Contacts of the helix formed by residues 189 - 208 (chain B) in PDB entry 3A9L
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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173B ALA 2.7 29.7 + - - +
174B PHE 2.8 11.5 + - - -
175B PHE 3.5 26.9 - - - +
176B GLN* 3.8 10.5 - - + +
188B VAL* 1.3 76.7 - - - +
190B GLN* 1.3 63.8 + - - +
191B GLU* 3.5 4.5 + - - +
192B PHE* 3.1 18.0 + - - +
193B LEU* 3.3 25.4 + - - +
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 1.3 74.9 - - - +
191B GLU* 1.3 60.0 + - - +
193B LEU* 2.9 27.1 + - - +
194B ASP* 2.8 57.4 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LYS* 2.8 33.5 + - - +
134B GLY 4.9 5.6 - - - +
135B ILE* 4.0 22.0 - - + +
170B GLN* 2.7 33.1 + - - +
173B ALA* 3.9 10.3 - - - +
174B PHE* 4.5 1.1 - - + -
189B THR* 3.5 8.1 + - - +
190B GLN* 1.3 78.1 - - - +
192B PHE* 1.3 56.4 + - - +
194B ASP* 3.3 10.1 + - - +
195B TYR* 2.9 31.8 + - - +
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Residues in contact with PHE 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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50B GLU* 3.3 29.8 - - + -
51B LEU* 3.6 29.6 - - + +
54B ARG* 3.6 30.3 - - + -
174B PHE* 3.4 57.5 - + + +
175B PHE* 5.7 0.2 - + - -
188B VAL* 3.6 35.9 - - + -
189B THR* 3.1 14.3 + - - +
191B GLU* 1.3 74.8 - - - +
193B LEU* 1.3 70.9 + - + +
195B TYR* 3.2 3.3 + - - +
196B ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 193 (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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54B ARG* 3.7 36.6 + - - +
58B LEU* 5.2 1.7 - - - +
188B VAL* 4.4 10.1 - - + +
189B THR 3.3 13.6 + - - +
190B GLN* 2.9 31.8 + - - +
192B PHE* 1.3 94.4 - - + +
194B ASP* 1.3 57.6 + - - +
196B ALA* 3.3 4.0 + - - +
197B GLU* 2.8 30.7 + - - +
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Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS* 3.8 29.3 - - + +
135B ILE* 3.9 13.5 - - + -
190B GLN* 2.8 44.9 + - - +
191B GLU* 3.5 12.2 - - - +
193B LEU* 1.3 69.5 - - - +
195B TYR* 1.3 61.4 + - - +
197B GLU* 3.2 7.6 + - - +
198B ALA* 2.9 30.8 + - - +
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Residues in contact with TYR 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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51B LEU* 3.7 31.2 - - + -
113B THR* 2.6 43.7 + - - +
130B LEU* 3.8 13.9 - - + +
135B ILE* 3.7 37.2 - - + -
164B LEU* 3.3 16.1 - - + +
166B ILE* 3.2 14.9 - - + +
170B GLN* 4.1 9.0 - - + -
174B PHE* 3.8 25.6 - + + -
191B GLU 2.9 17.3 + - - +
192B PHE 3.5 4.7 - - - +
193B LEU 3.2 0.2 - - - -
194B ASP* 1.3 79.9 - - - +
196B ALA* 1.3 61.9 + - - +
198B ALA* 3.2 10.7 + - - +
199B ILE* 3.4 14.7 + - + +
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Residues in contact with ALA 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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51B LEU* 3.7 11.8 - - + +
54B ARG* 3.5 32.8 - - + -
55B VAL* 3.6 26.8 - - + +
58B LEU* 3.6 11.6 - - + +
192B PHE 3.1 12.0 + - - +
193B LEU 3.9 2.2 - - - +
195B TYR* 1.3 76.0 - - - +
197B GLU* 1.3 63.0 + - - +
199B ILE* 3.2 12.9 + - - +
200B LYS* 3.3 9.5 + - - +
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Residues in contact with GLU 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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58B LEU* 3.8 15.8 - - + +
