Contacts of the helix formed by residues 195 - 213 (chain B) in PDB entry 4HYY
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 THR 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A SER* 4.1 17.7 - - - +
255A LYS* 5.6 5.6 - - - +
193B ALA 3.7 0.2 - - - -
194B TYR* 1.3 86.2 + - + +
196B SER* 1.3 64.5 + - - +
197B GLU* 3.3 8.3 + - - +
198B HIS* 2.9 27.7 + - + +
199B GLN 2.9 18.7 + - - -
228B LEU* 3.4 16.2 - - - +
232B ASP* 3.6 15.9 - - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B THR* 1.3 69.6 - - - +
197B GLU* 1.3 70.7 + - - +
199B GLN* 3.0 14.3 + - - +
200B MET* 3.0 13.2 + - - +
228B LEU* 3.6 25.2 + - - +
229B PHE* 3.5 37.4 - - - -
232B ASP* 2.9 22.7 + - - -
233B PHE* 3.6 15.9 - - - -
245B LYS* 6.1 0.7 - - - -
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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
----------------------------------------------------------
195B THR* 3.2 8.0 + - - +
196B SER* 1.3 81.6 - - - +
198B HIS* 1.3 68.6 + - - +
200B MET* 2.8 10.9 + - - +
201B GLU* 2.8 32.2 + - + +
232B ASP* 5.5 0.9 - - - +
233B PHE* 6.4 1.6 - - + -
245B LYS* 4.9 19.6 - - + +
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Residues in contact with HIS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LYS* 5.8 3.8 - - - -
192B ARG 3.4 13.7 + - - -
193B ALA* 3.4 8.3 - - - -
194B TYR* 3.1 41.8 - + + -
195B THR* 2.9 26.6 + - + +
197B GLU* 1.3 76.3 - - - +
199B GLN* 1.3 64.0 + - - +
201B GLU* 3.0 20.9 + - + +
202B LEU* 2.9 42.5 + - + +
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.7 9.2 - - + -
161B THR* 4.0 11.6 - - - +
193B ALA* 4.0 18.4 - - + -
195B THR 2.9 11.1 + - - +
196B SER 3.3 8.7 - - - +
197B GLU 3.0 0.4 - - - -
198B HIS* 1.3 79.2 - - - +
200B MET* 1.3 61.0 + - - +
202B LEU* 3.3 11.7 + - - +
203B LEU* 3.3 27.0 + - + +
222B ILE* 4.1 11.2 - - + +
224B SER 4.4 1.2 + - - -
225B ILE* 2.9 25.7 + - - +
228B LEU* 3.4 26.3 - - - +
229B PHE* 3.6 20.1 - - + -
249B MET* 3.3 19.0 - - - +
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER 3.0 10.2 + - - +
197B GLU* 2.8 11.3 + - - +
199B GLN* 1.3 77.4 - - - +
201B GLU* 1.3 61.5 + - + +
203B LEU* 3.1 22.5 + - - +
204B ASP* 3.4 16.6 + - - +
229B PHE* 5.6 2.5 - - + -
245B LYS* 6.0 1.8 - - + +
248B GLN* 3.6 27.8 - - + +
249B MET* 3.6 30.9 - - + +
252B ARG* 3.5 36.6 - - + +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU* 2.8 24.3 + - + +
198B HIS* 3.0 25.6 + - + +
200B MET* 1.3 71.0 - - + +
202B LEU* 1.3 64.3 + - + +
204B ASP* 3.1 24.4 + - - +
205B TYR* 3.3 12.0 + - - +
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Residues in contact with LEU 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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84A GLY* 5.0 8.5 - - - +
85A PHE* 3.5 24.6 - - + -
159B ILE* 4.1 24.9 - - + -
191B ALA* 4.0 12.6 - - + -
192B ARG 3.6 22.2 - - - +
193B ALA* 3.9 20.6 - - + -
198B HIS* 2.9 32.2 + - + +
199B GLN* 3.5 7.4 - - - +
200B MET 3.3 0.2 - - - -
201B GLU* 1.3 76.1 - - + +
203B LEU* 1.3 63.3 + - - +
205B TYR* 3.3 8.0 + - + +
206B VAL* 3.0 28.1 + - - +
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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
----------------------------------------------------------
159B ILE* 4.2 20.9 - - + -
199B GLN* 3.3 31.1 + - + +
200B MET* 3.1 17.2 + - - +
202B LEU* 1.3 77.8 - - - +
204B ASP* 1.3 53.3 + - - +
206B VAL* 3.3 5.6 + - + +
207B ALA* 2.7 36.4 + - - +
220B LEU* 3.6 30.7 - - + -
222B ILE* 4.4 9.4 - - + -
249B MET* 4.5 23.6 - - + +
252B ARG* 4.1 8.3 - - + +
