Contacts of the helix formed by residues 189 - 206 (chain B) in PDB entry 6EBT
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 ASP 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 SER 5.1 0.9 - - - +
185B GLN* 4.9 3.3 - - - -
186B SER* 3.1 23.6 + - - +
188B ASN* 1.3 77.8 - - - +
190B THR* 1.3 68.3 + - - +
192B PRO* 3.6 3.1 - - - +
193B THR* 2.8 24.9 + - - -
273B ALA* 3.7 17.2 - - - +
274B ALA* 3.7 5.6 + - - -
275B GLY* 3.0 19.7 + - - -
277B THR* 2.9 42.4 + - - +
289B PHE* 5.7 0.3 - - - -
315B LEU* 3.8 12.1 - - + -
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Residues in contact with THR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.3 4.0 - - - -
99B LEU* 3.6 20.0 - - + +
100B LYS* 4.1 0.7 - - - +
150B ASN* 3.3 29.6 + - - +
182B ASN* 4.5 0.4 - - - +
185B GLN* 3.5 35.9 - - + +
186B SER 3.0 21.8 + - - +
187B SER 4.3 3.6 + - - -
189B ASP* 1.3 86.2 + - - +
191B PHE* 1.3 63.2 + - - +
193B THR* 3.2 5.0 + - - -
194B ALA* 2.9 25.5 + - - +
274B ALA* 6.0 2.0 - - + -
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 3.7 39.0 - - + -
92B VAL* 4.0 13.9 - - + -
96B PHE* 3.7 27.3 - + + -
145B SER 3.2 20.6 - - - +
146B GLY* 3.6 19.7 - - - +
149B THR* 4.4 2.7 - - - -
187B SER 5.6 1.8 + - - +
188B ASN 4.7 0.4 + - - -
189B ASP 4.8 0.2 - - - +
190B THR* 1.3 82.7 + - - +
192B PRO* 1.3 66.0 - - + +
194B ALA* 3.0 1.6 + - - +
195B MET* 2.9 44.0 + - + +
409B LYS* 3.7 17.0 - - + -
410B PRO* 3.8 28.0 - - + -
413B ILE* 4.0 9.0 - - + -
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Residues in contact with PRO 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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145B SER 4.9 0.2 - - - +
188B ASN 3.0 26.9 - - - +
189B ASP* 3.6 3.8 - - - -
190B THR 3.5 3.1 - - - -
191B PHE* 1.3 94.1 - - + +
193B THR* 1.3 60.8 + - - +
195B MET* 3.2 16.7 - - + +
196B HIS* 3.2 28.8 + - + +
273B ALA* 3.9 15.9 - - + -
314B ALA 4.6 1.6 - - - +
315B LEU* 4.1 11.0 - - + -
318B HIS* 3.8 15.9 - - + +
409B LYS* 3.7 22.0 - - + +
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.8 28.5 - - + -
189B ASP 2.8 20.2 + - - -
190B THR 3.2 8.4 + - - -
191B PHE 3.2 0.6 - - - -
192B PRO* 1.3 78.3 - - - +
194B ALA* 1.3 64.2 + - - +
196B HIS* 3.2 4.0 + - - +
197B ILE* 3.0 34.2 + - + +
272B LEU* 4.0 26.9 - - + +
273B ALA* 3.5 5.1 + - - +
274B ALA* 2.9 24.0 + - + +
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Residues in contact with ALA 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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92B VAL* 4.3 4.0 - - + +
95B ALA* 3.1 16.9 - - + +
96B PHE* 3.5 52.9 - - + +
99B LEU* 4.6 2.2 - - + +
190B THR 2.9 12.6 + - - +
191B PHE 3.6 4.5 - - - +
193B THR* 1.3 76.2 - - - +
195B MET* 1.3 59.6 + - - +
197B ILE* 3.3 5.9 + - - -
198B ALA* 2.8 25.5 + - - +
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Residues in contact with MET 195 (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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92B VAL* 4.9 3.8 - - + +
191B PHE* 2.9 37.7 + - + +
192B PRO* 3.2 18.4 - - + +
194B ALA* 1.3 77.8 - - - +
196B HIS* 1.3 63.6 + - + +
198B ALA* 4.3 3.1 - - - -
199B ALA* 2.9 24.1 + - - +
318B HIS* 3.2 52.3 - - + +
321B LEU* 3.7 14.4 - - + -
409B LYS* 3.9 16.4 - - + +
413B ILE* 3.2 41.4 - - + +
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Residues in contact with HIS 196 (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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192B PRO* 3.2 21.2 + - + +
193B THR 3.7 3.1 - - - +
195B MET* 1.3 79.3 - - + +
197B ILE* 1.3 64.6 + - - +
199B ALA* 4.3 2.5 - - - -
200B ALA* 2.9 26.2 + - - +
268B ARG 3.6 16.4 - - - -
269B ILE* 3.0 23.7 + - + +
271B GLU* 2.7 26.0 + - + -
272B LEU* 3.9 9.6 - - + -
273B ALA 5.7 0.2 + - - -
305B PHE* 4.0 3.0 - - - -
318B HIS* 4.9 12.0 + - - +
320B ALA* 4.1 18.3 - - + +
321B LEU* 4.1 27.1 + - + +
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Residues in contact with ILE 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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95B ALA* 3.6 29.2 - - + +
98B ILE* 4.1 8.7 - - + -
99B LEU* 4.4 7.9 - - + +
193B THR* 3.0 36.7 + - + +
194B ALA* 3.5 6.7 - - - +
196B HIS* 1.3 76.6 - - - +
198B ALA* 1.3 63.0 + - - +
