Contacts of the helix formed by residues 189 - 204 (chain B) 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 THR 189 (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 4.9 4.9 - - - +
186B TYR* 3.4 10.7 + - - -
188B LYS* 1.3 86.1 + - - +
190B CYS* 1.3 64.2 + - - +
191B SER* 3.4 2.7 - - - +
192B LYS* 3.4 37.0 + - + +
193B VAL* 3.5 17.0 - - - +
301B SER* 5.4 1.1 - - - +
303B LEU* 3.3 31.6 - - + +
304B ILE* 3.7 28.9 - - + +
307B LEU* 5.7 1.6 - - - -
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Residues in contact with CYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 4.6 18.9 - - - +
185B LYS* 4.5 22.2 - - - +
186B TYR 3.8 3.8 + - - +
187B PRO* 3.7 18.9 + - + -
188B LYS 3.7 1.4 - - - -
189B THR* 1.3 78.3 - - - +
191B SER* 1.3 59.4 + - - +
193B VAL* 3.3 4.5 + - - +
194B GLU* 3.0 50.5 + - - +
18C ARG* 3.6 26.0 - - - +
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO 5.3 0.2 + - - -
188B LYS 5.6 0.3 + - - -
189B THR 3.4 0.7 - - - -
190B CYS* 1.3 79.8 - - - +
192B LYS* 1.3 62.8 + - - +
194B GLU* 3.5 7.3 - - - +
195B HIS* 2.9 29.7 + - - +
18C ARG* 4.1 25.3 - - - +
426C TYR* 3.5 16.0 + - - -
427C ASP* 5.2 2.3 + - - -
430C TYR* 5.7 0.9 + - - -
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Residues in contact with LYS 192 (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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188B LYS 3.9 13.7 + - - -
189B THR* 3.4 36.9 - - + +
191B SER* 1.3 83.8 + - - +
193B VAL* 1.3 65.2 + - + +
195B HIS* 3.3 9.4 + - - +
196B PHE* 2.9 25.3 + - - +
297B HIS* 4.4 23.8 - - + +
298B VAL* 4.4 29.4 - - + +
301B SER* 4.2 20.5 + - - +
304B ILE* 5.6 2.9 - - + -
427C ASP* 4.2 15.7 + - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.8 18.4 - - + -
183B TRP* 6.0 1.6 - - + -
184B PHE* 3.6 31.0 - - + -
189B THR 3.5 16.4 - - - +
190B CYS 3.3 5.6 + - - +
191B SER 3.3 0.4 - - - -
192B LYS* 1.3 82.9 - - + +
194B GLU* 1.3 61.7 + - - +
195B HIS 3.2 1.1 - - - -
196B PHE* 3.1 7.0 + - + +
197B VAL* 3.0 30.1 + - - +
304B ILE* 4.3 21.5 - - + -
419B LEU* 4.5 17.5 - - + -
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Residues in contact with GLU 194 (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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15B PRO* 5.9 2.6 - - - +
17B TYR* 2.4 35.9 + - - +
184B PHE* 4.6 3.9 - - + -
185B LYS* 5.1 5.4 + - - -
190B CYS* 3.0 40.3 + - - +
191B SER* 3.5 9.2 - - - +
193B VAL* 1.3 75.7 - - - +
195B HIS* 1.3 59.5 + - - +
197B VAL* 3.4 4.4 + - - +
198B SER* 3.0 27.2 + - - -
18C ARG* 5.5 1.1 - - - +
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER 2.9 18.4 + - - +
192B LYS* 3.4 9.9 - - - +
193B VAL 3.2 0.2 - - - -
194B GLU* 1.3 75.8 - - - +
196B PHE* 1.3 56.6 + - - +
198B SER* 3.1 15.5 + - - -
199B ILE* 2.8 30.6 + - + +
290B LYS* 5.1 7.2 - - + -
294B PHE* 3.3 43.0 - + - -
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.7 7.6 - - + -
192B LYS 2.9 14.6 + - - +
193B VAL* 3.1 13.4 + - + +
195B HIS* 1.3 74.5 - - - +
197B VAL* 1.3 67.8 + - + +
199B ILE* 3.1 37.0 + - + +
200B LEU* 3.1 25.1 + - + +
298B VAL* 5.8 5.8 - - + -
418B PHE* 4.9 16.4 - + - -
419B LEU* 3.6 47.6 - - + -
420B LEU* 4.3 24.0 - - + -
423B VAL* 3.9 14.8 - - + -
434B PHE* 5.0 15.5 - + - -
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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
