Contacts of the helix formed by residues 188 - 200 (chain B) in PDB entry 5HNK
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 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B LEU* 5.3 6.3 - - + -
180B MET* 3.9 12.3 - - - +
186B VAL* 3.6 4.0 - - - +
187B ASP* 1.3 82.3 - - - +
189B VAL* 1.3 64.1 + - - +
190B GLU* 3.4 11.4 + - - +
191B GLN* 3.0 31.3 + - - +
192B PHE* 3.1 21.8 + - - +
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Residues in contact with VAL 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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157B ASP 3.8 20.4 - - - +
158B THR* 3.3 26.5 - - - +
160B LEU 3.9 19.5 - - - +
177B LEU* 4.5 6.4 - - + +
180B MET* 4.0 9.4 - - + +
188B ASP* 1.3 76.2 - - - +
190B GLU* 1.3 62.1 + - + +
192B PHE* 3.2 8.3 + - - +
193B ILE* 2.9 46.5 + - + +
263B PRO* 4.9 3.1 - - + -
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Residues in contact with GLU 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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188B ASP* 3.4 11.2 + - - +
189B VAL* 1.3 79.5 - - + +
191B GLN* 1.3 58.6 + - - +
193B ILE* 3.4 22.8 + - - +
194B SER* 2.9 31.9 + - - -
226B ASN* 3.4 21.6 - - - +
261B ASP* 5.1 7.3 - - - +
264B THR* 5.7 0.9 + - - -
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Residues in contact with GLN 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 VAL* 3.7 14.2 - - + +
187B ASP* 2.8 48.2 + - - +
188B ASP* 3.0 22.3 + - - +
190B GLU* 1.3 73.4 - - - +
192B PHE* 1.3 60.4 + - - +
194B SER* 3.7 2.4 - - - -
195B LEU* 2.9 31.7 + - - +
218B TYR* 3.6 15.6 - - - -
221B ILE* 3.9 25.3 + - + +
222B ARG* 4.9 10.3 - - - +
226B ASN* 3.5 17.0 - - - +
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Residues in contact with PHE 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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154B GLY 3.5 27.1 - - - -
155B ASP* 3.9 19.1 - - + -
157B ASP* 4.0 8.1 - - + -
158B THR* 3.6 32.1 - - + -
180B MET* 4.4 10.1 - - - -
184B HIS* 3.6 40.8 - + + -
186B VAL* 3.7 15.0 - - + +
188B ASP 3.1 14.5 + - - +
189B VAL* 3.2 10.5 + - - +
191B GLN* 1.3 75.5 - - - +
193B ILE* 1.3 62.4 + - - +
195B LEU* 3.9 5.6 - - + +
196B LYS* 3.1 40.7 + - + +
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Residues in contact with ILE 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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158B THR* 3.7 18.2 - - + -
189B VAL* 2.9 39.6 + - + +
190B GLU* 3.7 20.6 - - - +
192B PHE* 1.3 73.9 - - - +
194B SER* 1.3 65.8 + - - +
196B LYS* 3.4 2.6 + - - -
197B ALA* 3.1 19.6 + - - +
257B LEU* 3.6 25.1 - - + -
260B VAL* 3.5 15.2 - - + +
261B ASP* 3.5 44.0 - - + +
263B PRO* 4.3 10.5 - - + -
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Residues in contact with SER 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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190B GLU* 2.9 14.3 + - - -
191B GLN 3.7 4.0 - - - -
193B ILE* 1.3 78.0 - - - +
195B LEU* 1.3 60.4 + - - +
197B ALA* 3.4 1.3 + - - -
198B ILE* 3.1 21.1 + - - +
221B ILE* 3.7 13.5 - - - -
226B ASN* 3.0 26.3 + - - +
227B VAL* 3.0 46.1 + - - +
257B LEU* 5.1 2.8 - - - +
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Residues in contact with LEU 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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184B HIS 4.2 10.3 - - - +
185B ASN* 5.2 2.0 - - + +
186B VAL* 3.8 22.0 - - + -
191B GLN 2.9 17.5 + - - +
192B PHE* 3.9 8.3 - - + +
194B SER* 1.3 73.2 - - - +
196B LYS* 1.3 61.6 + - - +
198B ILE* 3.5 2.8 + - + +
199B MET* 2.9 54.8 + - + +
213B GLY 4.3 1.6 - - - +
214B ALA* 4.3 12.6 - - + +
217B GLY* 3.7 37.9 - - - -
218B TYR* 3.8 5.2 - - + +
221B ILE* 3.3 10.7 - - + +
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Residues in contact with LYS 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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154B GLY* 5.5 0.6 - - - -
155B ASP* 4.2 30.3 + - + +
192B PHE* 3.1 35.1 + - + +
193B ILE* 3.8 5.2 - - - +
194B SER 3.4 0.2 - - - -
195B LEU* 1.3 76.0 - - - +
197B ALA* 1.3 56.9 + - - +
199B MET* 4.5 5.2 - - + +
200B GLY* 2.7 43.0 + - - +
201B ASP* 3.2 31.7 + - + -
256B ASN* 4.9 0.2 + - - -
260B VAL* 3.9 28.2 - - + +
7Y G 5.0 9.1 + - - -
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Residues in contact with ALA 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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193B ILE 3.1 14.1 + - - +
194B SER 3.6 8.7 - - - +
195B LEU 3.3 0.2 - - - -
196B LYS* 1.3 77.9 - - - +
198B ILE* 1.3 59.6 + - - +
227B VAL* 4.0 13.7 - - + -
252B LEU* 4.3 0.2 - - - +
253B LEU* 4.0 11.4 - - + +
256B ASN* 2.9 36.7 + - + +
257B LEU* 4.0 27.6 - - + +
260B VAL* 3.9 8.0 - - + +
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Residues in contact with ILE 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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194B SER 3.1 17.7 + - - +
195B LEU* 3.8 4.5 - - + +
197B ALA* 1.3 76.1 - - - +
199B MET* 1.3 60.9 + - + +
208B GLY* 3.3 1.7 - - - -
209B VAL* 2.9 35.0 + - + +
212B ILE* 3.5 41.7 - - + +
217B GLY* 4.6 8.5 - - - +
220B ILE* 5.1 7.4 - - + -
221B ILE* 3.8 29.2 - - + -
227B VAL* 4.0 10.3 - - + -
230B ILE* 4.3 12.8 - - + -
246B LEU* 5.2 5.8 - - + -
253B LEU* 3.9 21.3 - - + -
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Residues in contact with MET 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 LEU* 2.9 43.6 + - + +
196B LYS* 4.6 4.3 - - + -
198B ILE* 1.3 78.7 - - + +
200B GLY* 1.3 67.6 + - - +
206B ILE 4.8 0.2 - - - +
208B GLY* 3.4 11.9 + - - -
212B ILE 4.1 13.5 - - - +
213B GLY* 3.8 21.1 - - - +
214B ALA* 3.7 32.3 - - + +
6X C 5.6 1.9 + - - -
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Residues in contact with GLY 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 LYS* 2.7 35.7 + - - +
197B ALA 4.0 0.6 + - - -
198B ILE 3.3 3.2 + - - -
199B MET* 1.3 83.4 - - - +
201B ASP* 1.3 63.9 + - - +
206B ILE* 3.5 22.0 - - - -
207B ARG 4.2 0.4 - - - -
208B GLY* 3.8 7.2 - - - -
256B ASN* 4.3 2.5 - - - -
260B VAL* 6.0 0.7 - - - -
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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