Contacts of the helix formed by residues 187 - 203 (chain B) in PDB entry 6D1U
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B GLY* 3.0 26.0 + - - +
169B TYR* 3.5 19.0 + - - -
184B GLY* 3.2 19.2 + - - -
185B VAL 3.7 0.4 - - - -
186B ASP* 1.3 80.4 + - - +
188B ALA* 1.3 64.6 + - - +
189B GLY 3.3 4.8 + - - +
190B ALA* 3.0 22.3 + - - +
191B LYS* 3.1 22.0 + - - +
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.9 1.6 - - - -
187B ASN* 1.3 75.0 - - - +
189B GLY* 1.3 55.5 + - - +
191B LYS* 3.5 10.6 + - - +
192B ALA* 3.0 29.2 + - - +
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Residues in contact with GLY 189 (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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163B ILE 3.5 10.6 - - - +
166B ASP* 3.3 43.0 + - - +
167B GLY* 4.0 1.5 - - - -
168B GLY 4.1 1.6 - - - -
187B ASN* 3.2 7.7 + - - -
188B ALA* 1.3 77.4 - - - +
190B ALA* 1.3 64.3 + - - +
192B ALA* 3.5 2.8 + - - +
193B GLY* 3.1 17.7 + - - -
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Residues in contact with ALA 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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163B ILE* 3.5 31.5 + - + +
168B GLY* 3.8 2.3 - - - +
184B GLY 4.0 6.1 - - - +
185B VAL 3.4 29.4 - - - +
187B ASN* 3.0 19.5 + - - +
189B GLY* 1.3 72.3 - - - +
191B LYS* 1.3 61.0 + - - +
193B GLY* 3.4 1.2 + - - -
194B LEU* 3.0 31.0 + - - +
363B LEU* 3.9 3.9 - - + +
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Residues in contact with LYS 191 (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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186B ASP* 3.6 27.9 + - - +
187B ASN 3.1 15.1 + - - +
188B ALA* 3.7 11.0 - - - +
190B ALA* 1.3 77.3 - - - +
192B ALA* 1.3 57.0 + - - +
195B THR* 2.8 37.7 + - - +
359B VAL* 3.8 7.4 - - + +
360B ASP* 3.3 39.3 + - - +
363B LEU* 3.8 20.6 - - + -
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Residues in contact with ALA 192 (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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166B ASP* 4.0 3.6 - - - +
188B ALA 3.0 17.8 + - - +
189B GLY 3.8 5.2 - - - +
190B ALA 3.3 0.2 - - - -
191B LYS* 1.3 77.2 - - - +
193B GLY* 1.3 61.9 + - - +
195B THR* 3.7 5.1 - - - +
196B PHE* 3.1 18.7 + - - +
252B PHE* 3.4 21.9 - - + -
253B LYS* 3.8 25.6 - - + +
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Residues in contact with GLY 193 (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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162B LEU* 3.6 39.0 - - - +
163B ILE* 4.3 2.7 - - - -
189B GLY 3.1 12.7 + - - -
190B ALA 3.8 2.2 - - - -
191B LYS 3.3 0.2 - - - -
192B ALA* 1.3 76.8 - - - +
194B LEU* 1.3 61.1 + - - +
196B PHE* 3.3 5.2 + - - +
197B LEU* 3.1 16.5 + - - +
252B PHE* 3.6 12.5 - - - -
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Residues in contact with LEU 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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163B ILE* 4.2 15.6 - - + +
190B ALA 3.0 17.0 + - - +
193B GLY* 1.3 74.8 - - - +
195B THR* 1.3 56.6 - - - +
197B LEU* 3.2 29.5 + - + +
198B VAL* 2.9 32.3 + - + +
348B ALA 4.4 6.7 - - - +
349B VAL* 4.3 24.7 - - + +
352B ALA* 3.9 20.2 - - + -
359B VAL* 4.2 17.0 - - + -
362B ALA* 5.1 0.9 - - + -
363B LEU* 3.9 33.2 - - + -
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Residues in contact with THR 195 (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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191B LYS* 2.8 24.9 + - - +
192B ALA* 3.7 6.3 - - - +
