Contacts of the helix formed by residues 187 - 204 (chain B) in PDB entry 4K8T
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 ASP 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ALA 4.5 2.4 - - - +
32B ALA* 3.5 9.9 - - - +
33B MSE 3.0 35.6 + - - +
123B ARG* 5.7 2.1 + - - -
156B TYR* 3.6 21.4 + - + +
185B LEU 2.8 6.7 + - - -
186B SER* 1.3 76.2 - - - +
188B SER* 1.3 59.6 + - - +
189B PHE* 2.9 34.1 + - - +
190B CYS* 3.1 13.7 + - + +
191B VAL* 2.9 29.1 + - - +
193B ARG* 4.9 0.9 + - - -
216B GLU* 3.3 10.1 + - - -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 1.3 74.5 + - - +
189B PHE* 1.3 77.9 + - - +
191B VAL* 3.5 1.9 + - - -
192B ASP* 3.0 16.9 + - - -
215B GLN* 3.9 34.9 - - - +
216B GLU* 3.8 9.1 - - - +
219B SER* 3.0 30.4 + - - -
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Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.8 20.0 - - + -
30B LYS 5.7 0.7 - - - -
32B ALA* 3.8 27.4 - - + -
33B MSE 5.3 3.4 - - - +
187B ASP* 2.9 14.0 + - - +
188B SER* 1.3 87.8 - - - +
190B CYS* 1.3 68.5 + - - +
191B VAL 3.1 0.9 - - - -
192B ASP* 3.0 21.9 + - + +
193B ARG* 2.8 41.7 + - + +
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Residues in contact with CYS 190 (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 GLY 3.4 35.0 - - - -
156B TYR* 3.8 13.2 - - + -
159B ASP* 4.6 0.9 - - - -
185B LEU 4.1 5.6 - - - +
187B ASP* 3.1 27.9 + - + +
189B PHE* 1.3 74.6 - - - +
191B VAL* 1.3 62.7 + - - +
193B ARG* 3.1 26.4 + - - +
194B TYR* 3.1 38.0 + - - +
198B PHE* 4.0 9.4 - - - -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.7 33.7 - - + +
187B ASP 2.9 18.4 + - - +
188B SER* 3.5 8.7 - - - +
189B PHE 3.1 0.2 - - - -
190B CYS* 1.3 77.0 - - - +
192B ASP* 1.3 54.4 + - - +
195B ARG* 2.7 40.2 + - + +
198B PHE* 4.1 11.9 - - + -
216B GLU* 4.1 12.8 - - + +
219B SER* 3.6 8.1 - - - +
220B LEU* 3.4 48.9 - - + +
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER 3.0 16.0 + - - +
189B PHE* 3.0 31.8 + - + +
191B VAL* 1.3 75.8 - - - +
193B ARG* 1.3 64.1 + - + +
194B TYR 3.5 0.2 + - - -
195B ARG* 2.6 47.8 + - - +
219B SER* 2.9 8.5 + - - -
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B MSE 3.6 23.8 + - - +
35B LEU* 4.2 8.5 - - - +
159B ASP* 2.8 42.1 + - - -
187B ASP* 4.9 0.8 + - - -
189B PHE* 2.8 34.8 + - + +
190B CYS* 3.1 26.4 + - - +
192B ASP* 1.3 79.1 - - + +
194B TYR* 1.3 83.0 + - + +
195B ARG 3.7 0.2 - - - -
197B GLU* 4.3 3.1 - - - +
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Residues in contact with TYR 194 (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 TRP* 3.1 55.7 + + + -
159B ASP* 2.6 35.5 + - - -
164B LYS* 5.3 2.9 - - - -
190B CYS* 3.1 31.9 + - - -
191B VAL 3.5 1.8 - - - -
193B ARG* 1.3 103.0 + - + +
195B ARG* 1.3 64.8 + - - +
197B GLU* 3.0 23.1 + - - +
198B PHE* 2.9 44.3 + - + -
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 2.7 16.9 + - - +
192B ASP* 2.6 49.5 + - - +
193B ARG 3.7 1.2 + - - -
194B TYR* 1.3 73.3 - - - +
196B GLY* 1.3 64.0 + - - +
198B PHE* 3.4 3.0 + - - +
199B LEU* 3.1 38.1 + - + +
219B SER* 2.9 33.7 + - - +
220B LEU* 3.3 29.5 - - + +
222B GLN* 3.4 40.7 - - - +
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Residues in contact with GLY 196 (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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194B TYR 3.4 0.8 - - - -
195B ARG* 1.3 79.0 - - - +
197B GLU* 1.3 60.5 + - - +
199B LEU* 3.6 9.4 + - - +
200B ASP* 3.0 28.4 + - - +
