Contacts of the helix formed by residues 206 - 224 (chain B) in PDB entry 1D0N
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 ASN 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ARG* 3.5 29.1 + - - +
204B LYS 3.9 1.4 + - - -
205B SER* 1.3 75.4 - - - +
207B ARG* 1.3 70.8 + - - +
208B PHE* 3.2 4.6 + - - +
209B GLU* 2.8 34.0 + - - +
210B ARG* 3.2 14.5 + - - +
669B ASP* 3.7 14.9 + - - +
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Residues in contact with ARG 207 (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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205B SER 3.9 0.6 + - - -
206B ASN* 1.3 77.0 + - - +
208B PHE* 1.3 60.5 + - - +
210B ARG* 3.5 32.0 + - - +
211B LEU* 3.2 20.8 + - - +
744B ASP* 3.0 38.4 + - - +
746B LEU* 3.7 28.8 - - + +
747B ASP* 3.1 24.4 + - - -
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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
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168B ARG* 3.5 68.4 - - + +
169B ARG* 4.3 3.8 - - - -
206B ASN* 3.1 3.1 + - + +
207B ARG* 1.3 76.5 - - - +
209B GLU* 1.3 63.7 + - - +
211B LEU* 3.2 23.5 + - + +
212B LYS* 3.0 47.7 + - + +
664B GLU 3.3 23.8 - - - -
665B ASP* 4.4 9.0 - - - -
667B ALA* 4.0 28.7 - - + -
668B THR 5.7 0.2 - - - -
669B ASP* 4.9 1.6 - - - +
745B PRO* 6.3 0.7 - - + -
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 5.5 2.8 - - - +
166B LYS* 6.0 1.3 - - - -
167B GLY 3.9 17.3 - - - +
168B ARG* 2.7 53.8 + - - +
186B GLY 5.7 3.6 - - - +
187B ASP* 6.3 2.7 - - - -
188B CYS* 4.5 9.4 - - - +
205B SER* 5.2 3.4 - - - -
206B ASN* 2.8 30.5 + - - +
208B PHE* 1.3 76.1 - - - +
210B ARG* 1.3 56.0 + - - +
212B LYS* 3.0 9.8 + - - +
213B ALA* 2.8 34.8 + - - +
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Residues in contact with ARG 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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188B CYS* 3.9 9.9 - - - -
199B GLN* 3.6 4.8 + - - +
201B CYS* 3.6 26.1 - - - +
202B GLY 5.0 1.6 + - - -
203B SER* 4.8 7.7 + - - +
205B SER* 3.0 38.2 + - - +
206B ASN 3.2 8.9 + - - +
207B ARG* 3.6 41.4 - - - +
208B PHE 3.3 0.2 - - - -
209B GLU* 1.3 76.4 - - - +
211B LEU* 1.3 57.9 + - - +
213B ALA 3.2 0.3 + - - -
214B THR* 2.7 34.1 + - - -
233B VAL* 6.4 2.5 - - + -
235B GLU* 3.1 28.4 + - - -
746B LEU* 3.8 24.5 - - + +
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Residues in contact with LEU 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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207B ARG 3.2 10.7 + - - +
208B PHE* 3.2 34.3 + - + +
210B ARG* 1.3 79.6 - - - +
212B LYS* 1.3 67.9 + - + +
214B THR* 3.3 16.9 - - - -
215B GLN* 3.5 19.0 + - + +
664B GLU* 5.1 4.9 - - + +
740B TYR* 4.5 8.1 - - - +
745B PRO* 4.0 37.7 - - + +
746B LEU* 3.7 11.4 - - + +
749B ALA* 3.6 30.7 - - + -
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Residues in contact with LYS 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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136B SER 5.4 0.2 - - - +
165B VAL* 5.6 1.3 - - + -
167B GLY 4.5 6.3 - - - +
168B ARG 3.9 14.6 - - - +
169B ARG 5.4 2.2 - - - -
171B VAL* 3.6 32.7 - - + +
208B PHE* 3.0 44.7 + - + +
209B GLU* 3.0 11.3 + - - +
211B LEU* 1.3 80.6 - - + +
213B ALA* 1.3 63.7 + - - +
215B GLN* 3.1 29.9 + - + +
216B VAL* 3.6 9.8 + - - +
664B GLU* 4.1 20.2 + - - +
665B ASP* 3.7 20.0 + - - -
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Residues in contact with ALA 213 (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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165B VAL* 3.8 23.1 - - + +
188B CYS* 3.8 25.8 - - + -
190B ILE* 4.0 2.5 - - + +
199B GLN* 3.4 24.9 - - + +
209B GLU 2.8 19.0 + - - +
210B ARG 3.2 1.5 + - - +
212B LYS* 1.3 73.6 - - - +
214B THR* 1.3 62.7 + - - +
216B VAL* 3.1 16.3 + - - +
217B SER* 3.1 11.3 + - - -
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Residues in contact with THR 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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199B GLN* 3.2 20.1 + - - +
210B ARG 2.7 19.5 + - - -
211B LEU* 3.3 13.9 - - - -
213B ALA* 1.3 78.2 - - - +
215B GLN* 1.3 59.0 + - - +
217B SER* 3.5 1.6 + - - -
218B LYS* 3.1 27.0 + - - +
233B VAL* 5.6 1.3 - - + -
746B LEU* 4.3 1.2 - - - +
749B ALA* 4.4 20.6 - - + +
750B LEU* 4.1 17.2 - - + +
753B LEU* 3.8 29.8 - - + -
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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
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136B SER* 4.5 23.4 - - - +
211B LEU* 3.7 24.1 + - + +
