Contacts of the helix formed by residues 185 - 203 (chain B) in PDB entry 6DWN
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 ASN 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B PHE* 1.3 74.6 - - - +
186B PRO* 1.3 73.0 - - - +
187B TYR* 3.4 16.4 + - - +
188B ARG* 3.2 52.5 + - - +
189B TYR* 3.3 16.4 - - - -
500B HIS* 5.5 2.4 - - - -
502B CYS* 3.9 20.5 - - - +
503B CYS 3.1 27.9 + - - +
504B GLU* 4.1 12.0 + - + +
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Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 5.5 0.9 - - + -
184B PHE* 3.8 21.0 - - + +
185B ASN* 1.3 89.4 - - - +
187B TYR* 1.3 63.8 + - + +
189B TYR* 3.1 5.8 + - + +
190B VAL* 2.9 29.3 + - + +
327B SER* 5.4 6.3 - - - +
330B LEU* 3.7 28.3 - - + -
331B MET* 5.7 0.9 - - - -
480B PHE* 6.2 0.7 - - + -
500B HIS* 5.9 3.1 - - + -
503B CYS* 3.7 1.1 - - + +
506B PHE* 3.3 50.7 - - + -
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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
----------------------------------------------------------
185B ASN* 3.2 16.7 + - - +
186B PRO* 1.3 80.2 - - - +
188B ARG* 1.3 63.5 + - - +
189B TYR 3.1 0.9 + - - -
190B VAL* 4.5 4.9 - - - +
191B VAL* 3.2 34.2 + - + +
218B VAL 5.8 0.2 + - - -
219B ASN* 4.0 26.9 - - - -
319B PHE* 5.5 2.9 + - - -
320B ASP* 4.5 4.7 + - - -
323B THR* 3.6 30.6 - - + +
324B THR* 4.7 1.9 + - - -
327B SER* 3.7 31.6 + - - +
499B LYS* 3.3 38.5 - - + -
500B HIS* 5.2 7.6 - + + -
502B CYS* 6.4 0.7 - - - -
602B AQ4 5.5 1.0 - - - -
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN* 3.3 35.7 - - + +
186B PRO 3.1 0.8 - - - -
187B TYR* 1.3 78.8 - - + +
189B TYR* 1.3 80.0 + - + +
191B VAL* 3.4 14.2 - - - +
192B VAL* 3.7 9.9 - - - +
215B LEU* 4.8 4.7 - - - +
219B ASN* 4.3 18.1 + - - +
504B GLU* 2.1 42.4 + - - +
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.0 17.0 - - + -
173B THR* 3.6 23.8 - - + -
174B LEU* 4.5 11.2 - - + -
177B LEU* 3.2 47.1 - - + +
184B PHE* 4.3 6.8 - - + +
185B ASN 3.3 22.4 - - - -
186B PRO 3.1 3.1 + - - +
188B ARG* 1.3 101.0 + - + +
190B VAL* 1.3 63.0 + - + +
191B VAL 3.3 1.8 - - - -
192B VAL* 3.4 3.0 + - + +
193B SER* 3.3 24.3 + - - -
209B HIS* 3.7 19.1 - + + +
210B ASN* 5.6 10.5 - - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.5 24.2 - - + -
174B LEU* 6.3 1.8 - - + -
186B PRO* 2.9 26.9 + - + +
187B TYR* 4.5 3.8 - - - +
189B TYR* 1.3 74.1 - - - +
191B VAL* 1.3 60.6 + - - +
193B SER* 3.3 3.2 + - - +
194B VAL* 2.9 43.0 + - + +
323B THR* 4.3 10.5 - - + +
326B ILE* 3.6 29.6 - - + -
327B SER* 5.0 3.1 - - - +
330B LEU* 4.1 20.9 - - + -
470B PHE* 6.2 0.9 - - + -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.2 34.1 + - + +
188B ARG 3.4 13.5 - - - +
190B VAL* 1.3 76.8 - - - +
