Contacts of the helix formed by residues 212 - 234 (chain A) in PDB entry 5TSQ
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A VAL* 3.6 20.8 - - + +
211A ARG* 1.3 83.6 - - - +
213A LYS* 1.3 60.4 + - - +
214A PRO* 3.5 4.3 - - - +
215A ALA* 3.0 25.1 + - - +
216A ASP* 2.9 34.8 + - - +
307A LEU* 4.6 3.4 + - - +
308A GLN* 5.6 0.9 - - - +
311A GLY* 3.5 38.1 + - - -
312A ASP* 3.5 11.4 - - - +
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Residues in contact with LYS 213 (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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55A VAL* 4.6 4.4 - - + +
212A THR* 1.3 71.5 - - - +
214A PRO* 1.3 59.0 - - + +
216A ASP* 3.2 19.9 + - + +
217A PHE* 2.9 27.9 + - - +
312A ASP* 2.7 25.4 + - - +
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Residues in contact with PRO 214 (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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20A LEU* 4.5 13.2 - - + -
55A VAL* 3.6 37.9 - - + +
56A ALA* 4.3 2.0 - - - -
212A THR* 3.5 9.0 - - - +
213A LYS* 1.3 95.0 - - + +
215A ALA* 1.3 55.1 + - - +
217A PHE* 3.3 4.2 + - - +
218A ILE* 3.0 33.9 + - - +
307A LEU* 5.0 5.4 - - + +
310A ILE* 4.2 14.6 - - + -
311A GLY 3.5 19.7 - - - +
312A ASP* 3.5 3.6 - - - +
313A PRO* 3.9 10.3 - - + -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.4 29.7 - - + +
208A LYS* 6.2 0.2 - - - -
210A VAL* 3.7 18.6 - - + -
211A ARG 4.6 0.2 - - - +
212A THR* 3.0 24.6 + - - +
214A PRO* 1.3 73.8 - - - +
216A ASP* 1.3 57.9 + - - +
218A ILE* 3.2 6.0 + - - +
219A LEU* 2.8 35.9 + - - +
307A LEU* 4.3 11.6 - - + +
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Residues in contact with ASP 216 (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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208A LYS* 5.0 10.4 - - - +
211A ARG* 5.0 2.5 - - - -
212A THR 2.9 24.8 + - - +
213A LYS* 3.2 30.7 + - + +
215A ALA* 1.3 76.3 - - - +
217A PHE* 1.3 57.3 + - - +
219A LEU* 3.7 11.6 - - - +
220A LYS* 2.9 29.5 + - - +
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Residues in contact with PHE 217 (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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16A ALA* 4.6 0.2 - - + -
20A LEU* 5.0 2.2 - - + -
51A LEU* 4.1 18.2 - - + -
52A VAL* 4.0 36.8 - - + -
55A VAL* 3.9 32.5 - - + -
87A LEU* 4.2 12.1 - - + -
90A VAL* 4.1 26.0 - - + -
213A LYS 2.9 12.7 + - - +
214A PRO 3.4 8.3 - - - +
216A ASP* 1.3 75.9 - - - +
218A ILE* 1.3 82.8 + - + +
220A LYS* 3.2 9.7 + - + +
221A ILE* 3.1 35.8 + - + +
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Residues in contact with ILE 218 (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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16A ALA 4.5 1.3 - - - +
17A VAL* 4.1 31.4 - - + +
20A LEU* 3.7 27.6 - - + -
207A VAL* 4.2 10.5 - - + -
214A PRO 3.0 17.4 + - - +
215A ALA* 3.2 9.2 + - - +
217A PHE* 1.3 89.2 - - + +
219A LEU* 1.3 58.6 + - - +
221A ILE* 3.3 17.3 - - + +
222A LEU* 2.8 51.8 + - + +
303A VAL* 6.0 1.1 - - + -
307A LEU* 4.2 15.5 - - + -
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Residues in contact with LEU 219 (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 LEU* 3.8 37.7 - - + +
207A VAL* 3.9 10.7 - - + +
208A LYS* 3.7 38.6 - - + -
215A ALA 2.8 20.1 + - - +
216A ASP* 3.7 10.8 - - - +
218A ILE* 1.3 72.4 - - - +
220A LYS* 1.3 57.3 + - - +
