Contacts of the helix formed by residues 185 - 196 (chain B) in PDB entry 3HU6
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 ARG 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ARG* 4.6 7.0 - - - +
283A GLU* 5.6 4.4 - - - +
284A ARG* 4.4 19.5 - - + +
182B PRO* 4.0 20.2 - - - +
183B GLU 3.9 13.8 + - - +
184B CYS* 1.3 74.9 - - - +
186B LEU* 1.3 67.0 + - - +
187B ALA 3.5 1.8 - - - -
188B ASP* 3.3 18.7 + - + +
189B GLU* 3.2 52.2 + - + +
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Residues in contact with LEU 186 (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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186A LEU* 4.5 7.0 - - + -
187A ALA* 3.8 38.6 - - + +
190A LEU* 4.2 17.7 - - + -
217A ILE* 6.2 0.7 - - + -
221A ARG* 3.3 39.1 - - - +
258A ILE 3.9 2.2 - - - +
259A TYR 3.7 18.8 - - - +
260A THR 3.9 10.1 - - - +
184B CYS* 3.5 18.8 - - - -
185B ARG* 1.3 79.0 - - - +
187B ALA* 1.3 65.8 + - - +
188B ASP 3.0 1.6 + - - -
189B GLU* 3.2 2.3 + - - +
190B LEU* 3.1 29.4 + - + +
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Residues in contact with ALA 187 (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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186A LEU* 3.6 19.0 - - + +
184B CYS* 5.4 0.4 + - - -
185B ARG 3.5 0.2 - - - -
186B LEU* 1.3 80.1 - - - +
188B ASP* 1.3 62.3 + - - +
190B LEU* 3.8 1.1 + - - -
191B GLY 3.2 5.0 + - - -
259B TYR 3.8 2.3 - - - +
260B THR* 2.9 55.3 - - - +
262B LYS* 3.8 13.9 - - - +
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Residues in contact with ASP 188 (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 CYS 3.9 5.2 - - - +
185B ARG* 3.3 29.6 - - + +
186B LEU 3.0 0.6 + - - -
187B ALA* 1.3 75.8 + - - +
189B GLU* 1.3 67.7 + - + +
190B LEU 3.1 1.6 - - - -
191B GLY* 3.0 13.2 + - - -
192B GLY* 3.2 9.2 + - - -
260B THR* 5.1 1.3 - - - -
262B LYS* 3.6 18.6 + - - +
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Residues in contact with GLU 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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220A ALA* 3.1 46.9 - - + +
221A ARG* 2.5 47.4 + - - +
223A PRO* 6.1 0.9 - - - +
185B ARG* 3.2 36.5 + - + +
186B LEU 3.9 2.7 - - - +
188B ASP* 1.3 80.7 - - + +
190B LEU* 1.3 61.3 + - - +
192B GLY* 3.4 10.0 + - - +
193B LEU 3.7 3.6 + - - -
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Residues in contact with LEU 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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186A LEU* 4.7 3.8 - - + -
190A LEU* 3.1 42.0 - - + -
217A ILE* 4.8 13.9 - - + -
220A ALA* 4.8 4.5 - - + -
221A ARG* 4.7 11.4 - - - -
186B LEU* 3.1 30.8 + - + +
187B ALA* 4.0 1.6 - - - +
189B GLU* 1.3 76.5 - - - +
191B GLY* 1.3 65.0 + - - +
192B GLY 3.0 2.0 - - - -
193B LEU* 3.1 34.9 + - + +
217B ILE* 4.7 16.2 - - + -
259B TYR* 3.2 34.5 - - + +
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Residues in contact with GLY 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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187B ALA 3.2 4.9 + - - -
188B ASP 3.0 8.2 + - - -
190B LEU* 1.3 78.9 - - - +
192B GLY* 1.3 57.8 + - - +
194B TRP* 3.0 4.6 + - - +
195B GLU* 2.9 38.1 + - - +
259B TYR* 4.1 7.2 - - - -
260B THR* 3.4 25.5 - - - +
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Residues in contact with GLY 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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188B ASP 3.2 9.9 + - - -
189B GLU* 3.4 7.5 + - - -
190B LEU 3.0 1.4 - - - -
191B GLY* 1.3 74.8 - - - +
193B LEU* 1.3 65.5 + - - +
194B TRP 3.1 0.2 + - - -
195B GLU* 4.5 4.0 - - - -
196B ASN* 2.8 44.3 + - - +
198B ARG* 5.2 1.3 - - - -
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Residues in contact with LEU 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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216A ALA* 3.8 35.2 - - + +
217A ILE* 4.1 3.6 - - - +
220A ALA* 3.3 33.7 - - + +
189B GLU 3.7 1.2 + - - -
190B LEU* 3.1 17.8 + - + +
192B GLY* 1.3 74.7 - - - +
194B TRP* 1.3 57.9 + - - +
196B ASN 2.5 19.1 - - - +
197B SER* 3.7 1.9 - - - -
198B ARG* 3.3 29.8 + - + +
199B PHE* 5.3 2.0 - - + -
200B THR* 5.0 0.2 - - - +
212B GLN 5.6 0.2 - - - +
214B HIS* 3.5 29.1 - - + +
217B ILE* 3.9 22.2 - - + -
259B TYR* 4.4 2.2 - - + -
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Residues in contact with TRP 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 LEU 3.6 1.2 + - - -
191B GLY* 3.0 8.1 + - - +
193B LEU* 1.3 79.5 - - - +
195B GLU* 1.3 92.7 + - - +
196B ASN 3.7 1.9 - - - +
197B SER* 4.0 4.9 + - - -
211B PHE* 3.8 39.3 - + + -
212B GLN 3.4 26.5 - - - +
213B ALA* 4.1 2.7 - - + -
214B HIS* 5.0 0.7 - - - -
251B PHE* 4.1 1.6 - + - -
252B LYS* 4.1 28.9 + - + +
255B MET* 3.2 53.3 - - + +
256B CYS* 4.4 14.9 - - + +
259B TYR* 3.8 33.6 - + + -
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Residues in contact with GLU 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 GLY* 2.9 31.7 + - - +
192B GLY* 4.1 3.6 - - - +
194B TRP* 1.3 94.7 + - - +
196B ASN* 1.3 71.7 + - - +
197B SER* 3.3 2.9 + - - -
256B CYS* 5.1 11.4 - - - -
260B THR* 5.9 0.3 - - - +
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Residues in contact with ASN 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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192B GLY* 2.8 29.8 + - - +
193B LEU 2.5 25.6 - - - +
195B GLU* 1.3 80.1 - - - +
197B SER* 1.3 53.2 + - - +
198B ARG* 2.9 22.3 + - + +
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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