Contacts of the helix formed by residues 214 - 233 (chain B) in PDB entry 1N8T
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 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ILE* 3.3 38.8 - - + -
209B SER* 3.0 22.7 + - - -
210B LYS 5.2 0.7 + - - -
211B THR* 3.8 6.8 + - - -
212B PHE 3.7 0.6 - - - -
213B THR* 1.3 77.8 + - - +
215B GLN* 1.3 60.5 + - - +
216B GLU* 4.0 4.9 - - - +
217B THR* 3.9 17.0 - - - +
218B ILE* 2.9 29.6 + - - +
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 3.5 30.4 - - + +
427A ASN* 4.8 4.2 + - - -
213B THR 2.9 8.0 + - - +
214B THR* 1.3 73.1 - - - +
216B GLU* 1.3 72.6 + - - +
218B ILE* 4.4 2.0 - - - +
219B THR* 2.6 41.3 + - - +
521B ALA* 6.1 0.5 - - - +
522B LYS* 3.9 18.3 - - - +
525B GLU* 2.9 38.0 + - - +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR* 4.3 11.3 + - - +
388A HIS* 2.8 31.5 + - + +
423A ILE* 5.5 0.6 - - + +
427A ASN* 4.8 9.9 + - - +
156B ILE* 3.2 42.1 - - + +
184B SER 4.6 1.8 - - - +
186B ILE* 3.7 38.7 - - + +
214B THR* 4.0 1.4 - - - +
215B GLN* 1.3 92.0 + - + +
217B THR* 1.3 56.2 + - - +
219B THR* 3.7 1.2 - - - -
220B ASN* 2.9 35.5 + - - -
518B LYS* 5.9 2.6 - - - +
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.7 29.8 - - + +
155B GLY* 3.4 18.8 - - - -
156B ILE* 3.4 14.7 + - - +
207B ILE* 3.8 17.9 - - + -
208B ALA 3.8 13.7 + - - +
209B SER* 4.1 5.8 - - - -
214B THR* 3.4 19.9 + - - +
215B GLN 3.3 0.4 - - - -
216B GLU* 1.3 77.2 - - - +
218B ILE* 1.3 62.0 + - + +
220B ASN* 3.3 3.7 + - - +
221B ALA* 2.8 27.7 + - - +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.2 11.7 - - + -
209B SER* 5.1 0.7 - - - -
212B PHE* 3.3 63.0 - - + +
213B THR* 3.9 5.6 - - - +
214B THR* 2.9 25.7 + - - +
215B GLN* 4.4 2.0 - - - +
217B THR* 1.3 71.9 - - + +
219B THR* 1.3 60.8 + - - +
221B ALA* 3.5 5.1 - - + +
222B GLU* 2.9 49.8 + - + +
255B PHE* 5.2 5.2 - - + -
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Residues in contact with THR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 3.8 14.4 + - - +
419A LEU* 4.0 15.2 - - + +
420A HIS* 3.9 18.4 - - + +
423A ILE* 4.0 13.5 - - + +
186B ILE* 3.9 16.8 - - + -
215B GLN* 2.6 27.0 + - - +
216B GLU 3.7 3.6 - - - -
218B ILE* 1.3 77.7 - - - +
220B ASN* 1.3 62.9 + - - +
222B GLU* 3.3 12.1 + - - +
223B THR* 3.1 21.5 + - - -
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Residues in contact with ASN 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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420A HIS* 3.2 24.3 - - - -
154B ILE* 3.5 26.6 - - + +
183B VAL* 3.8 16.0 - - + +
184B SER* 4.0 7.7 + - - +
185B ASN 3.0 30.4 + - - +
186B ILE* 4.2 1.8 - - - +
191B ILE* 3.4 20.7 - - + +
216B GLU 2.9 23.7 + - - +
219B THR* 1.3 76.7 - - - +
221B ALA* 1.3 61.3 + - - +
223B THR* 3.2 3.1 + - - -
224B ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 4.0 12.1 - - + +
207B ILE* 3.6 34.1 - - + -
217B THR 2.8 21.1 + - - +
218B ILE* 3.5 7.6 - - + +
220B ASN* 1.3 72.0 - - - +
222B GLU* 1.3 59.3 + - - +
224B ALA* 3.2 4.3 + - - +
225B LYS 2.8 24.3 + - - -
242B PHE* 4.0 1.2 - - - -
255B PHE* 3.5 24.5 - - + -
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 3.1 29.2 + - - +
218B ILE* 2.9 33.9 + - + +
219B THR* 4.1 4.3 + - - -
220B ASN 3.3 0.2 - - - -
221B ALA* 1.3 73.4 - - - +
223B THR* 1.3 61.6 + - - +
225B LYS* 3.4 10.1 + - - +
226B ASP* 3.0 37.0 + - - +
255B PHE* 3.8 21.2 - - + -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 4.1 12.1 - - + -
416A ARG* 3.0 28.4 + - + +
420A HIS* 2.9 25.2 + - - -
191B ILE* 4.0 25.4 - - + -
195B LEU* 4.4 7.6 - - + -
219B THR 3.1 6.2 + - - -
220B ASN 3.6 7.4 - - - -
222B GLU* 1.3 74.3 - - - +
224B ALA* 1.3 68.3 + - - +
226B ASP* 3.2 4.6 + - - +
227B TRP* 2.9 22.6 + - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 4.1 7.4 - - + -
