Contacts of the helix formed by residues 199 - 216 (chain B) in PDB entry 3D8U
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 HIS 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B TYR* 4.3 29.2 - + + -
134B GLY* 4.9 15.4 - - - -
196B ARG* 3.2 48.8 + - + +
197B GLY 3.9 6.1 - - - +
198B ASN* 1.3 81.4 - - - +
200B SER* 1.3 81.8 + - - +
201B THR* 3.3 24.8 + - - -
202B LEU* 3.5 6.9 + - - +
203B GLN* 4.1 3.3 + - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 4.5 8.3 + - - -
158B LEU* 5.7 5.2 - - - +
198B ASN 4.1 1.2 + - - -
199B HIS* 1.3 83.2 + - - +
201B THR* 1.3 68.2 + - - +
203B GLN* 3.0 19.2 + - - +
204B ARG* 3.3 15.9 + - - +
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Residues in contact with THR 201 (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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157B GLU* 4.7 3.6 + - - -
171B HIS* 3.4 48.0 + - + +
196B ARG* 3.1 26.1 + - - +
199B HIS* 3.3 16.4 + - - -
200B SER* 1.3 79.9 + - - +
202B LEU* 1.3 62.6 + - - +
203B GLN 3.2 0.2 + - - -
204B ARG* 3.3 8.6 + - - +
205B GLN* 3.0 33.2 + - - +
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Residues in contact with LEU 202 (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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192B PHE* 3.6 26.0 - - + -
194B GLY* 3.7 18.6 - - - -
195B ALA 3.6 11.4 - - - +
196B ARG* 3.5 7.6 - - - +
197B GLY* 2.9 41.7 - - - +
199B HIS 3.5 1.0 + - - -
200B SER 3.2 1.0 - - - -
201B THR* 1.3 78.6 - - - +
203B GLN* 1.3 62.2 - - - +
205B GLN* 2.9 29.2 + - - +
206B LEU* 2.9 27.7 + - + +
225B THR* 3.2 27.8 - - + -
255B SER* 3.9 1.6 - - - -
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLY 3.8 19.8 + - - +
199B HIS 4.1 2.7 + - - +
200B SER* 3.0 15.4 + - - +
202B LEU* 1.3 82.4 - - - +
204B ARG* 1.3 57.1 + - + +
206B LEU* 3.6 18.4 - - + +
207B HIS* 3.0 61.0 + - + +
225B THR* 6.0 0.4 + - - +
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Residues in contact with ARG 204 (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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157B GLU* 3.7 28.9 - - - +
170B ASP* 4.6 5.2 + - - -
171B HIS* 4.1 13.2 - - + -
172B PHE* 3.2 59.8 - - - +
200B SER* 3.3 11.5 + - - +
201B THR 3.6 8.3 - - - +
202B LEU 3.2 0.6 - - - -
203B GLN* 1.3 77.4 - - + +
205B GLN* 1.3 57.0 + - - +
207B HIS* 4.4 12.8 + - - -
208B GLY 3.1 18.2 + - - -
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Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS* 4.0 33.2 + - + +
174B VAL* 5.8 1.4 - - + +
175B GLY* 4.0 5.5 - - - -
192B PHE* 4.2 6.0 - - + -
196B ARG* 5.1 0.4 - - - +
201B THR* 3.0 20.8 - - - +
202B LEU* 2.9 37.1 + - - +
204B ARG* 1.3 75.9 - - - +
206B LEU* 1.3 58.9 + - - +
207B HIS 3.2 0.2 - - - -
208B GLY* 3.1 1.6 + - - -
209B TRP* 2.9 28.2 + - - +
255B SER* 3.5 24.0 + - - +
256B HIS* 5.1 5.1 - - - -
283B LEU* 3.8 34.5 - - + +
284B GLU* 5.9 0.9 - - - +
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Residues in contact with LEU 206 (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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192B PHE* 3.4 38.0 - - + -
202B LEU* 2.9 12.7 + - + +
203B GLN* 3.6 25.8 - - - +
205B GLN* 1.3 74.8 - - - +
207B HIS* 1.3 60.7 + - + +
209B TRP* 2.9 30.5 + - + +
210B GLN* 2.8 50.2 + - - +
223B PHE* 4.0 25.6 - - + -
225B THR* 4.6 9.4 - - + -
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE* 3.6 18.4 - - + -
203B GLN* 3.0 42.9 + - + +
204B ARG* 3.9 15.0 + - - +
206B LEU* 1.3 82.1 - - + +
208B GLY* 1.3 66.0 + - - +
210B GLN* 3.1 20.8 + - - +
211B SER* 2.9 26.3 + - - -
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Residues in contact with GLY 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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172B PHE* 3.5 37.0 - - - -
