Contacts of the helix formed by residues 183 - 197 (chain B) in PDB entry 5M8L
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ALA 3.7 3.6 + - - -
152B LYS 3.0 28.9 + - - -
153B ARG 4.3 2.0 - - - -
154B THR 3.1 19.7 - - - -
155B THR* 4.1 0.9 - - - +
156B HIS* 3.9 1.1 - - - +
182B ILE* 1.3 80.9 - - - +
184B ILE* 1.3 59.8 + - - +
186B ASN* 3.1 29.9 + - - +
187B TYR* 2.8 29.1 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA* 3.2 21.3 + - + +
154B THR* 3.0 24.6 + - + +
156B HIS* 3.7 29.7 - - + +
157B PRO* 4.2 13.0 - - + -
183B SER* 1.3 73.9 - - - +
185B TYR* 1.3 62.2 + - - +
187B TYR* 3.6 5.0 + - - +
188B PHE* 3.4 16.8 + - - +
231B LEU* 4.2 11.0 - - + +
234B ASP* 3.8 30.3 - - + +
235B MET* 4.6 3.6 - - + -
238B MET* 3.8 38.4 - - + -
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.2 16.4 - - + +
151B ALA* 2.9 28.5 + - + +
152B LYS* 3.8 10.5 - - + +
184B ILE* 1.3 75.7 - - - +
186B ASN* 1.3 69.4 + - - +
188B PHE* 3.2 19.8 - + - +
189B VAL* 3.1 27.5 + - + -
231B LEU* 4.2 16.6 - - + -
286B TRP* 3.6 35.0 - + - -
395B PRO* 2.9 29.6 + - - +
396B ASN* 4.6 0.9 - - - -
397B ASP 4.0 0.7 + - - -
398B PRO* 3.3 18.0 - - + +
400B PHE* 4.6 0.5 - - - +
401B VAL* 3.4 27.1 - - + +
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Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LYS* 3.1 25.5 + - - +
182B ILE* 3.4 25.1 - - + +
183B SER* 3.1 25.6 + - - +
185B TYR* 1.3 75.9 - - - +
187B TYR* 1.3 54.9 + - - +
189B VAL* 3.0 11.0 + - - +
190B TRP* 2.7 35.7 + - - +
289B VAL* 3.8 26.5 - - + +
305B SER 5.0 2.4 + - - -
307B GLU* 2.9 26.7 + - - +
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Residues in contact with TYR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 4.1 17.8 + - - -
156B HIS* 3.9 21.1 - + + -
159B PHE* 3.5 51.7 - + + -
161B ILE* 4.3 14.8 - - + -
182B ILE* 3.8 14.8 - - + +
183B SER 2.8 17.6 + - - +
184B ILE 3.7 3.8 - - - +
186B ASN* 1.3 75.0 - - - +
188B PHE* 1.3 63.9 - - + +
190B TRP* 3.1 4.1 + - - +
191B THR* 3.1 52.2 + - + +
230B ARG* 3.9 26.9 + - + +
234B ASP* 4.3 3.8 - - - -
443B PHE* 4.7 10.3 - + - -
444B TRP 5.1 3.6 + - - -
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE 3.4 9.6 + - - +
185B TYR* 3.2 43.9 + + - +
186B ASN 3.2 0.2 - - - -
187B TYR* 1.3 84.2 - - + +
189B VAL* 1.3 59.7 + - - +
191B THR* 3.6 5.3 + - - -
192B HIS* 3.8 2.8 + - - +
227B HIS* 2.8 78.9 + + - -
228B LEU* 4.5 10.3 - - + -
230B ARG* 6.4 0.4 - - + -
231B LEU* 3.7 30.3 - - + -
395B PRO* 4.1 6.5 - - + -
400B PHE* 3.6 30.3 - + - -
401B VAL* 3.8 14.6 - - + -
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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
----------------------------------------------------------
185B TYR* 3.1 35.8 + - + +
186B ASN* 3.0 13.7 + - - +
188B PHE* 1.3 75.5 - - - +
190B TRP* 1.3 64.0 + - - +
192B HIS* 3.5 4.9 + - - +
193B TYR* 3.1 18.9 + - - +
289B VAL* 3.7 17.7 - - + +
290B CYS* 4.6 5.6 - - + -
392B HIS 5.1 3.2 - - - +
393B LEU 4.7 1.8 - - - +
395B PRO* 3.8 23.5 - - + +
396B ASN* 3.6 37.5 - - - +
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Residues in contact with TRP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 3.3 43.1 - - + -
161B ILE* 3.5 39.6 - - + +
162B ALA 3.4 21.8 - - - -
182B ILE* 4.3 6.3 - - + -
186B ASN 2.7 18.9 + - - +
187B TYR* 3.1 5.1 + - - +
189B VAL* 1.3 74.5 - - - +
191B THR* 1.3 68.6 + - + +
193B TYR* 3.0 10.0 + + - +
194B TYR* 2.8 66.0 + + + -