191B ILE* 4.7 5.3 - - + +
195B LEU* 4.3 13.2 - - - +
205B PHE* 3.7 34.5 - - + -
220B ASN 3.0 12.6 + - - +
221B ALA 3.4 8.1 - - - +
223B THR* 1.3 77.9 - - - +
225B LYS* 1.3 57.1 + - - +
227B TRP* 3.2 6.1 + - - +
228B PHE* 2.8 29.1 + - - +
242B PHE* 3.8 7.5 - - + -
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA 2.8 15.7 + - - +
222B GLU* 3.8 12.0 - - - +
224B ALA* 1.3 78.0 - - - +
226B ASP* 1.3 63.9 + - - +
228B PHE* 3.3 1.4 + - - +
229B LEU* 2.9 43.3 + - + +
238B VAL* 3.8 22.0 - - + -
242B PHE* 3.4 17.2 - - + -
254B GLU 4.9 1.6 + - - -
255B PHE* 2.8 60.6 + - + +
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Residues in contact with ASP 226 (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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416A ARG* 4.0 23.8 + - - -
222B GLU* 3.0 22.7 + - - +
223B THR* 3.2 4.9 + - + +
225B LYS* 1.3 86.1 - - - +
227B TRP* 1.3 63.7 + - - +
229B LEU* 3.4 9.4 + - - +
230B LEU* 3.1 30.4 + - + +
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Residues in contact with TRP 227 (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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195B LEU* 3.5 58.9 + - + +
196B ALA* 5.7 0.2 - - - +
198B LEU* 3.6 28.7 - - + -
199B ASN 4.0 0.4 - - - -
200B PRO* 3.5 45.0 - - + +
203B SER* 4.5 1.1 - - - -
205B PHE* 3.8 24.0 - + - -
223B THR* 2.9 13.8 + - + +
224B ALA 3.4 10.5 - - - +
226B ASP* 1.3 77.9 - - - +
228B PHE* 1.3 79.9 + - + +
230B LEU* 3.4 23.8 + - + +
231B SER* 4.0 5.0 + - - -
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Residues in contact with PHE 228 (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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143B TYR* 3.4 25.8 - + - -
200B PRO* 3.5 24.0 - - + -
205B PHE* 5.2 2.7 - + + -
224B ALA 2.8 16.3 + - - +
225B LYS 3.6 3.8 - - - +
227B TRP* 1.3 89.8 - + + +
229B LEU* 1.3 70.8 + - + +
231B SER* 3.1 9.5 + - - -
232B ALA* 3.0 28.1 + - + +
237B THR* 3.3 33.0 - - - -
238B VAL* 4.2 4.5 - - + -
241B HIS* 3.3 46.4 - + + -
242B PHE* 4.1 20.9 - + + -
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Residues in contact with LEU 229 (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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225B LYS* 2.9 37.4 + - + +
226B ASP* 4.0 10.8 - - - +
228B PHE* 1.3 97.3 - - + +
230B LEU* 1.3 68.7 + - - +
231B SER 3.1 0.2 - - - -
232B ALA* 3.7 4.5 - - + +
233B LYS* 2.8 35.6 + - - +
234B ASP 4.2 16.8 - - - +
235B PRO* 4.3 14.8 - - + -
237B THR* 4.3 0.4 - - - +
238B VAL* 4.1 15.0 - - + -
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Residues in contact with LEU 230 (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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226B ASP* 3.1 22.5 + - + +
227B TRP* 3.6 16.2 - - + +
228B PHE 3.2 0.6 - - - -
229B LEU* 1.3 77.4 - - + +
231B SER* 1.3 54.4 + - - +
233B LYS* 2.7 34.5 + - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 3.7 17.9 + - - -
200B PRO* 3.6 25.4 - - - +
227B TRP 4.0 1.8 + - - -
228B PHE 3.1 8.0 + - - -
229B LEU 3.1 0.2 - - - -
230B LEU* 1.3 81.1 - - - +
232B ALA* 1.3 61.5 + - - +
233B LYS* 3.3 18.4 + - - +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 3.8 24.9 - - + -
228B PHE* 3.0 46.6 + - + +
229B LEU* 4.4 2.9 - - + -
231B SER* 1.3 75.6 - - - +
233B LYS* 1.3 53.2 - - - +
234B ASP* 2.0 33.3 + - - +
237B THR* 3.6 9.9 - - - +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 2.8 24.5 + - - +
230B LEU 2.7 26.4 + - - +
231B SER* 3.5 13.2 - - - +
232B ALA* 1.3 71.8 - - - +
234B ASP* 1.3 56.8 + - + +
235B PRO* 3.0 16.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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