200B ALA* 3.8 1.2 - - - +
201B ILE* 3.0 46.8 + - + +
272B LEU* 4.2 4.7 - - + -
297B VAL* 3.6 33.4 - - + -
301B THR* 4.8 3.8 - - + -
305B PHE* 3.8 18.2 - - + -
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Residues in contact with ALA 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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91B PRO* 3.4 38.9 - - + +
92B VAL* 3.9 6.1 - - - +
95B ALA* 3.7 4.0 - - + +
194B ALA 2.8 19.7 + - - +
195B MET* 3.9 6.7 - - - +
197B ILE* 1.3 73.3 - - - +
199B ALA* 1.3 62.9 - - - +
201B ILE* 3.4 6.1 + - - +
202B GLU* 2.9 27.9 + - - +
417B LEU* 3.8 11.8 - - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MET 2.9 19.8 + - - +
196B HIS* 3.8 5.2 - - - +
197B ILE 3.3 0.2 - - - -
198B ALA* 1.3 77.6 - - - +
200B ALA* 1.3 61.7 + - - +
202B GLU* 3.4 1.7 + - - +
203B VAL* 3.0 30.5 + - - +
269B ILE* 4.2 13.0 - - + -
321B LEU* 4.4 8.3 - - + -
324B LEU* 4.2 15.7 - - + -
413B ILE* 4.1 10.1 - - + -
416B VAL* 4.5 3.8 - - + -
417B LEU* 4.1 10.2 - - - +
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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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196B HIS 2.9 17.7 + - - +
199B ALA* 1.3 77.6 - - - +
201B ILE* 1.3 62.7 + - - +
203B VAL* 3.3 1.4 + - - +
204B HIS* 3.1 29.6 + - - -
266B MET* 3.7 24.7 - - + -
269B ILE* 4.1 2.4 - - + +
270B TYR* 3.9 11.0 - - + -
303B LEU* 4.0 4.9 - - + -
305B PHE* 3.6 25.8 - - + -
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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
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91B PRO* 6.5 0.7 - - + -
94B LYS* 6.5 0.7 - - + -
95B ALA* 5.5 2.0 - - + +
98B ILE* 3.6 30.1 - - + -
197B ILE* 3.0 30.4 + - + +
198B ALA* 3.9 6.3 - - - +
200B ALA* 1.3 74.6 - - - +
202B GLU* 1.3 64.8 + - - +
204B HIS* 3.3 1.6 + - - +
205B GLU* 2.9 60.2 + - - +
301B THR* 4.4 9.9 - - + -
303B LEU* 4.1 18.4 - - + -
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Residues in contact with GLU 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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91B PRO* 3.9 27.8 - - - +
198B ALA 2.9 18.0 + - - +
199B ALA 3.8 3.1 - - - +
201B ILE* 1.3 81.5 - - - +
203B VAL* 1.3 58.2 + - - +
205B GLU* 5.6 1.2 - - - +
206B VAL* 3.0 50.7 + - + +
207B LEU* 3.0 9.6 + - - +
417B LEU* 3.9 17.9 - - + +
420B ALA* 4.1 20.9 - - + -
421B ARG* 4.0 26.9 + - - +
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Residues in contact with VAL 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 ALA 3.0 21.6 + - - +
200B ALA 3.7 4.3 - - - +
202B GLU* 1.3 78.3 - - - +
204B HIS* 1.3 63.5 + - + +
207B LEU* 3.9 16.2 - - + -
208B LEU* 2.9 45.5 + - + +
262B ILE* 3.8 23.3 - - + -
266B MET* 3.8 29.4 - - + -
324B LEU* 4.0 22.2 - - + -
328B MET* 5.8 0.2 - - - -
420B ALA* 5.2 5.8 - - + -
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Residues in contact with HIS 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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200B ALA 3.1 29.0 + - - +
201B ILE* 4.1 2.2 - - - +
203B VAL* 1.3 86.4 - - + +
205B GLU* 1.3 63.1 + - + +
208B LEU* 4.4 18.6 - - + +
209B PRO* 3.2 19.7 - - - +
263B LYS* 5.9 2.9 - - + -
266B MET* 4.5 6.6 - - + +
270B TYR* 2.4 31.9 + + - -
303B LEU* 3.6 29.3 - - + +
304B PRO* 6.0 0.2 - - + -
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Residues in contact with GLU 205 (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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201B ILE* 2.9 40.3 + - + +
202B GLU* 5.6 0.9 - - - +
204B HIS* 1.3 82.4 - - + +
206B VAL* 1.3 66.7 + - + +
209B PRO* 3.4 17.2 - - - +
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Residues in contact with VAL 206 (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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202B GLU* 3.0 36.9 + - + +
204B HIS 3.7 0.2 - - - -
205B GLU* 1.3 89.5 - - + +
207B LEU* 1.3 68.1 + - - +
208B LEU 3.6 0.7 - - - -
209B PRO* 3.8 2.0 - - - +
210B GLY* 3.1 17.7 + - - -
420B ALA 4.1 14.4 - - - +
421B ARG* 4.2 13.5 - - - -
424B GLY* 3.5 11.9 - - - -
425B ASP* 3.8 23.1 - - - +
428B VAL* 5.7 0.3 - - - +
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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