Contacts of the helix formed by residues 188 - 204 (chain B) in PDB entry 4HNE
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 GLN 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLU* 3.8 0.2 + - - -
185B VAL* 3.3 35.2 + - + +
186B LEU 3.7 2.2 + - - -
187B ASN* 1.3 78.4 - - - +
189B GLY* 1.3 64.3 + - - +
190B TYR* 3.3 8.7 - - - -
191B LEU* 3.3 21.0 + - + +
192B SER* 3.1 21.2 + - - -
405B PHE* 4.5 17.7 + - - +
408B ASP* 3.4 30.3 + - - +
410B GLY 4.1 5.1 + - - -
411B PHE* 4.1 22.1 - - - +
412B ASP 5.0 0.4 - - - +
415B GLN* 4.5 8.1 + - - -
419B GLN* 4.7 5.7 + - - +
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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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157B GLU* 3.0 20.0 + - - -
188B GLN* 1.3 75.8 - - - +
190B TYR* 1.3 64.1 + - - +
192B SER* 3.0 6.2 + - - -
193B GLU* 2.9 22.4 + - - +
348B GLY* 3.6 25.0 - - - -
349B LEU* 6.1 0.4 - - - -
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LYS* 4.0 8.3 - - - +
154B LYS* 3.6 28.7 - - + +
157B GLU* 2.7 22.4 + - - +
187B ASN 3.8 6.5 - - - -
188B GLN* 4.1 6.3 - - - -
189B GLY* 1.3 73.8 - - - +
191B LEU* 1.3 85.7 + - + +
193B GLU* 3.3 5.4 - - - +
194B ALA* 3.0 26.2 + - - +
213B VAL* 4.1 7.6 - - + +
257B VAL* 3.9 22.5 - - + +
258B GLY* 4.0 19.3 - - - -
259B SER* 3.8 30.0 - - - +
407B LYS 4.9 1.0 + - - -
408B ASP* 2.5 42.6 + - - +
409B PRO* 4.2 3.1 - - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN* 3.3 26.4 + - + +
189B GLY 3.2 1.0 - - - -
190B TYR* 1.3 104.1 - - + +
192B SER* 1.3 56.9 + - - +
193B GLU 3.1 1.3 - - - -
194B ALA* 3.8 2.8 - - - +
195B GLY* 2.6 34.8 + - - -
213B VAL* 3.6 20.2 - - + -
404B LEU* 3.8 18.6 - - + +
405B PHE* 3.6 35.6 - - + +
407B LYS* 5.3 2.2 - - + -
408B ASP* 3.4 33.9 - - + +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN 3.1 11.2 + - - -
189B GLY 3.0 9.3 + - - -
191B LEU* 1.3 74.7 - - - +
193B GLU* 1.3 63.4 + - - +
196B ALA* 3.1 20.1 + - - +
347B ASN 2.8 22.8 + - - +
348B GLY 3.6 13.0 - - - -
350B ALA* 2.9 38.4 + - - +
351B PHE* 3.4 15.3 - - - -
405B PHE* 4.7 1.6 - - - -
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LYS* 3.0 29.2 + - - +
189B GLY 2.9 10.1 + - - +
190B TYR* 3.3 11.9 - - - +
192B SER* 1.3 80.1 - - - +
194B ALA* 1.3 60.4 + - - +
196B ALA* 3.5 13.3 - - - +
197B SER 3.6 3.5 + - - -
211B THR* 3.2 18.1 + - - +
259B SER* 3.6 23.8 - - - +
261B GLN* 3.7 10.9 + - + +
345B ILE 2.8 27.2 - - - +
347B ASN* 3.2 16.0 + - + +
348B GLY* 2.9 26.0 + - - -
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Residues in contact with ALA 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 TYR 3.0 16.7 + - - +
191B LEU* 3.2 3.3 + - - +
193B GLU* 1.3 75.0 - - - +
195B GLY* 1.3 60.0 + - - +
197B SER* 3.1 6.1 + - - -
198B LEU* 3.0 25.8 + - - +
211B THR* 3.3 23.2 + - - +
212B LYS* 4.2 8.3 - - - -
213B VAL* 4.2 19.1 - - + +
259B SER* 5.7 0.4 - - - -
404B LEU* 3.9 17.2 - - + +
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Residues in contact with GLY 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 LEU 2.6 21.6 + - - -
194B ALA* 1.3 72.4 - - - +
196B ALA* 1.3 56.3 + - - +
198B LEU* 3.2 6.1 + - - +
199B VAL* 2.8 34.5 + - - +
351B PHE* 3.5 17.3 - - - -
401B LEU* 4.2 6.2 - - - +
404B LEU* 3.5 14.0 - - - +
405B PHE* 4.4 0.7 - - - -
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Residues in contact with ALA 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 SER 3.1 13.7 + - - +
193B GLU 3.5 11.2 - - - +
195B GLY* 1.3 75.9 - - - +
