Contacts of the helix formed by residues 185 - 204 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D PHE* 1.3 73.9 - - - +
186D PRO* 1.3 71.4 - - - +
187D TYR* 3.2 21.3 + - - +
188D ARG* 3.4 14.8 + - + +
189D TYR* 3.3 20.2 - - + -
500D HIS* 5.7 2.6 - - - -
502D CYS* 3.8 20.8 - - - +
503D CYS 3.2 26.6 + - - +
504D GLU* 3.5 26.2 + - - +
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Residues in contact with PRO 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D LEU* 5.7 0.9 - - + -
184D PHE* 3.7 19.9 - - + +
185D ASN* 1.3 90.5 - - - +
187D TYR* 1.3 63.7 + - + +
189D TYR* 2.9 7.9 + - + +
190D VAL* 2.9 28.0 + - + +
327D SER* 5.6 6.1 - - - +
330D LEU* 3.7 28.0 - - + -
331D MET* 6.0 0.7 - - - -
480D PHE* 6.3 0.7 - - + -
500D HIS* 6.1 2.9 - - + -
503D CYS* 3.7 0.9 - - + +
506D PHE* 3.3 49.4 - - + -
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Residues in contact with TYR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ASN* 3.2 17.2 + - - +
186D PRO* 1.3 80.9 - - + +
188D ARG* 1.3 64.3 + - - +
190D VAL* 4.5 5.8 - - - +
191D VAL* 3.1 32.3 + - + +
219D ASN* 4.1 23.6 + - - -
319D PHE* 5.9 1.7 - - - -
320D ASP* 4.3 7.1 + - - -
323D THR* 3.8 27.4 - - + +
324D THR* 4.9 2.9 + - - -
327D SER* 3.7 30.9 + - - +
499D LYS* 3.4 36.6 - - + -
500D HIS* 5.4 7.0 - + + -
502D CYS* 6.3 1.1 - - + -
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Residues in contact with ARG 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ASN* 3.4 23.1 + - + +
186D PRO 3.1 0.8 - - - -
187D TYR* 1.3 81.9 - - - +
189D TYR* 1.3 94.9 + - + +
191D VAL* 3.2 19.2 - - - +
192D VAL* 3.5 12.4 - - - +
219D ASN* 5.5 8.1 - - - +
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Residues in contact with TYR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 3.6 21.2 - - + +
173D THR* 3.4 26.0 - - + -
174D LEU* 4.4 11.9 - - + -
177D LEU* 3.2 44.6 - - + +
184D PHE* 4.3 7.6 - + + +
185D ASN 3.3 24.9 - - - -
186D PRO* 2.9 5.2 + - + +
188D ARG* 1.3 115.3 + - + +
190D VAL* 1.3 62.4 + - + +
191D VAL 3.3 1.6 - - - -
192D VAL* 3.5 9.2 + - + +
193D SER* 3.3 24.9 + - - -
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Residues in contact with VAL 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 4.5 17.9 - - + -
186D PRO* 2.9 25.2 + - + +
187D TYR* 4.4 3.1 - - - +
189D TYR* 1.3 73.9 - - - +
191D VAL* 1.3 60.7 + - - +
193D SER* 3.4 5.0 + - - +
194D VAL* 2.9 44.3 + - + +
323D THR* 4.1 13.5 - - + +
326D ILE* 3.7 28.7 - - + -
327D SER* 5.0 3.6 - - - +
330D LEU* 4.1 22.4 - - + -
470D PHE* 6.5 0.4 - - + -
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 3.1 37.2 + - + +
188D ARG* 3.2 16.6 - - - +
190D VAL* 1.3 79.1 - - - +
192D VAL* 1.3 65.7 + - + +
194D VAL* 4.3 0.5 - - - +
195D THR* 2.6 39.4 + - - +
218D VAL* 5.5 8.5 - - + +
219D ASN* 5.0 20.6 - - + +
319D PHE* 4.5 16.2 - - + -
323D THR* 3.7 23.5 - - + +
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ARG* 3.5 20.6 - - - +
189D TYR* 3.5 9.6 + - + +
190D VAL 3.2 0.8 - - - -
191D VAL* 1.3 79.3 - - + +
193D SER* 1.3 67.6 + - - +
195D THR* 3.2 5.3 + - - -
196D ASN* 3.0 44.4 + - - +
207D TYR* 5.3 8.1 - - + -
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Residues in contact with SER 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU* 3.9 14.9 + - - +
169D VAL* 5.9 1.0 - - - +
170D LEU* 3.5 28.7 + - - +
189D TYR 3.3 14.6 + - - -
190D VAL* 3.4 4.2 + - - -
192D VAL* 1.3 79.2 - - - +
194D VAL* 1.3 63.5 + - - +
195D THR 3.4 0.2 + - - -
196D ASN* 3.4 13.7 + - - +
197D VAL* 3.3 19.9 + - - +
470D PHE* 4.1 23.8 - - - -
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D VAL* 2.9 32.5 + - + +
191D VAL 4.4 0.2 - - - +
193D SER* 1.3 75.8 - - - +
195D THR* 1.3 62.3 + - - +
197D VAL* 3.4 6.2 + - - +
198D ILE* 3.3 19.3 + - + +
318D GLY 4.2 1.6 - - - +
319D PHE* 3.7 17.5 - - - +
322D VAL* 3.9 14.1 - - + -
323D THR* 3.2 29.4 - - - +
326D ILE* 3.9 20.2 - - + -
466D GLU* 3.5 19.1 - - - +
470D PHE* 4.4 7.0 - - + -