253B LEU* 3.8 17.0 - - + -
256B ILE* 4.0 14.2 - - + +
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Residues in contact with ASP 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 MET* 3.4 16.2 + - - +
201B GLU* 3.1 17.7 + - - +
203B LEU* 1.3 76.3 - - - +
205B TYR* 1.3 64.5 + - - +
207B ALA* 3.5 2.1 + - - +
208B ALA* 3.1 24.0 + - - +
252B ARG* 2.4 41.0 + - - +
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Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 4.3 5.2 - - - -
85A PHE* 3.4 36.6 - + + -
157B ILE* 6.4 1.3 - - + -
201B GLU 3.3 6.8 + - - +
202B LEU* 3.3 12.2 + - + +
204B ASP* 1.3 81.3 - - - +
206B VAL* 1.3 51.5 + - + +
208B ALA* 3.2 6.3 + - - +
209B LYS* 2.8 49.1 + - + +
205D TYR* 3.7 34.7 + + - -
208D ALA* 3.4 38.7 + - + -
209D LYS* 4.4 3.2 + - - +
212D GLU* 2.7 39.6 + - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.5 24.7 - - + -
157B ILE* 3.7 22.7 - - + -
159B ILE* 4.5 8.3 - - + -
202B LEU 3.0 18.4 + - - +
203B LEU* 3.6 10.8 - - + +
205B TYR* 1.3 68.8 - - + +
207B ALA* 1.3 69.1 + - - +
209B LYS* 3.7 6.2 - - - +
210B PHE* 2.9 54.6 + - + -
220B LEU* 4.2 17.5 - - + -
256B ILE* 5.0 2.7 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU 2.7 20.9 + - - +
204B ASP 3.9 3.4 - - - +
206B VAL* 1.3 74.0 - - - +
208B ALA* 1.3 65.5 + - - +
210B PHE* 3.1 5.1 + - - +
211B HIS* 2.9 22.5 + - - +
252B ARG* 4.1 14.4 - - - +
256B ILE* 3.8 27.5 - - + +
260B TYR* 4.0 15.7 - - + +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASP 3.1 18.6 + - - +
205B TYR 3.4 1.1 - - - +
207B ALA* 1.3 74.8 - - - +
209B LYS* 1.3 61.7 + - - +
211B HIS* 3.3 9.8 + - - +
212B GLU* 3.1 26.3 + - - +
205D TYR* 3.3 34.3 - - + -
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Residues in contact with LYS 209 (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 ILE* 4.6 9.2 - - + -
189B LEU* 4.8 8.7 - - - +
205B TYR* 2.8 32.7 + - + +
206B VAL* 3.7 5.8 - - - +
208B ALA* 1.3 70.9 - - - +
210B PHE* 1.3 72.1 + - + +
212B GLU* 3.0 20.6 + - + +
213B GLU 3.8 4.2 + - - +
216B ILE* 5.3 0.5 - - - +
217B PHE* 3.7 34.9 - - + -
205D TYR* 4.0 13.0 + - - +
209D LYS* 5.0 9.1 - - - +
212D GLU* 3.1 39.6 + - - -
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 3.8 21.5 - - + -
206B VAL* 2.9 35.0 + - + -
207B ALA* 3.5 6.1 - - - +
209B LYS* 1.3 73.6 - - + +
211B HIS* 1.3 57.7 + - - +
213B GLU 2.8 26.8 - - - +
214B ALA* 4.0 8.0 + - - +
216B ILE* 4.7 4.5 - - + -
217B PHE* 3.3 41.1 - + + -
219B LEU 4.4 9.0 - - - -
220B LEU* 4.5 7.6 - - + -
256B ILE* 3.7 28.7 - - + -
260B TYR* 3.7 25.6 - + + -
262B VAL* 3.6 31.4 - - + -
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA 2.9 13.1 + - - +
208B ALA* 3.4 13.7 - - - +
209B LYS 3.1 0.2 - - - -
210B PHE* 1.3 72.5 - - - +
212B GLU* 1.3 64.8 + - + +
213B GLU* 3.1 4.3 + - - -
214B ALA* 4.8 2.5 + - - +
259B GLU* 4.6 6.1 - - - -
260B TYR* 2.6 37.8 + + - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA 3.1 6.7 + - - +
209B LYS* 3.0 15.4 + - + +
211B HIS* 1.3 80.5 - - + +
213B GLU* 1.3 63.5 + - - +
189D LEU* 3.8 26.4 - - - +
205D TYR* 3.0 34.1 + - + +
209D LYS* 3.2 26.5 + - - -
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS 3.8 2.9 + - - +
210B PHE 2.8 16.5 - - - +
211B HIS 3.1 3.3 + - - -
212B GLU* 1.3 81.9 - - - +
214B ALA* 1.3 66.8 + - - +
216B ILE* 2.9 40.3 - - + +
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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
------------------------------------------------------------
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