* 3.8 8.0 - - - +
209A LYS 3.3 0.2 - - - -
210A ALA* 1.3 97.2 - - + +
212A PRO* 1.3 65.9 - - - +
213A ASP 3.1 8.7 - - - +
214A LEU* 3.1 29.1 - - + +
237A ARG* 4.6 1.2 + - - -
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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