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Residues in contact with THR 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D VAL* 2.6 26.7 + - - +
192D VAL* 3.2 5.1 + - - -
194D VAL* 1.3 76.7 - - - +
196D ASN* 1.3 58.2 + - - +
198D ILE* 3.2 7.7 - - - +
199D CYS* 2.5 43.9 + - + +
207D TYR* 6.0 5.4 - - + -
218D VAL* 5.1 15.0 - - + +
315D PHE* 3.6 29.4 - - + -
319D PHE* 3.5 21.9 - - + +
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Residues in contact with ASN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D HIS* 5.5 0.2 - - - +
166D GLU* 3.2 38.8 + - - +
192D VAL* 3.0 39.1 + - - +
193D SER* 3.4 1.5 + - - +
195D THR* 1.3 80.1 - - - +
197D VAL* 1.3 57.2 + - - +
199D CYS* 3.9 5.8 - - - +
200D ALA* 3.0 29.1 + - - +
205D ARG 4.0 2.4 - - - +
206D ARG* 3.7 17.4 - - + +
207D TYR* 2.7 42.4 + - - +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 3.9 18.2 - - + -
162D HIS* 4.1 14.8 - - + -
163D VAL* 3.8 28.5 - - + +
166D GLU* 3.6 19.1 - - + -
193D SER 3.3 15.3 - - - +
194D VAL 3.4 6.9 + - - +
195D THR 3.1 0.8 - - - -
196D ASN* 1.3 74.1 - - - +
198D ILE* 1.3 65.8 + - - +
200D ALA* 3.2 4.0 + - - +
201D ILE* 3.0 31.2 + - + +
466D GLU* 3.9 10.8 - - - +
470D PHE* 4.0 18.6 - - + -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 5.5 1.6 - - + -
194D VAL* 3.3 12.2 + - + +
195D THR* 3.2 19.1 - - - +
197D VAL* 1.3 80.4 - - + +
199D CYS* 1.3 60.8 + - - +
201D ILE* 3.5 18.6 + - + -
202D CYS* 3.1 35.3 + - - -
314D LEU* 3.9 6.5 - - + +
315D PHE* 3.9 27.6 - - + -
318D GLY* 4.1 7.6 - - - -
319D PHE* 3.9 21.1 - - + +
462D ILE* 6.3 1.1 - - + -
466D GLU* 5.1 4.0 + - - +
601D HEM 3.8 28.3 - - + -
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Residues in contact with CYS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D THR* 2.5 29.3 + - + +
196D ASN* 3.9 4.0 - - - +
198D ILE* 1.3 72.6 - - - +
200D ALA* 1.3 56.0 + - - +
203D PHE* 2.6 61.5 + - - +
204D GLY 3.2 2.9 + - - -
205D ARG 3.5 15.3 - - - +
207D TYR* 3.7 32.8 - - - -
315D PHE* 3.9 16.4 - - + -
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D HIS* 3.8 33.1 + - + +
165D LYS* 5.9 2.7 - - - +
166D GLU* 6.0 0.4 - - - +
196D ASN 3.0 20.0 + - - +
197D VAL 3.2 4.5 + - - +
199D CYS* 1.3 73.6 - - - +
201D ILE* 1.3 63.6 + - - +
204D GLY* 2.8 30.1 + - - +
205D ARG* 3.5 16.7 + - - +
206D ARG* 5.1 1.3 - - + +
279D ARG 5.2 1.0 - - - +
280D ASP* 4.2 3.1 - - - +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.7 7.6 - - + +
145D PHE* 3.5 34.8 - - + +
146D SER* 4.2 14.1 - - - -
159D LEU* 4.1 26.0 - - + -
162D HIS* 3.9 14.8 - - + -
197D VAL* 3.0 24.0 + - + +
198D ILE* 3.8 17.5 - - + +
199D CYS 3.3 0.2 - - - -
200D ALA* 1.3 75.7 - - - +
202D CYS* 1.3 58.6 + - - +
280D ASP* 3.6 4.3 - - - +
281D ILE* 3.4 39.9 + - + +
462D ILE* 5.0 7.2 - - + -
466D GLU* 6.0 0.2 - - - +
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ILE* 3.1 37.4 + - - +
201D ILE* 1.3 80.8 - - - +
203D PHE* 1.3 81.5 + - + +
280D ASP* 3.0 13.2 - - - +
281D ILE* 4.2 21.1 - - + -
282D THR* 3.0 25.3 + - - -
311D VAL* 4.5 8.1 - - + -
314D LEU* 4.4 6.3 - - - -
315D PHE* 4.3 20.4 - - + -
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Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D CYS* 2.6 41.4 + - - +
202D CYS* 1.3 91.3 - - + +
204D GLY* 1.3 60.0 + - - +
205D ARG* 3.5 11.0 + - + +
207D TYR* 4.6 1.6 - - - -
261D PHE* 4.8 10.3 - + - -
262D MET* 6.4 2.2 - - + -
265D MET* 3.4 49.5 - - + +
269D HIS* 3.6 11.7 + - - -
280D ASP* 3.1 17.3 - - - +
282D THR* 3.7 14.1 - - - -
311D VAL* 4.7 14.4 - - + -
315D PHE* 4.0 38.4 - + + -
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Residues in contact with GLY 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D HIS* 6.3 0.2 - - - -
199D CYS 3.2 1.4 + - - -
200D ALA* 2.8 25.7 + - - -
202D CYS 3.8 0.2 - - - -
203D PHE* 1.3 77.4 - - - +
205D ARG* 1.3 62.8 + - - +
279D ARG* 5.2 4.3 - - - -
280D ASP* 3.8 7.4 + - - -
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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