197B SER* 1.3 56.4 + - - +
199B VAL* 3.5 1.7 + - - -
200B ASP* 3.0 28.1 + - - +
208B VAL* 4.2 4.3 - - + +
300B LEU* 3.9 14.2 - - + +
304B ILE* 4.2 14.6 - - + -
347B ASN* 3.7 29.4 - - + +
351B PHE* 3.7 6.0 - - - -
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Residues in contact with SER 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU 3.6 1.6 + - - -
194B ALA 3.1 4.4 + - - -
196B ALA* 1.3 77.9 - - - +
198B LEU* 1.3 60.8 + - - +
200B ASP* 3.7 4.1 - - - +
201B GLN* 3.1 31.5 + - - +
208B VAL* 3.9 13.7 + - - +
209B PRO 3.8 0.7 + - - -
210B ARG* 3.4 17.8 - - - +
211B THR* 3.1 54.7 + - - -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ALA 3.0 11.7 + - - +
195B GLY 3.2 8.9 + - - +
197B SER* 1.3 75.8 - - - +
199B VAL* 1.3 66.8 + - - +
201B GLN* 3.2 7.7 + - - +
202B LYS* 3.2 25.7 + - + +
397B LEU* 3.9 20.4 - - + -
400B ASP* 3.6 46.2 - - + +
401B LEU* 4.1 12.3 - - + +
404B LEU* 4.1 24.0 - - + -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLY 2.8 22.2 + - - +
196B ALA 4.0 3.6 - - - +
198B LEU* 1.3 73.7 - - - +
200B ASP* 1.3 63.6 + - - +
202B LYS* 3.5 1.7 + - - +
203B LEU* 3.2 44.4 + - + +
300B LEU* 4.1 9.4 - - + -
303B ILE* 4.4 11.4 - - + -
304B ILE* 4.0 28.0 - - + -
351B PHE* 4.4 7.0 - - + -
397B LEU* 4.1 17.0 - - + -
401B LEU* 4.5 5.2 - - + -
423B MET* 4.1 19.5 - - + -
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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 ALA 3.0 18.6 + - - +
197B SER 3.7 5.6 - - - +
199B VAL* 1.3 77.0 - - - +
201B GLN* 1.3 62.1 + - - +
203B LEU 3.3 1.4 + - - -
204B GLU 2.8 24.4 + - - -
205B LEU* 3.0 18.8 + - + +
206B ASN* 2.8 29.0 + - - +
207B ILE* 2.9 18.2 + - - +
208B VAL* 2.8 44.7 + - + +
300B LEU* 4.4 2.4 - - + +
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Residues in contact with GLN 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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107B ASP* 5.1 1.9 - - - +
197B SER* 3.1 28.1 + - - +
198B LEU* 3.2 7.8 + - - +
200B ASP* 1.3 81.6 + - - +
202B LYS* 1.3 65.0 + - + +
204B GLU* 3.1 20.6 + - - +
206B ASN* 4.4 14.3 + - - -
210B ARG* 3.4 35.4 + - + +
212B LYS* 5.8 4.4 + - - +
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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 LEU* 3.2 18.8 + - + +
199B VAL 4.1 4.0 - - - +
200B ASP 3.4 0.2 - - - -
201B GLN* 1.3 81.4 - - + +
203B LEU* 1.3 58.4 + - + +
204B GLU* 3.6 2.6 + - - +
387B LYS* 3.4 20.6 - - - -
393B PHE* 3.5 35.1 - - + -
396B ASP* 3.7 24.7 + - - +
397B LEU* 4.3 20.6 - - + +
400B ASP* 2.8 32.2 + - - +
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Residues in contact with LEU 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 VAL* 3.2 39.4 + - + +
202B LYS* 1.3 76.8 - - + +
204B GLU* 1.3 70.2 + - - +
205B LEU* 3.3 20.9 + - + +
299B VAL* 4.4 7.4 - - + -
300B LEU* 5.7 0.2 - - - -
303B ILE* 3.7 23.8 - - + -
383B LEU* 3.6 21.8 - - - +
384B ILE* 4.4 16.3 - - + +
387B LYS* 3.6 10.6 + - + +
388B ILE* 4.4 12.6 - - + -
393B PHE* 3.5 32.3 - - + -
397B LEU* 5.3 5.2 - - + -
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Residues in contact with GLU 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 8.7 + - - -
201B GLN* 3.1 16.4 + - - +
202B LYS 4.1 3.6 - - - +
203B LEU* 1.3 82.1 - - - +
205B LEU* 1.3 57.9 + - - +
206B ASN* 3.5 16.7 + - - +
296B ARG* 3.1 17.2 + - - -
383B LEU* 3.9 12.9 - - + +
387B LYS* 3.0 22.8 + - - +
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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