Contacts of the helix formed by residues 186 - 205 (chain D) in PDB entry 6M04
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 TYR 186 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PHE* 3.8 23.5 + + - +
183D TRP 4.3 0.4 + - - +
184D PHE 3.5 2.0 - - - -
185D LYS* 1.3 78.5 - - - +
187D PRO* 1.3 68.1 - - + +
188D LYS* 3.7 39.0 - - + +
189D THR* 2.9 29.0 + - - +
190D CYS* 2.6 35.7 + - - +
303D LEU* 4.7 7.0 - - + -
307D LEU* 4.4 13.7 - - + -
23E TRP* 4.8 14.6 - - + +
27E PHE* 4.3 27.4 - + - -
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Residues in contact with PRO 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS 3.9 4.0 - - - +
186D TYR* 1.3 98.2 - - + +
188D LYS* 1.3 63.9 + - + +
189D THR 3.4 0.2 + - - -
190D CYS* 3.9 9.0 + - + +
191D SER* 3.9 3.5 + - - -
21E LYS* 4.4 17.3 - - + +
22E PRO* 3.9 6.7 - - + +
23E TRP* 3.6 32.8 - - + +
26E VAL* 4.1 17.9 - - + -
27E PHE* 5.9 0.7 - - + -
425E GLN 5.4 5.8 - - - +
426E TYR* 3.9 34.2 - - + +
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Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D TYR* 3.4 24.8 - - + +
187D PRO* 1.3 77.8 - - + +
189D THR* 1.3 60.7 + - - +
191D SER* 3.4 13.6 + - - -
192D LYS* 4.1 13.0 + - - -
303D LEU* 4.0 26.7 - - + +
23E TRP* 5.1 19.0 - - + -
425E GLN 5.3 8.1 - - - +
426E TYR 4.8 6.7 - - - +
427E ASP* 5.3 0.4 - - - +
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Residues in contact with THR 189 (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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183D TRP* 3.3 24.2 - - + +
184D PHE* 4.9 3.6 - - - +
186D TYR* 2.9 23.7 + - - +
188D LYS* 1.3 78.0 - - - +
190D CYS* 1.3 67.2 + - - +
191D SER 3.1 3.4 + - - -
192D LYS* 3.5 8.7 + - - +
193D VAL* 3.3 23.9 + - + +
303D LEU* 4.3 14.0 - - - +
304D ILE* 3.7 24.9 - - + -
307D LEU* 3.4 19.5 - - + +
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Residues in contact with CYS 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D PHE* 3.9 25.6 - - - +
185D LYS* 4.0 14.1 - - - -
186D TYR 2.6 21.5 + - - +
187D PRO* 3.9 4.5 + - + +
188D LYS 3.7 0.2 - - - -
189D THR* 1.3 73.1 - - - +
191D SER* 1.3 57.7 + - - +
193D VAL* 3.9 6.3 - - - -
194D GLU* 2.9 34.6 + - - +
18E ARG* 2.8 48.0 - - - -
426E TYR* 4.1 2.9 - - + +
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Residues in contact with SER 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO 3.9 8.9 + - - -
188D LYS 3.4 15.2 + - - -
190D CYS* 1.3 78.9 - - - +
192D LYS* 1.3 73.3 + - - +
194D GLU* 3.7 2.3 - - - +
195D HIS* 2.9 29.1 + - - +
297D HIS* 5.7 1.9 - - - -
426E TYR* 3.2 21.8 + - - -
427E ASP* 3.2 39.6 + - - -
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Residues in contact with LYS 192 (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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188D LYS 4.1 15.6 + - - +
189D THR* 3.6 11.7 - - - +
191D SER* 1.3 81.2 + - - +
193D VAL* 1.3 67.2 + - + +
195D HIS* 3.7 9.2 - - + +
196D PHE* 2.8 30.1 + - - +
294D PHE* 4.3 4.8 - - + -
297D HIS* 4.5 16.4 - - + -
298D VAL* 3.7 37.6 - - + +
300D ASP* 5.4 5.7 + - - +
302D ASP* 4.7 16.2 + - - +
303D LEU* 5.7 5.6 - - - +
304D ILE* 4.6 17.9 - - + -
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Residues in contact with VAL 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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17D TYR* 5.1 2.2 - - + -
20D LEU* 3.7 29.4 - - + -
183D TRP* 5.4 6.7 - - + -
184D PHE* 4.2 23.6 - - + +
189D THR* 3.3 24.4 + - + +
190D CYS* 4.0 7.2 - - - +
191D SER 3.2 0.6 - - - -
192D LYS* 1.3 74.8 - - + +
194D GLU* 1.3 61.4 + - - +
196D PHE* 3.2 6.2 + - + +
197D VAL* 3.0 32.4 + - + +
304D ILE* 3.8 24.5 - - + -
419D LEU* 5.9 5.6 - - + -
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Residues in contact with GLU 194 (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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17D TYR* 2.3 35.5 + - - -
190D CYS* 2.9 20.5 + - - +
191D SER* 3.7 4.5 - - - +
193D VAL* 1.3 76.4 - - - +
195D HIS* 1.3 58.8 + - - +
197D VAL* 3.3 2.3 + - - +
198D SER* 3.0 48.3 + - - +
18E ARG* 3.5 35.2 + - + +
426E TYR* 4.9 3.6 - - - +
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Residues in contact with HIS 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 SER 2.9 19.2 + - - +
192D LYS* 3.8 7.6 - - + +
193D VAL 3.2 0.4 - - - -
194D GLU* 1.3 77.4 - - - +
196D PHE* 1.3 57.0 + - - +
198D SER* 3.3 9.6 + - - -
199D ILE* 2.8 53.2 + - + +
290D LYS* 5.2 6.3 + - + -