192B VAL* 1.3 63.3 + - + +
194B VAL* 4.0 0.7 - - - +
195B THR* 2.4 41.9 + - - +
215B LEU* 4.9 1.3 - - + -
218B VAL* 4.1 23.3 - - + -
219B ASN* 4.3 20.6 - - + +
319B PHE* 4.3 14.4 - - + -
323B THR* 3.6 24.5 + - + +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG 3.7 19.1 - - - +
189B TYR* 3.7 6.7 - - + +
190B VAL 3.2 0.8 - - - -
191B VAL* 1.3 81.7 - - + +
193B SER* 1.3 65.2 + - - +
195B THR* 3.1 5.0 + - - -
196B ASN* 2.9 46.6 + - - +
207B TYR* 6.1 0.2 - - + -
208B ASP 4.0 6.7 - - - +
209B HIS* 3.6 50.7 - - + +
215B LEU* 4.4 11.2 - - + -
218B VAL* 5.9 2.2 - - + -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 3.8 13.2 + - - +
170B LEU* 3.4 31.1 - - - +
189B TYR 3.3 11.5 + - - -
190B VAL* 3.9 5.2 - - - -
192B VAL* 1.3 80.7 - - - +
194B VAL* 1.3 62.1 + - - +
196B ASN* 3.4 14.7 + - - +
197B VAL* 3.3 20.8 + - - +
209B HIS* 3.6 10.6 + - - -
470B PHE* 4.1 20.9 - - - -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 2.9 25.7 + - + +
191B VAL 4.2 0.2 - - - +
193B SER* 1.3 76.0 - - - +
195B THR* 1.3 62.1 + - - +
197B VAL* 3.5 4.3 + - - +
198B ILE* 3.4 19.3 + - + +
318B GLY 4.1 1.8 - - - +
319B PHE* 4.0 10.3 - - - -
322B VAL* 3.9 18.4 - - + -
323B THR* 3.2 29.6 - - - +
326B ILE* 3.7 29.4 - - + -
466B GLU* 3.8 16.6 - - - +
470B PHE* 4.4 10.3 - - + -
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 2.4 31.2 + - - +
192B VAL* 3.1 6.5 + - - -
194B VAL* 1.3 75.0 - - - +
196B ASN* 1.3 55.7 + - - +
197B VAL 3.2 0.2 + - - -
198B ILE* 3.2 7.7 - - - +
199B CYS* 2.7 39.9 + - + +
214B LEU* 4.3 22.0 - - + -
218B VAL* 4.3 12.1 - - + +
315B PHE* 3.7 29.6 - - + -
319B PHE* 3.5 17.8 - - + +
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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
----------------------------------------------------------
166B GLU* 3.3 37.9 + - - +
192B VAL* 2.9 35.3 + - - +
193B SER* 3.8 2.1 - - - +
194B VAL 3.4 0.4 - - - -
195B THR* 1.3 76.5 - - - +
197B VAL* 1.3 61.0 + - - +
199B CYS* 3.9 5.5 - - - +
200B ALA* 3.1 24.6 + - - +
205B ARG 4.1 2.4 - - - +
206B ARG* 3.5 27.8 - - + +
207B TYR* 3.2 30.0 + - - +
209B HIS* 4.8 1.0 - - - -
214B LEU* 5.1 6.9 - - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 4.1 12.6 - - + -
162B HIS* 4.1 16.9 - - + +
163B VAL* 3.9 25.1 - - + +
166B GLU* 3.6 19.5 - - + -
193B SER 3.3 16.3 + - - +
194B VAL 3.7 6.5 - - - +
195B THR 3.1 0.6 - - - -
196B ASN* 1.3 78.2 - - - +
198B ILE* 1.3 63.2 + - - +
200B ALA* 3.3 4.7 + - - +
201B ILE* 3.2 30.1 + - + +
466B GLU* 3.7 19.1 - - - +
470B PHE* 3.9 18.4 - - + -
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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
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142B LEU* 5.0 2.7 - - + -
