Contacts of the helix formed by residues 185 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PHE* 1.3 73.9 - - - +
186A PRO* 1.3 71.9 - - - +
187A TYR* 3.2 17.5 + - - +
188A ARG* 3.4 36.8 + - + +
189A TYR* 3.3 21.8 - - - -
500A HIS* 5.6 2.3 - - - -
502A CYS* 3.8 16.9 - - - +
503A CYS 3.1 24.9 + - - +
504A GLU* 3.3 29.7 + - - +
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Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 5.7 1.1 - - + -
184A PHE* 3.6 21.5 - - + +
185A ASN* 1.3 91.1 - - - +
187A TYR* 1.3 63.8 + - + +
189A TYR* 3.1 6.5 + - + +
190A VAL* 2.8 28.6 + - + +
327A SER* 5.5 6.1 - - - +
330A LEU* 3.8 27.6 - - + -
331A MET* 5.9 0.9 - - + -
480A PHE* 5.9 0.9 - - + -
500A HIS* 6.1 2.9 - - + -
503A CYS* 3.7 0.9 - - + +
506A PHE* 3.3 48.2 - - + -
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASN* 3.2 17.4 + - - +
186A PRO* 1.3 79.8 - - + +
188A ARG* 1.3 65.8 + - + +
190A VAL* 4.5 4.9 - - - +
191A VAL* 3.0 43.5 + - + +
218A VAL 4.9 5.2 + - - -
219A ASN* 4.0 25.1 - - + -
319A PHE* 5.9 1.9 - - - -
320A ASP* 4.9 3.8 + - - -
323A THR* 3.5 35.7 - - + +
324A THR* 4.7 2.7 + - - -
327A SER* 3.8 27.1 - - - +
499A LYS* 3.2 38.2 - - + -
500A HIS* 5.4 6.5 - + + -
502A CYS* 6.4 1.1 - - + -
602A AQ4 5.5 2.3 - - - -
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.5 32.0 - - - +
186A PRO 3.2 1.0 + - - -
187A TYR* 1.3 77.9 - - + +
189A TYR* 1.3 80.6 + - + +
191A VAL* 3.4 14.8 - - - +
192A VAL* 3.5 11.1 - - - +
215A LEU* 4.3 6.2 - - + +
219A ASN* 3.9 24.9 - - - +
502A CYS* 6.0 0.2 - - - -
504A GLU* 2.6 34.4 + - - -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.6 16.1 - - + +
173A THR* 4.1 13.7 - - + -
174A LEU* 4.5 12.1 - - + -
177A LEU* 3.4 42.4 - - + +
184A PHE* 4.3 8.0 - - + +
185A ASN 3.3 25.6 - - - -
186A PRO 3.1 4.3 + - - +
188A ARG* 1.3 101.3 + - + +
190A VAL* 1.3 62.9 + - + +
191A VAL 3.3 1.6 - - - -
192A VAL* 3.5 2.0 + - + +
193A SER* 3.3 24.3 + - - -
209A HIS* 3.6 29.7 - + + -
210A ASN* 5.9 2.5 - - - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.3 25.1 - - + -
174A LEU* 6.3 1.6 - - + -
186A PRO* 2.8 26.2 + - + +
187A TYR* 4.3 4.0 - - + +
189A TYR* 1.3 75.0 - - + +
191A VAL* 1.3 61.1 + - - +
193A SER* 3.4 2.5 + - - +
194A VAL* 2.9 41.9 + - + +
323A THR* 4.4 10.1 - - + +
326A ILE* 3.7 29.2 - - + -
327A SER* 5.1 2.7 - - - +
330A LEU* 4.2 20.6 - - + -
470A PHE* 6.1 1.3 - - + -
474A LEU* 6.1 0.9 - - + -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.0 36.4 + - + +
188A ARG* 3.4 15.9 - - - +
190A VAL* 1.3 76.9 - - - +
192A VAL* 1.3 62.2 + - + +
