Contacts of the helix formed by residues 190 - 206 (chain B) in PDB entry 5M7S
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 SER 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B MET* 3.7 10.7 - - - +
188B PHE* 3.3 4.3 + - - +
189B SER* 1.3 81.0 + - - +
191B PHE* 1.3 65.1 + - - +
192B ALA* 3.5 9.5 + - - +
193B HIS* 2.8 34.7 + - - +
194B ALA* 3.2 21.0 + - - +
232B PRO 5.6 0.2 + - - -
233B TYR* 6.0 0.2 - - - -
236B THR* 4.5 2.4 + - - -
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY 5.3 2.7 - - - -
145B PHE* 4.0 23.3 - + - -
176B ILE* 3.6 20.9 - - + -
177B ASP 3.6 14.1 - - - -
178B HIS* 3.6 41.5 - - + +
179B ASN 5.5 1.1 - - - -
180B MET* 3.5 32.6 - - + +
190B SER* 1.3 73.7 - - - +
192B ALA* 1.3 64.0 + - - +
194B ALA* 3.1 5.0 + - - +
195B GLN* 3.1 53.1 + - - +
217B THR* 3.6 16.8 - - + -
233B TYR* 4.5 10.3 - + + -
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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
----------------------------------------------------------
190B SER* 3.2 6.6 + - - +
191B PHE* 1.3 79.1 - - - +
193B HIS* 1.3 63.1 + - - +
195B GLN* 3.3 3.2 + - - +
196B VAL* 2.9 30.6 + - - +
233B TYR* 3.5 53.6 - - + +
236B THR* 3.7 17.0 - - + +
237B VAL* 4.5 4.7 - - + -
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Residues in contact with HIS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 3.9 13.5 - - + -
189B SER* 3.1 27.1 + - - +
190B SER* 2.8 36.0 + - - +
192B ALA* 1.3 77.4 - - - +
194B ALA* 1.3 58.3 + - - +
196B VAL* 3.8 3.4 - - - +
197B SER* 2.9 31.9 + - - -
236B THR* 3.8 30.3 + - + +
240B LYS* 3.9 23.8 + - + +
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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
----------------------------------------------------------
145B PHE* 3.5 30.2 - - + +
180B MET* 3.8 26.2 - - - -
188B PHE* 3.7 28.2 - - + -
190B SER 3.2 2.2 + - - +
191B PHE 3.1 10.4 + - - +
193B HIS* 1.3 78.0 - - - +
195B GLN* 1.3 65.3 + - - +
197B SER* 3.5 2.6 + - - -
198B ILE* 3.4 17.7 + - - +
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Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.9 16.6 - - + -
173B PHE* 3.8 30.8 - - + +
191B PHE* 3.1 42.4 + - - +
192B ALA* 3.3 4.4 + - - +
194B ALA* 1.3 74.2 - - - +
196B VAL* 1.3 56.2 + - - +
198B ILE* 3.3 3.8 + - - +
199B THR* 2.7 37.4 + - - -
214B PHE* 3.4 18.8 - - + -
217B THR* 2.9 23.6 + - - -
233B TYR* 2.3 34.3 + - - -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ALA 2.9 22.9 + - - +
193B HIS* 4.0 5.2 - - - +
195B GLN* 1.3 71.8 - - - +
197B SER* 1.3 65.7 + - - +
199B THR* 4.4 5.4 - - - -
200B ASN* 2.9 30.4 + - - +
214B PHE* 4.8 4.3 - - + -
236B THR* 4.5 3.4 - - + +
237B VAL* 4.1 34.8 - - + +
240B LYS* 3.5 41.7 - - + +
241B LEU* 3.6 15.0 - - + +
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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
----------------------------------------------------------
188B PHE* 3.4 29.5 - - - -
193B HIS 2.9 19.7 + - - -
194B ALA 3.7 2.2 - - - -
195B GLN 3.3 0.2 - - - -
196B VAL* 1.3 78.7 - - - +
198B ILE* 1.3 60.5 + - - +
200B ASN* 3.7 5.0 - - - +
201B GLU* 3.0 32.4 + - - +
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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
----------------------------------------------------------
139B PRO* 5.3 0.2 - - + -
143B ILE* 3.5 31.9 - - + -
145B PHE* 3.7 46.4 - - + +
151B VAL* 4.0 20.6 - - + -
154B LEU* 3.9 18.2 - - + -
171B LEU* 4.8 1.3 - - + -