194B VAL 3.4 11.6 + - - +
195B THR* 3.2 20.2 - - - +
197B VAL* 1.3 80.6 - - - +
199B CYS* 1.3 61.7 + - - +
201B ILE* 3.5 18.3 + - + -
202B CYS* 3.1 34.3 + - - -
314B LEU 3.9 6.1 - - - +
315B PHE* 3.9 33.4 - - + -
318B GLY* 4.2 8.5 - - - -
319B PHE* 4.0 14.4 - - + +
462B ILE* 6.2 1.3 - - + -
466B GLU* 5.1 4.7 + - - +
601B HEM 3.8 28.5 - - + -
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Residues in contact with CYS 199 (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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195B THR* 2.7 27.7 + - + +
196B ASN* 3.9 5.6 - - - +
198B ILE* 1.3 72.0 - - - +
200B ALA* 1.3 56.4 + - - +
203B PHE* 2.5 57.9 + - - -
204B GLY 3.2 3.1 + - - -
205B ARG* 3.3 31.2 - - - +
206B ARG* 5.4 1.1 - - - -
207B TYR* 5.6 3.8 - - - -
214B LEU* 5.2 11.9 - - + -
261B PHE* 6.1 2.9 - - - -
315B PHE* 4.1 15.7 - - + -
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Residues in contact with ALA 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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162B HIS* 4.1 29.9 + - + +
165B LYS* 5.7 5.2 - - - +
196B ASN 3.1 18.8 + - - +
197B VAL 3.3 4.0 + - - +
199B CYS* 1.3 76.3 - - - +
201B ILE* 1.3 62.4 + - - +
204B GLY* 3.1 26.0 + - - +
205B ARG 3.6 15.4 + - - +
206B ARG* 5.8 1.1 - - + -
279B ARG 5.2 0.7 - - - +
280B ASP* 4.0 5.7 - - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.5 10.8 - - + -
145B PHE* 3.6 30.4 - - + +
146B SER* 4.3 10.8 - - - -
159B LEU* 4.2 24.9 - - + -
162B HIS* 4.0 14.8 - - + -
197B VAL* 3.2 21.7 + - + +
198B ILE* 3.8 16.8 - - + +
199B CYS 3.3 0.2 - - - -
200B ALA* 1.3 76.7 - - - +
202B CYS* 1.3 59.5 + - - +
280B ASP* 3.5 4.2 - - - +
281B ILE* 3.1 47.5 + - + +
462B ILE* 5.1 7.0 - - + -
466B GLU* 5.8 0.4 - - - +
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Residues in contact with CYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.1 39.9 + - - +
199B CYS 4.0 1.1 - - - +
201B ILE* 1.3 80.6 - - - +
203B PHE* 1.3 76.6 + - + +
280B ASP* 3.3 3.6 - - - +
281B ILE* 4.3 14.6 - - - -
282B THR* 2.3 39.5 + - - -
311B VAL* 4.2 23.6 - - + -
314B LEU* 4.3 12.3 - - - -
315B PHE* 4.3 3.6 - - - -
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B CYS* 2.5 38.7 + - - +
202B CYS* 1.3 91.4 - - + +
204B GLY* 1.3 60.7 + - - +
205B ARG* 3.7 5.8 + - + +
261B PHE* 4.3 26.2 - + - -
262B MET* 6.2 4.0 - - + -
265B MET* 3.9 34.6 - - + +
266B VAL* 6.6 0.4 - - + -
269B HIS* 2.8 27.8 + - - -
280B ASP* 2.9 8.1 - - - -
282B THR* 3.4 12.3 - - + -
311B VAL* 4.2 20.6 - - + -
312B LEU* 5.6 6.7 - - + -
315B PHE* 4.0 38.1 - + + -
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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