176B LYS* 3.4 19.6 - - - -
204B ARG 3.1 12.4 + - - -
205B GLN 3.1 4.9 + - - -
207B HIS* 1.3 78.3 - - - +
209B TRP* 1.3 61.0 + - - +
211B SER* 3.5 2.8 + - - -
212B ALA 3.3 15.4 + - - -
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Residues in contact with TRP 209 (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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175B GLY* 5.1 1.6 - - - -
176B LYS 4.2 0.4 - - - +
179B THR* 3.4 34.8 - - + -
190B VAL* 3.5 38.5 - - + +
191B GLY 4.5 0.2 - - - -
192B PHE* 3.8 22.7 - + + -
205B GLN 2.9 11.2 + - - +
206B LEU* 2.9 18.9 + - + +
208B GLY* 1.3 78.3 - - - +
210B GLN* 1.3 82.2 + - + +
212B ALA* 3.4 4.0 + - - +
213B MSE 3.2 40.5 + - + +
220B PRO* 3.4 33.9 - - + -
222B HIS 3.8 20.4 - - - -
223B PHE* 3.7 26.0 - + + -
253B VAL* 3.8 12.5 - - + +
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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
----------------------------------------------------------
206B LEU* 2.8 28.8 + - - +
207B HIS* 3.7 24.7 - - - +
209B TRP* 1.3 87.7 - - + +
211B SER* 1.3 70.0 + - - +
213B MSE 3.3 0.7 + - - +
214B ILE* 3.0 39.6 + - + +
220B PRO* 3.4 28.9 + - + +
223B PHE* 3.6 24.4 - - - -
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE* 3.9 22.2 - - - -
176B LYS* 4.5 9.9 - - - +
207B HIS 2.9 15.8 + - - -
208B GLY 3.5 5.6 - - - -
210B GLN* 1.3 77.3 - - - +
212B ALA* 1.3 66.4 + - - +
213B MSE 2.9 0.9 + - - -
214B ILE* 3.7 4.8 - - - +
215B GLU* 2.9 31.8 + - - +
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Residues in contact with ALA 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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176B LYS* 4.0 18.7 - - + +
179B THR* 3.4 33.9 - - + +
180B ARG* 4.2 8.7 - - + +
183B ILE* 3.6 8.3 - - + +
208B GLY 3.3 5.5 + - - +
209B TRP 3.4 4.7 + - - +
211B SER* 1.3 79.5 + - - +
213B MSE 1.3 61.3 + - - +
215B GLU* 3.9 11.9 - - - +
216B ASN* 3.0 27.3 + - - +
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Residues in contact with MSE 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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179B THR* 4.3 7.4 - - - -
183B ILE* 4.4 4.3 - - - -
188B LYS 4.0 7.6 - - - +
189B ASN* 4.7 1.8 - - + -
190B VAL* 3.9 41.7 - - - +
209B TRP* 3.2 41.2 + - + +
210B GLN 3.6 5.2 - - - +
211B SER 2.9 1.6 + - - -
212B ALA* 1.3 73.1 - - - +
214B ILE* 1.3 57.7 + - - +
216B ASN* 2.8 24.6 + - - -
218B LEU* 3.0 50.3 + - + +
219B THR 4.5 13.5 - - - +
220B PRO* 3.6 19.7 - - + -
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Residues in contact with ILE 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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210B GLN* 3.0 28.8 + - + +
211B SER* 3.9 4.3 - - - +
213B MSE 1.3 74.1 - - - +
215B GLU* 1.3 55.7 + - - +
217B TYR* 2.7 27.4 + - - +
218B LEU 3.7 7.2 - - - +
220B PRO* 3.6 25.8 - - + -
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Residues in contact with GLU 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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176B LYS* 4.7 5.5 - - - +
180B ARG* 3.8 33.6 + - - +
211B SER* 2.9 24.5 + - - +
212B ALA* 3.9 12.6 + - - +
214B ILE* 1.3 70.5 - - - +
216B ASN* 1.3 67.2 + - - +
217B TYR* 3.5 10.1 + - - -
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Residues in contact with ASN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ARG* 5.6 4.3 - - - +
183B ILE* 3.9 23.3 - - + +
188B LYS* 5.6 6.3 + - - +
212B ALA 3.0 18.9 - - - +
213B MSE 2.8 15.3 + - - +
215B GLU* 1.3 83.2 + - - +
217B TYR* 1.3 71.7 + - - +
218B LEU* 3.1 29.5 + - + +
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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