290B CYS* 4.4 4.9 - - - -
302B LEU* 4.3 7.0 - - + -
303B CYS* 2.8 46.1 + - + +
442B PRO* 4.1 4.0 - - + -
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN 4.4 1.6 - - - +
187B TYR* 3.1 49.7 + - + +
188B PHE* 3.6 7.4 + - - -
190B TRP* 1.3 89.1 - - + +
192B HIS* 1.3 63.3 + - - +
194B TYR* 3.4 0.6 + - - -
195B SER* 3.1 24.4 + - - -
223B TRP* 3.7 2.8 - - - -
227B HIS* 3.7 15.8 - - - -
442B PRO* 3.6 27.0 - - + +
443B PHE* 4.0 11.9 - - + -
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE 3.8 0.8 + - - +
189B VAL 3.5 4.4 + - - +
190B TRP 3.2 0.4 - - - -
191B THR* 1.3 78.0 + - - +
193B TYR* 1.3 65.9 + - - +
195B SER* 3.1 15.4 + - - -
196B VAL* 3.4 14.2 - - - +
214B SER* 4.9 0.4 - - - -
215B HIS* 3.1 15.1 + + - -
223B TRP* 3.5 31.8 - + + -
224B HIS* 3.6 2.5 - - - -
227B HIS* 3.9 6.3 - + + -
391B THR* 3.3 29.3 + - + -
392B HIS 5.2 0.2 - - - -
394B SER* 3.8 13.7 - - - -
395B PRO* 3.6 25.4 - - + +
400B PHE* 3.7 12.4 - + - -
516B ZN 1.9 38.1 - - - -
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL 3.1 13.2 + - - +
190B TRP* 3.0 16.4 + - - +
192B HIS* 1.3 78.1 + - - +
194B TYR* 1.3 83.6 + + + +
196B VAL* 3.2 6.1 + - - +
197B LYS* 3.0 61.9 + - + +
290B CYS* 3.8 21.1 - - + -
293B LEU* 4.0 10.5 - - + -
296B TYR* 3.6 29.3 - + - +
297B ASP* 6.2 0.2 - - - -
302B LEU* 3.7 8.3 - - + -
303B CYS* 3.5 36.9 + - + -
392B HIS* 3.8 30.5 + - + +
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Residues in contact with TYR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 4.7 5.2 - - - -
86B ASP* 3.7 21.5 + - - +
87B ARG* 2.7 68.9 + - + +
90B TRP* 3.9 13.4 - + - -
94B PHE* 4.1 6.8 - - - -
165B ARG* 6.3 0.9 - - + -
190B TRP* 2.8 50.7 + + + +
191B THR 3.8 3.8 - - - +
193B TYR* 1.3 84.0 - + + +
195B SER* 1.3 50.3 + - - +
197B LYS* 3.5 13.5 - - + +
302B LEU* 3.8 28.3 - - + -
441B VAL* 4.2 0.4 - - + -
442B PRO* 3.5 33.4 - - + -
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.6 5.5 + - - +
191B THR 3.1 11.2 + - - -
192B HIS* 3.1 12.0 + - - -
193B TYR 3.2 0.4 - - - -
194B TYR* 1.3 79.0 - - - +
196B VAL* 1.3 56.9 + - - +
212B ASP* 4.1 0.2 - - - -
213B PHE* 2.9 43.2 + - - +
214B SER* 2.4 30.7 + - - -
223B TRP* 3.6 9.6 - - - -
441B VAL 3.4 25.8 - - - -
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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
----------------------------------------------------------
87B ARG* 4.0 0.2 - - - -
192B HIS* 3.4 15.7 - - + +
193B TYR 3.4 9.9 - - - +
195B SER* 1.3 84.3 - - - +
197B LYS* 1.3 69.7 + - - +
198B LYS* 5.4 1.0 - - - +
211B VAL 4.1 11.0 - - - +
212B ASP* 3.5 17.8 - - - +
214B SER* 3.6 0.9 - - - +
215B HIS* 3.4 38.4 - - + +
391B THR* 3.8 8.7 - - + +
392B HIS* 3.8 34.1 - - + +
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 5.1 2.6 + - - -
87B ARG* 2.9 40.1 + - - +
165B ARG* 4.6 11.9 - - - +
193B TYR* 3.0 48.0 + - + +
194B TYR* 3.5 17.0 - - + +
196B VAL* 1.3 82.7 - - - +
198B LYS* 1.3 82.3 + - - +
199B THR* 3.8 0.8 + - - +
200B PHE* 4.3 10.3 - - - +
211B VAL* 4.1 6.4 - - - +
293B LEU* 6.0 2.5 - - + -
296B TYR* 5.1 1.9 + - - -
297B ASP* 4.8 8.9 + - - +
301B THR 4.5 4.6 + - - -
302B LEU* 3.4 31.8 - - + +
392B HIS* 6.1 0.9 - - - -
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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
------------------------------------------------------------
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