Contacts of the helix formed by residues 205 - 224 (chain B) in PDB entry 1D7K
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 PRO 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B CYS* 4.2 8.2 - - - -
203B THR 3.9 3.4 - - - +
204B ASP* 1.3 90.0 - - - +
206B GLU* 1.3 56.2 + - + +
207B THR 3.1 0.7 - - - -
208B PHE* 3.0 32.1 + - + +
209B VAL 4.0 0.2 + - - -
246B LEU* 3.8 28.3 - - + -
250B GLU* 4.4 11.0 - - - +
251B ILE* 4.3 13.2 - - + -
254B VAL* 3.4 37.3 - - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASP* 2.9 19.4 + - - +
205B PRO* 1.3 71.5 - - + +
207B THR* 1.3 59.8 + - - +
208B PHE 3.2 0.7 - - - -
209B VAL* 3.0 40.3 + - - +
210B GLN* 3.0 30.2 + - - +
254B VAL* 5.2 6.8 - - + +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B THR* 5.1 1.3 - - - -
158B ASP* 3.8 14.6 - - + +
159B ASP* 3.0 49.7 + - + +
198B VAL* 4.1 14.2 - - + +
202B CYS* 4.5 0.4 - - - -
204B ASP* 2.9 19.2 + - - +
205B PRO 3.1 0.4 + - - -
206B GLU* 1.3 74.6 - - - +
208B PHE* 1.3 60.7 + - - +
210B GLN* 3.8 10.7 - - + -
211B ALA* 2.9 27.0 + - - +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 4.1 14.6 - + - -
198B VAL* 4.1 30.1 - - + -
199B GLY 6.0 0.4 - - - -
202B CYS* 4.9 9.9 - - + -
205B PRO 3.0 16.2 + - - +
207B THR* 1.3 77.6 - - - +
209B VAL* 1.3 56.3 + - + +
211B ALA* 2.8 6.3 + - - +
212B ILE* 2.7 42.4 + - + +
234B ILE* 3.8 24.7 - - + -
236B GLY 4.4 10.5 - - - -
237B GLY 5.8 3.1 - - - -
238B PHE* 4.0 22.4 - + - -
251B ILE* 3.7 26.7 - - + -
254B VAL* 5.0 1.1 - - + -
255B ILE* 3.6 33.0 - - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO 4.4 3.4 - - - +
206B GLU* 3.0 43.6 + - - +
208B PHE* 1.3 71.6 - - + +
210B GLN* 1.3 65.0 + - - +
212B ILE* 2.9 12.9 + - - +
213B SER* 2.8 26.2 + - - -
254B VAL* 4.2 26.5 - - + +
258B ALA* 4.3 11.9 - - + -
262B TYR* 4.8 15.4 - - + +
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Residues in contact with GLN 210 (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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158B ASP 6.3 0.7 - - - +
206B GLU 3.0 13.9 + - - +
207B THR* 3.8 12.6 - - + +
209B VAL* 1.3 77.3 - - - +
211B ALA* 1.3 56.4 + - - +
213B SER* 3.5 11.6 + - - -
214B ASP* 2.9 55.0 + - - +
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Residues in contact with ALA 211 (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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155B ILE* 4.2 3.6 - - - +
156B ALA 6.1 0.2 - - - -
157B THR* 4.2 14.1 - - + +
196B PHE* 3.5 43.4 - - + -
198B VAL* 4.5 1.1 - - + -
207B THR 2.9 16.3 + - - +
208B PHE* 2.8 15.2 + - - +
210B GLN* 1.3 71.1 - - - +
212B ILE* 1.3 60.7 + - - +
214B ASP* 3.5 6.6 + - - +
215B ALA* 3.3 22.3 + - - +
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Residues in contact with ILE 212 (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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196B PHE* 4.2 18.2 - - + -
208B PHE* 2.7 37.2 + - + +
209B VAL* 2.9 7.9 + - - +
211B ALA* 1.3 68.9 - - - +
213B SER* 1.3 59.8 + - - +
215B ALA* 3.4 2.6 + - - -
216B ARG* 3.0 21.1 + - - +
232B LEU* 5.8 1.1 - - + -
234B ILE* 4.9 1.8 - - + -
255B ILE* 4.4 13.0 - - + +
258B ALA* 3.5 35.2 - - + +
259B LEU* 4.7 15.5 - - + +
262B TYR* 3.9 15.4 - - + +
263B PHE* 3.3 33.4 - - + -
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 2.8 19.4 + - - -
210B GLN* 3.7 14.4 + - - -
212B ILE* 1.3 70.0 - - - +
214B ASP* 1.3 67.8 + - - +
215B ALA 3.1 0.2 - - - -
216B ARG* 3.0 13.5 + - - +
217B CYS* 3.3 9.5 + - - +
262B TYR* 3.8 37.7 + - - -
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Residues in contact with ASP 214 (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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155B ILE* 4.0 16.4 - - + -
156B ALA 4.6 9.0 - - - +
157B THR* 5.8 0.9 - - - -
174B LEU* 4.1 23.9 - - + +
210B GLN* 2.9 48.3 + - - +
211B ALA* 3.9 6.9 - - - +
212B ILE 3.4 0.2 - - - -
213B SER* 1.3 72.1 + - - +
215B ALA* 1.3 57.5 + - - +
217B CYS* 3.1 26.7 + - - +
218B VAL* 3.3 9.9 + - - +
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Residues in contact with ALA 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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155B ILE* 4.2 3.5 - - + +
194B VAL* 3.3 33.6 - - + +