294D PHE* 3.3 41.7 - + - +
297D HIS* 6.2 2.2 - + + -
204E PHE* 3.4 36.9 - + - -
429E LEU* 5.4 12.5 - - + +
430E TYR* 5.6 2.4 + - - +
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Residues in contact with PHE 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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20D LEU* 4.8 3.4 - - + -
192D LYS 2.8 19.6 + - - +
193D VAL* 3.2 5.6 + - - +
195D HIS* 1.3 75.7 - - - +
197D VAL* 1.3 68.5 + - + +
199D ILE* 3.2 6.6 + - + +
200D LEU* 2.9 40.6 + - + +
294D PHE* 3.5 31.9 - + + -
418D PHE* 4.0 22.4 - + - -
419D LEU* 3.6 35.4 - - + -
420D LEU* 3.7 27.4 - - + -
423D VAL* 4.0 12.3 - - + -
434D PHE* 4.6 14.4 - + - -
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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
----------------------------------------------------------
17D TYR* 3.6 46.4 - - + +
19D ILE* 5.1 14.1 - - + -
20D LEU* 3.9 31.0 - - + -
193D VAL 3.0 17.2 + - - +
194D GLU 3.9 3.6 - - - +
196D PHE* 1.3 79.2 - - + +
198D SER* 1.3 57.4 + - - +
200D LEU* 3.4 4.2 + - - +
201D GLY* 2.9 27.0 + - - -
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Residues in contact with SER 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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194D GLU* 3.0 32.9 + - - +
195D HIS* 3.5 11.8 - - - -
197D VAL* 1.3 78.6 - - - +
199D ILE* 1.3 57.8 + - - +
201D GLY* 3.4 0.8 + - - -
202D LYS* 2.9 39.2 + - - +
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Residues in contact with ILE 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 HIS* 2.8 49.7 + - + +
196D PHE* 3.6 11.7 - - + +
198D SER* 1.3 77.1 - - - +
200D LEU* 1.3 56.7 + - - +
202D LYS* 3.4 5.2 + - + +
203D CYS* 2.8 29.8 + - - +
287D LEU* 4.5 8.5 - - + +
290D LYS* 4.3 31.0 - - + +
291D VAL* 4.4 13.2 - - + -
294D PHE* 4.5 14.1 - - + -
434D PHE* 4.0 26.2 - - + -
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Residues in contact with LEU 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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19D ILE* 5.5 9.9 - - + -
196D PHE* 2.9 42.5 + - + +
197D VAL* 4.1 5.2 - - - +
199D ILE* 1.3 78.5 - - - +
201D GLY* 1.3 58.5 + - - +
203D CYS* 3.3 6.3 + - - +
204D PHE* 3.0 26.6 + - + +
420D LEU* 4.5 3.4 - - + -
423D VAL* 4.1 18.6 - - + -
430D TYR* 3.8 40.6 - - + +
433D ARG* 3.8 21.9 + - - +
434D PHE* 5.1 8.5 - - + -
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Residues in contact with GLY 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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197D VAL 2.9 18.0 + - - -
198D SER* 3.8 1.3 - - - -
200D LEU* 1.3 79.2 - - - +
202D LYS* 1.3 64.9 + - - +
204D PHE* 3.5 9.6 + - - +
205D GLU* 3.4 26.8 - - - +
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Residues in contact with LYS 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 SER* 2.9 24.7 + - - +
199D ILE* 3.9 5.4 - - + +
201D GLY* 1.3 78.5 - - - +
203D CYS* 1.3 60.7 + - - +
205D GLU* 3.4 36.1 + - - +
206D SER* 4.2 4.5 + - - -
287D LEU* 3.4 30.9 - - + +
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Residues in contact with CYS 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 ILE 2.8 18.3 + - - +
200D LEU* 3.7 6.3 - - - +
201D GLY 3.3 0.2 - - - -
202D LYS* 1.3 74.9 - - - +
204D PHE* 1.3 61.7 + - - +
205D GLU 3.3 0.4 + - - -
206D SER* 4.1 8.0 + - - -
209D THR* 4.4 7.3 + - - +
287D LEU* 4.2 13.0 - - + +
433D ARG* 2.9 41.7 + - - +
434D PHE* 3.6 24.7 - - + -
437D PHE* 3.8 36.5 - - - -
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Residues in contact with PHE 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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200D LEU* 3.0 14.6 + - + +
201D GLY* 3.5 6.5 + - - +
202D LYS 3.3 0.6 - - - -
203D CYS* 1.3 77.0 - - - +
205D GLU* 1.3 63.3 + - + +
206D SER 3.3 8.3 + - - +
209D THR* 5.1 1.0 + - - -
429D LEU* 5.1 12.1 - - + -
430D TYR* 3.5 34.1 - + + -
433D ARG* 3.3 41.3 + - + +
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Residues in contact with GLU 205 (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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201D GLY* 3.4 18.0 - - - +
202D LYS* 3.4 35.7 + - - +
203D CYS 3.3 1.2 - - - -
204D PHE* 1.3 85.5 - - + +
206D SER* 1.3 57.5 + - - +
207D PRO* 3.6 8.9 - - - +
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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
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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