222A LEU* 3.3 3.6 + - - -
223A GLU* 2.8 63.0 + - + +
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Residues in contact with LYS 220 (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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89A THR* 3.2 38.6 + - - +
90A VAL* 3.8 25.6 - - + +
91A SER 5.8 0.2 - - - +
216A ASP 2.9 17.3 + - - +
217A PHE* 3.2 8.3 + - + +
219A LEU* 1.3 76.3 - - - +
221A ILE* 1.3 62.0 + - - +
223A GLU* 3.2 21.3 + - - +
224A PHE* 3.2 12.1 + - - +
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Residues in contact with ILE 221 (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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13A ILE* 3.6 33.5 - - + +
16A ALA* 3.8 28.7 - - + -
17A VAL* 4.9 0.7 - - + -
87A LEU* 3.6 20.0 - - + +
89A THR 6.3 0.2 - - - +
90A VAL* 3.5 30.7 - - + -
217A PHE* 3.1 21.1 + - + +
218A ILE* 3.3 28.7 - - + +
220A LYS* 1.3 77.2 - - - +
222A LEU* 1.3 58.5 + - + +
224A PHE* 3.4 7.7 + - - +
225A TYR* 2.9 28.4 + - - +
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Residues in contact with LEU 222 (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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13A ILE* 4.2 9.6 - - + -
17A VAL* 4.4 13.2 - - + -
199A ALA* 5.0 7.6 - - + -
203A VAL* 5.6 0.4 - - + -
204A LEU* 4.0 25.1 - - + -
207A VAL* 4.7 12.1 - - + -
218A ILE* 2.8 44.4 + - + +
219A LEU* 3.8 4.0 - - - +
221A ILE* 1.3 75.5 - - + +
223A GLU* 1.3 52.7 + - - +
225A TYR* 3.6 17.9 - - + +
226A THR* 2.6 38.5 + - - -
237A ALA* 5.0 0.5 - - - +
239A VAL* 3.9 27.6 - - + -
300A TRP* 5.1 9.4 - - + -
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Residues in contact with GLU 223 (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 LEU* 4.9 10.1 - - + +
219A LEU* 2.8 48.4 + - + +
220A LYS* 3.2 10.6 + - - +
222A LEU* 1.3 74.8 - - - +
224A PHE* 1.3 65.1 + - - +
226A THR* 3.4 6.8 + - - -
227A LYS* 3.1 37.3 + - - +
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Residues in contact with PHE 224 (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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13A ILE* 3.7 9.6 - - + -
79A PRO 5.3 0.7 - - - -
80A GLN 5.8 0.2 - - - -
81A ILE 3.7 20.0 - - - -
82A HIS 3.9 0.7 - - - -
83A GLY* 3.9 21.1 - - - -
88A GLY* 3.6 35.4 - - - -
89A THR* 4.1 27.4 - - + +
220A LYS 3.2 11.5 + - - +
221A ILE* 3.6 9.2 - - - +
223A GLU* 1.3 75.7 - - - +
225A TYR* 1.3 65.2 + - - +
227A LYS* 3.0 21.0 + - + +
228A VAL* 3.1 27.8 + - + +
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Residues in contact with TYR 225 (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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13A ILE* 3.9 16.8 - - + -
14A ASP* 3.8 15.4 + - + -
81A ILE* 3.7 30.4 - - + +
82A HIS* 3.8 13.5 + + - -
221A ILE 2.9 17.9 + - - +
222A LEU* 3.6 20.2 - - + +
224A PHE* 1.3 79.1 - - - +
226A THR* 1.3 61.7 + - - +
228A VAL* 3.4 4.5 + - + +
229A TYR* 3.0 48.2 + + - -
237A ALA* 3.5 21.3 - - + -
238A LYS 2.8 30.9 + - - -
239A VAL* 4.3 8.5 - - + -
240A HIS* 3.3 18.4 + - - -
402A BDR 4.8 1.4 + - - -
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Residues in contact with THR 226 (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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199A ALA* 4.7 4.3 + - - +
204A LEU* 3.9 24.7 - - + +
222A LEU 2.6 25.3 + - - -
223A GLU* 3.5 9.0 - - - +
224A PHE 3.2 0.2 - - - -