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Residues in contact with GLU 197 (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 TRP* 3.7 27.6 - - + +
164B LYS* 4.7 8.5 + - - +
193B ARG 4.3 2.1 - - - +
194B TYR* 3.0 36.7 + - - +
196B GLY* 1.3 79.2 + - - +
198B PHE* 1.3 66.5 + - - +
200B ASP* 3.3 8.9 + - - +
201B LEU* 3.0 28.1 + - - +
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Residues in contact with PHE 198 (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 GLY* 3.5 31.6 - - - -
158B TRP* 4.0 17.9 - + - -
183B MSE 3.8 22.6 - - + +
185B LEU* 3.9 38.8 - - + -
190B CYS* 4.0 7.2 - - - -
191B VAL* 4.1 31.0 - - + -
194B TYR* 2.9 35.1 + - + +
195B ARG 3.8 4.3 - - - +
197B GLU* 1.3 76.7 - - + +
199B LEU* 1.3 65.8 + - - +
201B LEU* 3.2 14.9 + - + +
202B MSE 3.1 27.2 + - - +
220B LEU* 4.6 5.8 - - + -
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Residues in contact with LEU 199 (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 ARG* 3.1 37.8 + - + +
196B GLY* 3.8 7.2 - - - +
198B PHE* 1.3 74.9 - - - +
200B ASP* 1.3 58.3 + - - +
202B MSE 3.2 8.2 + - - +
203B ARG* 2.8 62.0 + - - +
220B LEU* 3.9 21.5 - - + +
221B TYR* 3.7 32.5 - - + +
236B ASP* 3.7 14.4 - - - +
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Residues in contact with ASP 200 (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 GLY 3.0 18.0 + - - +
197B GLU* 3.5 9.1 - - - +
198B PHE 3.2 0.2 - - - -
199B LEU* 1.3 73.4 - - - +
201B LEU* 1.3 58.1 + - - +
203B ARG* 4.5 4.6 - - - +
204B SER* 2.8 48.3 + - - -
206B LYS* 5.2 5.8 + - - +
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Residues in contact with LEU 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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153B PHE* 3.9 8.3 - - + -
158B TRP* 3.7 38.4 - - + -
167B ILE* 5.3 2.5 - - + -
168B LEU* 4.3 18.2 - - + -
183B MSE 3.8 23.6 - - - -
197B GLU 3.0 18.3 + - - +
198B PHE* 3.4 14.6 - - + +
200B ASP* 1.3 78.5 - - - +
202B MSE 1.3 61.8 + - - +
204B SER* 3.4 5.9 + - - -
206B LYS* 3.1 30.9 + - + -
207B VAL* 3.0 34.6 + - + -
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Residues in contact with MSE 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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183B MSE 5.3 2.7 - - - +
185B LEU* 5.0 5.4 - - - -
198B PHE* 3.1 18.9 + - - +
199B LEU* 3.2 12.1 + - - +
201B LEU* 1.3 78.6 - - + +
203B ARG* 1.3 62.7 + - - +
205B GLY* 3.3 13.3 + - - -
207B VAL* 4.0 17.0 - - + +
210B VAL* 3.6 38.8 - - + -
220B LEU* 4.3 16.8 - - + -
221B TYR* 4.1 3.8 - - - +
233B ILE* 3.6 31.9 - - + -
236B ASP* 3.3 39.9 - - + +
237B CYS* 3.9 10.4 - - + -
238B LYS* 5.6 0.9 + - - -
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Residues in contact with ARG 203 (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 LEU* 2.8 48.6 + - - +
200B ASP* 4.3 3.6 - - - +
202B MSE 1.3 79.3 - - - +
204B SER* 1.3 58.9 + - - +
205B GLY 3.5 0.5 + - - -
232B ARG* 4.0 18.8 - - - +
236B ASP* 2.8 48.4 + - - +
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Residues in contact with SER 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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200B ASP* 2.8 29.8 + - - -
201B LEU 3.4 8.3 + - - -
203B ARG* 1.3 75.6 - - - +
205B GLY* 1.3 58.7 + - - +
206B LYS* 3.2 38.8 + - - +
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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
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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