194A VAL* 4.0 0.7 - - - +
195A THR* 2.5 39.9 + - - +
215A LEU* 4.6 0.9 - - + -
218A VAL* 4.1 29.6 - - + +
219A ASN* 4.3 16.6 - - + -
319A PHE* 4.4 7.9 - - + -
323A THR* 3.5 28.3 + - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG 3.5 19.5 - - - +
189A TYR* 3.5 6.2 + - + +
190A VAL 3.2 0.6 - - - -
191A VAL* 1.3 76.6 - - + +
193A SER* 1.3 66.8 + - - +
195A THR* 3.2 2.3 + - - -
196A ASN* 3.0 39.9 + - - +
207A TYR 4.2 1.8 - - - +
209A HIS* 3.8 38.1 - - + +
214A LEU* 3.4 30.5 - - + -
215A LEU* 3.9 25.8 - - + -
218A VAL* 5.6 0.7 - - + -
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU* 3.8 15.8 + - - +
169A VAL* 5.7 0.5 - - - +
170A LEU* 3.5 25.8 - - - +
189A TYR 3.3 12.5 + - - -
190A VAL* 3.4 6.5 + - - -
192A VAL* 1.3 79.1 - - - +
194A VAL* 1.3 63.1 + - - +
195A THR 3.4 0.2 + - - -
196A ASN* 3.4 15.0 + - - +
197A VAL* 3.4 19.8 + - - +
209A HIS* 4.0 9.5 + - - -
470A PHE* 4.1 22.2 - - - -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 2.9 24.4 + - + +
191A VAL 4.1 0.2 - - - +
193A SER* 1.3 77.0 - - - +
195A THR* 1.3 62.1 + - - +
197A VAL* 3.4 11.1 + - - +
198A ILE* 3.5 12.5 + - - +
318A GLY 4.1 7.0 - - - +
319A PHE* 4.1 6.5 - - - +
322A VAL* 3.8 20.6 - - + -
323A THR* 3.3 27.1 - - - +
326A ILE* 3.8 28.5 - - + -
466A GLU* 3.7 16.2 - - - +
470A PHE* 4.3 9.9 - - + -
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL 2.5 24.4 + - - -
192A VAL* 3.2 5.3 + - - -
194A VAL* 1.3 76.5 - - - +
196A ASN* 1.3 53.8 + - - +
197A VAL 3.2 0.3 + - - -
198A ILE* 3.2 7.3 - - - +
199A CYS* 2.6 42.5 + - + +
214A LEU* 3.3 32.8 - - + -
218A VAL* 3.9 13.1 - - + +
315A PHE* 3.6 27.8 - - + -
319A PHE* 3.4 15.8 - - + +
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS* 5.6 0.2 - - - +
166A GLU* 3.4 37.6 + - - +
192A VAL* 3.0 30.2 + - - +
193A SER* 3.8 1.9 - - - +
194A VAL 3.4 0.4 - - - -
195A THR* 1.3 76.6 - - - +
197A VAL* 1.3 56.9 + - - +
199A CYS* 3.8 6.9 - - - +
200A ALA* 2.9 29.8 + - - +
205A ARG 4.1 1.7 - - - +
206A ARG* 3.5 15.2 - - + +
207A TYR* 2.9 48.7 + - - +
209A HIS* 5.5 1.6 + - - -
214A LEU* 4.3 6.8 - - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 3.8 27.1 - - + -
162A HIS* 4.0 15.9 - - + +
163A VAL* 4.0 15.7 - - + +
166A GLU* 3.8 17.0 - - + -
193A SER 3.4 16.2 - - - +
194A VAL 3.7 1.6 - - - +
195A THR 3.1 0.6 - - - -
196A ASN* 1.3 78.2 - - - +
198A ILE* 1.3 62.3 + - - +
200A ALA* 3.3 2.6 + - - +
201A ILE* 3.1 29.9 + - + +
466A GLU* 3.6 26.9 - - - +
470A PHE* 4.1 12.3 - - + -
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.9 1.8 - - + -
194A VAL* 3.5 12.0 + - + +
195A THR* 3.2 15.3 - - - +