212B LYS* 3.1 22.3 + - + +
213B ALA 3.1 0.4 - - - -
214B THR* 1.3 78.9 - - - +
216B VAL* 1.3 60.1 + - - +
218B LYS* 3.5 14.7 + - - +
219B GLY* 2.9 25.6 + - - -
664B GLU* 6.2 1.8 - - - +
749B ALA* 5.8 3.6 - - - +
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Residues in contact with VAL 216 (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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136B SER* 4.1 14.4 - - - +
137B GLY* 5.6 1.3 - - - -
139B LYS* 4.8 10.1 - - - -
163B LEU* 5.0 0.9 - - + -
165B VAL* 4.6 4.9 - - + -
171B VAL* 3.9 22.7 - - + -
173B ALA* 4.0 21.5 - - + -
190B ILE* 3.8 17.5 - - + -
212B LYS 3.8 12.8 - - - +
213B ALA* 3.1 10.5 + - - +
215B GLN* 1.3 74.7 - - - +
217B SER* 1.3 60.7 + - - +
219B GLY* 3.0 2.9 + - - -
220B ILE* 2.8 44.1 + - + +
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Residues in contact with SER 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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190B ILE* 3.3 24.2 - - - +
197B ILE* 4.2 10.3 - - - +
199B GLN* 2.7 33.2 + - - +
213B ALA 3.1 1.8 + - - -
214B THR* 3.7 5.6 - - - -
215B GLN 3.3 0.2 - - - -
216B VAL* 1.3 79.1 - - - +
218B LYS* 1.3 63.2 + - - +
220B ILE* 3.1 9.7 + - - +
221B ARG* 3.0 21.7 + - - +
231B VAL* 4.2 20.8 - - - +
753B LEU* 4.6 2.5 - - - -
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Residues in contact with LYS 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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214B THR 3.1 15.3 + - - +
215B GLN* 4.0 14.4 - - - +
217B SER* 1.3 79.6 - - - +
219B GLY* 1.3 57.0 + - - +
221B ARG* 3.2 36.6 - - - +
222B ASP* 2.8 40.8 + - - +
752B GLU* 2.5 33.9 + - + +
753B LEU* 3.7 29.6 - - + +
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Residues in contact with GLY 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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136B SER* 5.8 5.4 - - - -
139B LYS* 5.5 3.1 - - - -
215B GLN 2.9 15.5 + - - -
216B VAL* 3.0 5.8 + - - -
218B LYS* 1.3 78.8 - - - +
220B ILE* 1.3 56.1 + - - +
222B ASP* 4.7 1.8 - - - -
223B ASN* 2.8 48.9 + - - +
224B GLU* 5.5 0.2 - - - +
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Residues in contact with ILE 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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139B LYS* 4.0 19.1 - - - +
161B ARG* 3.8 11.9 - - - +
163B LEU* 3.4 32.8 - - + -
190B ILE* 4.4 17.9 - - + -
192B ASP* 3.9 5.4 - - - +
197B ILE* 3.8 9.6 - - + -
216B VAL* 2.8 26.3 + - + +
217B SER* 3.1 6.9 + - - +
219B GLY* 1.3 75.6 - - - +
221B ARG* 1.3 53.0 + - - +
224B GLU* 2.5 58.0 + - - +
225B ARG* 3.8 23.1 - - - +
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Residues in contact with ARG 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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197B ILE* 3.9 15.0 - - + +
217B SER 3.0 12.3 + - - +
218B LYS* 3.2 33.4 + - - +
220B ILE* 1.3 78.4 - - - +
222B ASP* 1.3 85.2 + - - +
224B GLU 2.7 14.3 - - - +
225B ARG* 3.7 5.3 - - - +
227B GLY* 2.7 39.5 + - - +
229B ALA* 3.6 33.9 - - + +
231B VAL* 4.0 12.1 - - + +
752B GLU 3.9 15.6 + - - -
753B LEU* 3.8 21.7 + - - +
755B ALA* 5.3 2.8 + - - -
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Residues in contact with ASP 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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218B LYS* 2.8 39.8 + - - +
219B GLY* 4.1 2.0 - - - +
221B ARG* 1.3 114.5 + - - +
223B ASN* 1.3 68.1 + - - +
226B SER* 3.7 7.1 - - - -
227B GLY* 3.7 17.2 + - - +
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Residues in contact with ASN 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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57B ASN* 2.8 61.0 + - + +
136B SER* 5.5 6.1 + - - -
219B GLY* 2.8 28.5 + - - +
222B ASP* 1.3 79.8 - - - +
224B GLU* 1.3 63.2 + - + +
226B SER* 4.6 1.8 + - - -
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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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57B ASN* 5.1 0.2 - - - +
58B LEU* 3.6 26.4 - - + +
61B ASP* 4.4 5.3 - - - +
139B LYS* 2.8 30.5 + - - +
141B LYS* 5.2 2.9 + - - -
161B ARG* 3.2 27.0 + - - -
219B GLY 3.9 0.2 + - - -
220B ILE* 2.5 32.4 + - + +
221B ARG 2.7 21.1 - - - +
223B ASN* 1.3 75.1 - - + +
225B ARG* 1.3 72.3 + - - +
226B SER 3.0 6.2 + - - -
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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
------------------------------------------------------------
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