Contacts of the helix formed by residues 218 - 232 (chain A) in PDB entry 6TPN
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 ILE 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY 5.2 1.3 - - - +
216A GLY* 4.5 9.4 - - - +
217A GLU* 1.3 79.8 - - - +
219A ALA* 1.3 72.6 + - + +
220A PRO 3.5 0.4 - - - -
221A LYS* 3.7 5.3 + - + +
222A MET* 3.1 51.4 + - + +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.9 20.1 - - + -
215A GLY 4.6 8.1 - - - +
216A GLY 3.6 4.6 + - - +
218A ILE* 1.3 86.0 - - + +
220A PRO* 1.3 67.7 - - + +
222A MET* 3.1 9.3 + - - +
223A TYR* 3.0 22.2 + - - +
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Residues in contact with PRO 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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214A TRP* 3.6 46.4 - - + +
216A GLY 3.2 17.3 - - - +
217A GLU* 3.8 17.3 - - + +
218A ILE 3.6 2.2 - - - -
219A ALA* 1.3 91.4 - - + +
221A LYS* 1.3 59.4 + - + +
224A HIS* 2.9 41.7 + - + +
328A ARG* 4.7 9.2 - - - +
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Residues in contact with LYS 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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217A GLU* 3.8 25.6 - - - +
218A ILE* 3.7 6.9 + - + +
219A ALA 3.3 0.6 - - - -
220A PRO* 1.3 78.7 - - + +
222A MET* 1.3 66.3 + - + +
225A ILE* 3.1 32.6 + - + +
328A ARG 3.4 21.5 - - - +
329A VAL* 3.4 34.8 + - + +
330A PHE 5.0 5.3 + - - -
331A GLY* 5.3 5.6 - - - +
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Residues in contact with MET 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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218A ILE* 3.1 46.4 - - + +
219A ALA* 3.1 8.2 + - - +
221A LYS* 1.3 79.9 - - + +
223A TYR* 1.3 61.4 + - - +
225A ILE* 3.5 9.9 + - - +
226A CYS* 3.2 28.0 + - - -
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Residues in contact with TYR 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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183A ILE 4.2 5.4 + - - -
184A MET* 3.8 19.3 - - - -
186A PRO* 3.7 27.6 - - + -
187A GLN* 3.3 43.1 + - + +
214A TRP* 3.5 35.9 - + + -
219A ALA 3.0 11.1 + - - +
220A PRO 3.2 2.4 + - - +
222A MET* 1.3 77.4 - - - +
224A HIS* 1.3 66.7 + + - +
226A CYS* 2.9 12.8 + - + +
227A PHE* 2.7 53.3 + + + +
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Residues in contact with HIS 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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212A GLU* 2.8 40.4 + - - -
214A TRP* 4.8 0.2 - + - -
220A PRO* 2.9 32.1 + - + +
223A TYR* 1.3 86.2 - + - +
225A ILE* 1.3 60.4 + - - +
227A PHE* 3.7 8.4 - - - +
228A PHE* 3.2 24.9 + - - +
324A ASN* 4.6 8.4 + - - +
325A VAL* 4.6 4.4 - - - +
328A ARG* 3.6 36.2 - - + +
329A VAL* 4.0 18.1 - - + +
1201A NU8 3.7 31.6 - + - -
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Residues in contact with ILE 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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221A LYS* 3.1 23.2 + - + +
222A MET* 3.7 9.9 - - - +
223A TYR 3.1 0.4 - - - -
224A HIS* 1.3 78.3 - - - +
226A CYS* 1.3 60.5 + - - +
228A PHE* 3.3 6.6 + - + +
229A LEU* 3.0 45.4 + - + +
325A VAL* 6.0 1.3 - - + -
329A VAL* 3.8 27.8 - - + -
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Residues in contact with CYS 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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222A MET* 3.2 16.3 + - - +
223A TYR* 2.9 14.3 + - + +
225A ILE* 1.3 82.9 - - - +
227A PHE* 1.3 61.7 + - - +
229A LEU* 4.3 9.9 - - - -
230A VAL* 3.1 29.7 + - - +
1208A OLA 4.5 20.0 - - + -
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Residues in contact with PHE 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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135A THR* 3.8 21.1 - - + -
138A VAL* 4.7 5.8 - - + -
184A MET* 3.8 28.3 - - + -
223A TYR* 2.7 38.1 + + + +
224A HIS* 4.0 12.8 - - - +
225A ILE 3.1 0.4 - - - -
226A CYS* 1.3 72.9 - - - +
228A PHE* 1.3 61.3 + - - +
230A VAL* 5.2 0.2 - - - -
231A THR* 2.4 55.0 + - + -
1201A NU8 3.4 74.9 - + - -
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Residues in contact with PHE 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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224A HIS 3.2 16.0 + - - +
225A ILE* 3.3 6.7 + - + +
227A PHE* 1.3 84.3 - - - +
229A LEU* 1.3 64.2 + - + +
231A THR* 4.1 2.7 - - - -
232A TYR* 3.1 29.5 + + + +
233A ALA* 2.8 42.8 + - + -
321A SER* 3.7 38.8 - - - -
322A ILE* 4.6 9.6 - - + -
325A VAL* 3.6 28.3 - - + -
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Residues in contact with LEU 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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225A ILE* 3.0 40.1 + - + +
226A CYS* 4.0 10.5 - - - +
228A PHE* 1.3 81.2 - - + +
230A VAL* 1.3 69.3 + - + +
231A THR 3.4 0.3 + - - -
233A ALA* 3.8 18.6 - - + -
234A ALA* 2.8 35.9 + - + +
235A PRO* 3.3 2.1 - - - +
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Residues in contact with VAL 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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139A SER* 5.1 3.6 - - - +
142A ALA* 4.4 2.6 - - - +
143A LEU* 5.0 10.2 - - + +
183A ILE* 4.2 17.5 - - + -
184A MET* 5.5 0.9 - - + -
226A CYS* 3.1 17.9 + - - +
227A PHE* 4.6 0.7 - - - +
229A LEU* 1.3 80.1 - - + +
231A THR* 1.3 63.8 + - + +
234A ALA* 4.9 3.1 - - - -
235A PRO* 3.2 20.0 - - - +
1208A OLA 3.6 61.7 - - + -
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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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138A VAL* 4.0 22.5 - - + +
139A SER* 4.7 8.1 - - - +
142A ALA* 3.1 26.2 - - - +
184A MET* 3.9 28.7 - - + -
227A PHE* 2.4 47.6 + - + +
228A PHE* 4.1 2.3 - - - -
230A VAL* 1.3 82.7 - - + +
232A TYR* 1.3 63.2 + - - +
235A PRO* 4.0 2.1 - - - +
313A PHE* 4.1 10.4 - - - -
317A TYR* 5.8 0.2 - - - -
321A SER* 5.1 1.0 + - - -
1201A NU8 4.3 4.1 - - - -
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Residues in contact with TYR 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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228A PHE* 3.1 35.2 + + + +
231A THR* 1.3 83.8 + - - +
233A ALA* 1.3 73.4 + - - +
235A PRO* 3.3 4.1 - - - +
236A LEU* 3.2 43.5 + - + +
313A PHE* 4.1 16.1 - + - -
314A ALA* 2.8 36.7 + - - +
317A TYR* 3.6 34.5 - + + -
318A ALA* 3.5 16.6 - - - +
321A SER* 3.8 18.8 - - - +
322A ILE* 6.2 2.2 - - + -
1201A NU8 5.5 0.9 - - - -
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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