197A VAL* 1.3 80.4 - - + +
199A CYS* 1.3 61.3 + - - +
201A ILE* 4.3 19.7 - - + -
202A CYS* 3.0 45.6 + - - -
314A LEU* 3.9 14.8 - - + +
315A PHE* 4.0 15.7 - - + -
318A GLY* 4.0 9.4 - - - -
319A PHE* 3.9 18.4 - - + +
462A ILE* 5.9 2.2 - - + -
466A GLU* 5.7 3.8 - - - +
601A HEM 3.5 29.2 - - + -
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Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A THR* 2.6 30.5 + - + +
196A ASN* 3.9 4.7 - - - +
198A ILE* 1.3 71.6 - - - +
200A ALA* 1.3 56.2 + - - +
203A PHE* 2.7 55.4 + - - -
204A GLY 3.2 4.0 + - - -
205A ARG* 3.2 23.3 - - - +
206A ARG* 5.1 2.0 - - - -
207A TYR* 5.1 15.9 - - - -
214A LEU* 5.8 0.7 - - - -
261A PHE* 5.9 1.3 - - - -
265A MET* 5.1 2.9 - - - -
315A PHE* 4.1 15.7 - - + -
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS* 3.9 30.2 + - + +
165A LYS* 6.1 2.0 - - - +
196A ASN 2.9 19.0 + - - +
197A VAL 3.3 4.5 + - - +
199A CYS* 1.3 75.9 - - - +
201A ILE* 1.3 64.3 + - - +
204A GLY* 3.2 22.5 + - - +
205A ARG 3.4 15.2 + - - +
206A ARG* 5.7 1.8 - - + -
279A ARG 5.2 1.4 - - - +
280A ASP* 4.1 4.2 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.4 10.1 - - + -
145A PHE* 3.6 31.7 - - + +
146A SER* 4.4 10.5 - - - -
159A LEU* 4.2 25.1 - - + -
162A HIS* 4.1 13.9 - - + -
197A VAL* 3.1 22.3 + - + +
198A ILE* 3.7 19.7 - - + +
199A CYS 3.3 0.4 - - - -
200A ALA* 1.3 76.1 - - - +
202A CYS* 1.3 58.0 + - - +
280A ASP* 3.6 5.1 - - - +
281A ILE* 3.2 46.1 + - + +
462A ILE* 4.9 7.4 - - + -
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Residues in contact with CYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.0 40.6 + - - +
201A ILE* 1.3 79.1 - - - +
203A PHE* 1.3 78.5 + - + +
280A ASP* 3.3 4.8 - - - +
281A ILE* 4.3 13.9 - - - -
282A THR* 2.6 37.8 + - - -
311A VAL* 4.4 9.0 - - + -
314A LEU* 4.2 11.0 - - - -
315A PHE* 4.2 18.8 - - - -
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A CYS* 2.7 36.4 + - - +
202A CYS* 1.3 91.8 - - + +
204A GLY* 1.3 60.2 + - - +
205A ARG* 4.2 5.9 - - - +
261A PHE* 4.1 21.1 - + - -
262A MET* 6.2 4.0 - - + -
265A MET* 3.4 42.0 - - + -
269A HIS* 3.1 20.0 + - - +
280A ASP* 2.8 14.5 - - - +
282A THR* 3.5 11.7 - - - -
311A VAL* 4.2 18.6 - - + -
312A LEU* 5.7 5.8 - - + -
315A PHE* 3.7 40.8 - + + -
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A CYS 3.2 1.0 + - - -
200A ALA* 3.2 23.8 + - - -
203A PHE* 1.3 78.9 - - - +
205A ARG* 1.3 63.8 + - - +
279A ARG* 5.5 3.6 - - - -
280A ASP* 3.3 8.6 + - - -
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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