173B PHE* 4.6 9.2 - - + -
188B PHE* 5.2 1.3 - - + -
194B ALA 3.4 8.6 + - - +
195B GLN 3.3 6.5 + - - +
197B SER* 1.3 79.3 - - - +
199B THR* 1.3 62.4 + - - +
201B GLU* 4.3 7.2 - - - +
202B ILE* 2.8 39.3 + - + +
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.5 20.4 - - + +
173B PHE* 3.7 2.8 - - - -
195B GLN 2.7 22.5 + - - -
196B VAL 3.9 2.5 - - - -
198B ILE* 1.3 76.5 - - - +
200B ASN* 1.3 57.4 + - - +
202B ILE* 3.8 1.0 - - - +
203B TYR* 2.8 32.7 + - - +
212B PHE* 3.8 22.1 - - + -
214B PHE* 3.2 39.5 - - + -
241B LEU* 3.9 14.4 - - + -
245B ILE* 4.0 6.1 - - + -
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Residues in contact with ASN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 2.9 26.6 + - - +
197B SER* 3.7 5.1 - - - +
199B THR* 1.3 76.8 - - - +
201B GLU* 1.3 61.3 + - - +
203B TYR* 3.5 3.0 - - - +
204B GLN* 3.2 33.3 + - - +
240B LYS 2.9 26.7 + - - -
241B LEU* 3.8 3.3 - - - +
242B LEU* 3.1 40.7 + - + +
245B ILE* 3.5 11.3 - - - +
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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
----------------------------------------------------------
151B VAL* 3.6 23.3 - - + +
155B LYS* 3.0 31.0 + - - +
197B SER* 3.0 22.7 + - - +
198B ILE* 3.3 9.4 + - - +
200B ASN* 1.3 71.7 - - - +
202B ILE* 1.3 60.2 + - - +
204B GLN* 3.4 9.3 + - - +
205B TYR* 3.0 29.9 + - - +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.3 12.6 - - + -
154B LEU* 4.0 33.9 - - + -
155B LYS* 3.5 33.4 - - + +
158B LEU* 3.5 25.8 - - + -
171B LEU* 4.1 7.2 - - + -
198B ILE* 2.8 26.9 + - + +
199B THR 3.8 2.5 - - - +
201B GLU* 1.3 71.8 - - - +
203B TYR* 1.3 64.6 + - - +
205B TYR* 3.3 5.3 + - + +
206B LEU* 3.1 29.3 + - + +
212B PHE* 3.8 17.9 - - + -
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Residues in contact with TYR 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 THR 2.8 22.7 + - - +
200B ASN 3.5 3.1 - - - +
202B ILE* 1.3 75.1 - - - +
204B GLN* 1.3 57.9 + - - +
206B LEU* 3.6 0.4 + - - -
207B GLY 3.6 1.9 + - - -
208B GLU* 3.0 67.7 + - + +
209B PRO* 3.5 27.0 + - + +
212B PHE* 3.7 36.3 - + + -
242B LEU* 3.9 26.0 - - + -
244B GLY* 3.5 28.4 + - - -
245B ILE* 3.8 26.9 - - + -
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Residues in contact with GLN 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 ASN* 3.2 20.3 + - - +
201B GLU* 4.1 5.6 - - - +
203B TYR* 1.3 75.5 - - + +
205B TYR* 1.3 65.8 + - - +
206B LEU 3.2 0.2 - - - -
207B GLY* 3.1 13.2 + - - -
208B GLU* 4.0 27.8 + - + +
242B LEU* 3.9 28.6 - - + +
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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
----------------------------------------------------------
155B LYS* 3.8 65.7 + - + +
159B ASP* 4.4 21.1 + - + +
201B GLU* 3.0 18.8 + - + +
202B ILE* 3.6 6.5 - - + +
204B GLN* 1.3 77.6 - - - +
206B LEU* 1.3 71.7 + - + +
207B GLY* 3.2 4.0 + - - -
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Residues in contact with LEU 206 (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 LEU* 4.4 28.5 - - + +
159B ASP* 4.8 7.6 - - - +
162B SER* 5.0 4.7 - - - +
169B PHE* 3.9 32.2 - - + -
202B ILE* 3.1 23.5 + - + +
203B TYR 3.9 5.6 - - - +
204B GLN 3.2 0.6 - - - -
205B TYR* 1.3 89.4 - - + +
207B GLY* 1.3 58.1 + - - +
208B GLU 3.6 1.3 - - - -
209B PRO* 3.7 18.3 - - + +
212B PHE* 3.7 28.5 - - + -
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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