196B PHE* 5.0 2.5 - - + -
211B ALA 3.3 16.5 + - - +
212B ILE* 3.6 5.6 - - - +
213B SER 3.1 0.6 - - - -
214B ASP* 1.3 75.0 - - - +
216B ARG* 1.4 65.1 + - - +
218B VAL* 4.0 6.7 - - - +
219B PHE* 3.5 18.2 + - - -
232B LEU* 4.5 7.2 - - + -
263B PHE* 3.4 17.0 - - + -
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE 3.0 8.4 + - - +
213B SER 3.0 10.0 + - - +
215B ALA* 1.4 74.4 - - - +
217B CYS* 1.3 76.0 - - - +
219B PHE* 2.9 32.6 + - - +
220B ASP* 2.9 43.0 + - - +
262B TYR* 2.6 57.8 + - + +
263B PHE* 3.3 27.2 - - + +
264B PRO* 4.1 7.9 - - - +
267B SER* 5.3 8.3 - - - -
269B VAL* 6.2 0.2 - - - +
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Residues in contact with CYS 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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174B LEU* 3.9 18.6 - - + -
213B SER 3.3 5.5 + - - +
214B ASP* 3.1 17.5 + - - +
216B ARG* 1.3 86.2 - - - +
218B VAL* 1.3 50.9 + - - +
220B ASP* 2.6 28.9 + - - +
221B MET* 3.0 34.4 + - - -
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Residues in contact with VAL 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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153B LEU* 4.7 7.2 - - + -
155B ILE* 4.1 22.7 - - + -
174B LEU* 4.5 11.2 - - + -
177B SER* 4.2 15.0 - - - +
181B LEU* 4.1 16.7 - - + +
194B VAL* 3.6 24.5 - - + -
214B ASP 3.3 12.4 + - - +
215B ALA* 4.0 3.3 - - - -
216B ARG 3.2 0.6 - - - -
217B CYS* 1.3 73.4 - - - +
219B PHE* 1.3 54.9 + - - +
221B MET* 3.3 26.7 - - + -
222B GLY* 2.9 22.0 + - - -
229B MET* 4.6 4.4 - - + +
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Residues in contact with PHE 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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193B GLY* 4.2 2.7 - - - -
194B VAL* 3.7 24.0 - - + -
215B ALA 3.5 18.2 + - - +
216B ARG* 2.9 37.6 + - - +
217B CYS 2.9 2.0 + - - -
218B VAL* 1.3 71.4 - - - +
220B ASP* 1.3 56.6 - - - +
222B GLY* 2.7 18.8 + - - +
223B ALA* 3.1 13.5 + - - +
227B PHE 5.0 0.7 - - - +
229B MET* 3.1 46.2 - - + +
230B TYR* 3.7 17.9 - - - -
231B LEU 3.6 27.4 - - - -
232B LEU* 4.5 3.8 - - + -
263B PHE* 4.2 20.2 - + - -
269B VAL* 5.0 2.7 - - + -
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Residues in contact with ASP 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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216B ARG* 2.9 44.3 + - - +
217B CYS* 2.6 16.7 + - - +
219B PHE* 1.3 71.6 - - - +
221B MET* 1.3 54.5 - - - +
223B ALA* 3.1 27.2 + - - +
224B GLU* 3.4 16.2 + - - +
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Residues in contact with MET 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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174B LEU* 3.8 20.9 - - + +
177B SER* 4.7 0.2 - - - -
178B ARG* 3.2 66.6 + - - +
181B LEU* 3.3 14.8 - - + +
217B CYS* 3.0 31.6 + - - +
218B VAL* 3.3 40.6 - - + +
220B ASP* 1.3 70.5 - - - +
222B GLY* 1.3 60.5 + - - +
223B ALA 3.3 0.4 - - - -
224B GLU* 4.5 6.5 + - - +
225B VAL* 3.4 5.8 - - - +
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Residues in contact with GLY 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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181B LEU* 4.1 7.4 - - - -
218B VAL 2.9 7.0 + - - -
219B PHE 2.7 15.7 + - - -
221B MET* 1.3 73.6 - - - +
223B ALA* 1.3 53.7 + - - +
224B GLU 3.6 0.4 - - - -
225B VAL* 3.2 9.3 - - - +
227B PHE* 2.7 42.3 + - - +
229B MET* 3.7 22.9 - - - -
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Residues in contact with ALA 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 PHE 3.1 9.0 + - - +
220B ASP* 3.1 18.4 - - - +
222B GLY* 1.3 74.9 - - - +
224B GLU* 1.3 57.8 + - + +
226B GLY* 2.8 21.5 + - - -
227B PHE 3.5 10.8 - - - +
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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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178B ARG* 4.1 28.4 + - - +
220B ASP* 3.4 15.5 + - - +
221B MET* 5.2 3.6 - - - +
222B GLY 3.6 0.2 - - - -
223B ALA* 1.3 75.7 - - + +
225B VAL* 1.3 58.8 + - - +
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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
------------------------------------------------------------
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