194B LEU* 1.3 74.4 - - - +
196B PHE* 1.3 60.1 + - - +
198B VAL* 3.2 2.8 + - + +
199B ASP* 2.9 47.2 + - - +
359B VAL* 3.6 25.6 - - + +
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Residues in contact with PHE 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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131B TRP* 3.3 50.9 - + + -
132B GLU* 3.9 19.5 - - + -
135B PRO* 4.4 16.4 - - + -
162B LEU* 4.4 6.1 - - + -
192B ALA 3.1 14.2 + - - +
193B GLY* 3.3 8.9 + - - +
195B THR* 1.3 76.9 - - - +
197B LEU* 1.3 63.0 + - - +
199B ASP* 3.4 10.4 + - + +
200B LEU* 3.0 45.2 + - + +
252B PHE* 3.8 23.6 - + + -
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Residues in contact with LEU 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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151B PHE* 3.9 20.2 - - + -
153B LEU* 4.2 5.6 - - + -
159B THR* 3.8 24.9 - - + -
162B LEU* 4.1 15.7 - - + +
163B ILE* 6.5 0.2 - - + -
193B GLY 3.1 12.2 + - - +
194B LEU* 3.2 30.5 + - + +
196B PHE* 1.3 77.4 - - - +
198B VAL* 1.3 62.3 + - + +
200B LEU* 3.2 20.7 + - + +
201B ILE* 3.3 22.9 + - + +
206B MET* 3.6 25.6 - - + -
349B VAL* 4.1 10.3 - - + -
353B ALA* 5.0 5.2 - - + -
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 2.9 23.9 + - + +
195B THR* 3.2 4.7 + - + +
197B LEU* 1.3 75.9 - - + +
199B ASP* 1.3 58.6 + - - +
201B ILE* 3.1 11.3 + - + +
202B LYS* 2.8 55.6 + - + +
352B ALA* 3.6 46.0 - - + +
353B ALA* 4.1 6.5 - - + +
359B VAL* 4.0 14.6 - - + -
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Residues in contact with ASP 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 THR* 2.9 35.9 + - - +
196B PHE* 3.7 11.4 - - + +
198B VAL* 1.3 77.3 - - - +
200B LEU* 1.3 64.5 + - - +
202B LYS* 4.3 18.4 + - - +
203B ASN* 3.0 40.0 + - - +
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Residues in contact with LEU 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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131B TRP* 4.1 19.1 - - + -
134B ILE* 4.5 10.1 - - + -
135B PRO* 3.9 30.7 - - + -
149B LEU* 5.1 2.9 - - + -
196B PHE* 3.0 43.5 + - + +
197B LEU* 3.2 11.9 + - + +
199B ASP* 1.3 74.7 - - - +
201B ILE* 1.3 60.2 + - - +
203B ASN 3.8 0.5 - - - -
204B LYS 3.3 3.1 + - - -
205B HIS* 2.9 50.9 + - + +
206B MET* 3.4 31.3 + - + -
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Residues in contact with ILE 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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175A ASN* 6.0 4.7 - - + -
153B LEU* 4.1 17.9 - - + -
197B LEU* 3.3 19.3 + - + +
198B VAL* 3.1 10.2 + - + +
200B LEU* 1.3 75.4 - - - +
202B LYS* 1.3 68.6 + - + +
204B LYS* 3.0 17.7 + - - +
206B MET* 3.6 32.4 - - + +
207B ASN* 5.0 0.2 - - - -
208B ALA* 4.2 14.6 - - + +
353B ALA* 3.6 48.9 - - + +
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Residues in contact with LYS 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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198B VAL* 2.8 41.1 + - + +
199B ASP* 3.4 18.0 + - - +
201B ILE* 1.3 75.8 - - + +
203B ASN* 1.3 63.7 + - - +
204B LYS* 3.4 15.6 + - - +
355B GLY* 6.4 2.2 - - - -
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Residues in contact with ASN 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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135B PRO* 6.2 0.2 - - - +
199B ASP* 3.0 29.9 + - - +
202B LYS* 1.3 80.6 + - - +
204B LYS* 1.3 69.4 + - - +
205B HIS* 3.3 34.3 + - + +
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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