225A TYR* 1.3 77.0 - - - +
227A LYS* 1.3 59.9 + - + +
229A TYR* 3.3 1.0 + - - +
230A GLU* 2.9 61.9 + - + +
236A TYR* 5.0 6.7 - - + -
237A ALA* 4.0 19.0 - - - +
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Residues in contact with LYS 227 (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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223A GLU* 3.1 23.7 + - - +
224A PHE* 3.0 11.4 + - + +
226A THR* 1.3 78.7 - - + +
228A VAL* 1.3 59.4 + - + +
230A GLU* 3.9 8.1 - - - +
231A THR* 3.0 35.9 + - - +
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Residues in contact with VAL 228 (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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80A GLN 3.3 27.6 - - - +
81A ILE* 3.4 35.7 - - + +
224A PHE* 3.1 41.7 + - + +
225A TYR 3.7 7.6 - - - +
227A LYS* 1.3 77.9 - - + +
229A TYR* 1.3 60.1 + - + +
231A THR* 4.7 2.5 - - - -
232A GLN* 2.8 41.4 + - - +
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Residues in contact with TYR 229 (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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81A ILE* 4.5 9.9 - - + +
160A ASN* 4.9 3.1 + - - -
225A TYR* 3.0 54.9 + + - +
226A THR 3.9 1.1 - - - +
228A VAL* 1.3 80.4 - - + +
230A GLU* 1.3 59.1 + - - +
233A ARG* 2.8 65.0 + - + +
234A ASN 2.9 8.8 + - - -
235A THR* 3.3 30.3 - - - +
236A TYR 3.7 3.4 - - - -
237A ALA* 3.6 21.3 - - + +
238A LYS* 3.9 27.3 - - + +
240A HIS* 2.9 28.2 + - - -
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Residues in contact with GLU 230 (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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226A THR* 2.9 39.8 + - + +
227A LYS* 4.0 7.6 - - - +
229A TYR* 1.3 75.8 - - - +
231A THR* 1.3 64.1 + - - +
234A ASN* 3.2 21.7 + - - +
235A THR 3.4 18.6 - - - +
236A TYR* 3.5 28.3 - - + -
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Residues in contact with THR 231 (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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227A LYS* 3.0 19.9 + - - +
228A VAL* 4.0 2.7 - - - -
230A GLU* 1.3 79.5 - - - +
232A GLN* 1.3 71.5 + - + +
234A ASN 4.6 0.9 + - - -
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Residues in contact with GLN 232 (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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80A GLN* 2.9 46.3 + - - +
81A ILE* 3.3 17.0 - - - +
228A VAL* 2.8 29.9 + - - +
231A THR* 1.3 83.3 - - + +
233A ARG* 1.3 74.2 + - + +
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Residues in contact with ARG 233 (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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80A GLN* 5.3 4.4 - - - +
81A ILE* 3.2 35.0 - - + +
160A ASN* 4.1 31.7 + - - +
228A VAL 4.7 0.2 - - - +
229A TYR* 2.8 57.3 + - + +
232A GLN* 1.3 94.0 + - + +
234A ASN* 1.3 71.6 + - - +
235A THR* 3.3 12.7 + - + +
238A LYS* 6.3 0.7 - - - +
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Residues in contact with ASN 234 (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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229A TYR 2.9 4.6 + - - -
230A GLU* 3.2 17.5 + - - +
231A THR 4.6 1.2 + - - +
232A GLN 3.8 0.6 - - - -
233A ARG* 1.3 79.1 - - - +
235A THR* 1.3 64.6 + - - +
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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