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16B THR* 4.7 10.5 - - + +
17B TYR* 3.7 36.1 - - + +
19B ILE* 4.6 19.5 - - + +
20B LEU* 3.7 32.5 - - + -
193B VAL 3.0 15.7 + - - +
194B GLU 3.8 4.9 - - - +
196B PHE* 1.3 76.0 - - + +
198B SER* 1.3 57.7 + - - +
200B LEU* 3.9 4.0 - - - +
201B GLY* 2.9 27.5 + - - -
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Residues in contact with SER 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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194B GLU* 3.0 16.5 + - - -
195B HIS* 3.1 20.6 + - - -
197B VAL* 1.3 74.7 - - - +
199B ILE* 1.4 61.9 + - - +
201B GLY* 3.9 1.3 - - - -
202B LYS* 3.0 33.3 + - - +
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Residues in contact with ILE 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 HIS* 2.8 19.1 + - + +
196B PHE* 3.1 36.7 + - + +
198B SER* 1.4 76.1 - - - +
200B LEU* 1.3 58.3 + - + +
202B LYS* 3.7 3.0 - - - +
203B CYS* 2.8 27.5 + - - +
287B LEU* 5.1 8.3 - - + +
291B VAL* 4.8 6.5 - - + -
294B PHE* 3.4 57.4 - - + -
298B VAL* 6.1 3.8 - - + -
434B PHE* 3.5 28.3 - - + -
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Residues in contact with LEU 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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19B ILE* 4.6 22.0 - - + -
196B PHE* 3.1 27.4 + - + +
197B VAL* 4.3 3.6 - - - +
199B ILE* 1.3 81.6 - - - +
201B GLY* 1.3 61.4 + - - +
203B CYS* 2.9 21.4 + - + +
204B PHE* 3.0 15.8 + - - +
420B LEU* 5.2 3.4 - - + -
423B VAL* 4.0 23.3 - - + -
430B TYR* 3.6 46.0 - - + +
434B PHE* 4.6 24.2 - - + -
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Residues in contact with GLY 201 (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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19B ILE* 6.1 4.0 - - - +
197B VAL* 2.9 17.5 + - - -
198B SER* 3.9 1.3 - - - -
200B LEU* 1.3 79.6 - - - +
202B LYS* 1.3 64.7 + - - +
204B PHE* 4.3 4.9 + - - +
205B GLU* 2.8 17.3 - - - +
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Residues in contact with LYS 202 (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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198B SER* 3.0 23.9 + - - +
199B ILE* 3.9 3.6 - - - +
201B GLY* 1.3 79.8 - - - +
203B CYS* 1.3 62.0 + - - +
205B GLU* 3.0 43.4 + - - +
206B SER* 4.6 3.5 + - - -
287B LEU* 4.2 19.6 - - + +
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Residues in contact with CYS 203 (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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199B ILE 2.8 18.4 + - - +
200B LEU* 2.9 12.5 + - + +
202B LYS* 1.3 78.4 - - - +
204B PHE* 1.3 61.3 - - - +
205B GLU 3.4 0.5 + - - -
206B SER* 3.7 8.0 + - - -
287B LEU* 4.7 4.7 - - + -
433B ARG* 3.0 44.8 + - - -
434B PHE* 3.6 28.3 - - + -
437B PHE* 3.7 31.9 - - + -
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Residues in contact with PHE 204 (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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195A HIS* 3.4 36.1 - + - -
290A LYS* 3.5 22.6 + - + -
293A LYS* 5.0 6.1 - - - -
200B LEU 3.0 12.7 + - - +
201B GLY* 4.7 4.5 - - - +
202B LYS 3.3 1.0 - - - -
203B CYS* 1.3 78.4 - - - +
205B GLU* 1.3 66.5 + - + +
429B LEU* 4.5 15.7 - - + -
430B TYR* 3.5 38.1 - + + +
433B ARG* 2.7 46.8 + - + +
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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