133B LYS* 4.0 10.8 - - - +
193B LEU 2.8 18.9 + - - +
194B ASP* 3.6 8.3 - - - +
196B ALA* 1.3 76.7 - - - +
198B ALA* 1.3 61.9 + - - +
200B LYS* 2.9 42.6 + - - +
201B GLU* 3.1 43.5 + - - +
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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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129B LYS* 3.4 41.2 - - - +
130B LEU* 3.7 19.3 - - + +
133B LYS* 4.0 6.5 - - + +
194B ASP 2.9 12.0 + - - +
195B TYR 3.4 9.9 - - - +
197B GLU* 1.3 74.7 - - - +
199B ILE* 1.3 61.1 + - - +
201B GLU* 3.3 7.5 + - - +
202B ALA* 3.0 24.3 + - - +
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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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36B TYR* 3.8 29.6 - - + +
55B VAL* 3.9 19.3 - - + -
100B VAL* 5.2 0.2 - - + -
102B PHE* 4.4 13.9 - - + -
126B ILE* 3.4 45.5 - - + -
130B LEU* 4.5 7.9 - - + -
164B LEU* 3.9 15.9 - - + -
195B TYR* 3.4 18.6 + - + +
196B ALA 3.2 7.8 + - - +
198B ALA* 1.3 79.0 - - - +
200B LYS* 1.3 56.1 + - - +
202B ALA* 3.3 3.5 + - - +
203B GLU* 3.0 28.1 + - + +
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Residues in contact with LYS 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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55B VAL* 5.1 0.4 - - - +
58B LEU* 3.7 32.3 - - + +
59B THR* 3.6 29.5 - - + +
196B ALA 3.3 11.5 + - - +
197B GLU* 2.9 46.3 + - - +
198B ALA 3.3 0.2 - - - -
199B ILE* 1.3 73.7 - - - +
201B GLU* 1.3 64.3 + - - +
203B GLU* 3.6 2.1 + - - +
204B ALA* 2.9 31.7 + - + +
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Residues in contact with GLU 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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129B LYS* 4.0 25.0 + - + +
132B SER* 4.8 4.3 + - - -
133B LYS* 2.9 34.5 + - - -
197B GLU* 3.1 36.2 + - - +
198B ALA* 3.7 7.9 - - - +
199B ILE 3.3 0.2 - - - -
200B LYS* 1.3 80.2 - - - +
202B ALA* 1.3 53.7 + - - +
204B ALA* 3.7 5.4 - - - +
205B GLU* 2.8 37.1 + - - +
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Residues in contact with ALA 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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122B LEU* 4.0 7.0 - - + -
125B LEU* 3.7 7.9 - - - +
126B ILE* 3.7 36.3 - - + +
129B LYS* 3.7 19.0 - - + +
198B ALA 3.0 13.1 + - - +
199B ILE 3.5 8.5 - - - +
201B GLU* 1.3 74.0 - - - +
203B GLU* 1.3 53.4 + - - +
205B GLU* 3.3 2.3 + - - +
206B TYR* 2.8 36.2 + - - +
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Residues in contact with GLU 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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31B ASN* 5.3 5.5 + - - -
34B MET* 3.9 20.0 - - + +
36B TYR* 2.5 33.8 + - - +
59B THR* 3.2 30.5 - - - +
61B GLY* 5.2 1.3 + - - -
122B LEU* 4.0 7.1 - - + +
199B ILE 3.0 9.9 + - - +
200B LYS 3.7 4.9 - - - +
202B ALA* 1.3 77.8 - - - +
204B ALA* 1.3 63.7 + - - +
206B TYR* 3.0 21.8 + - - +
207B TYR* 3.2 43.0 + - + -
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Residues in contact with ALA 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 LYS* 2.9 27.3 + - + +
201B GLU* 3.7 6.3 - - - +
203B GLU* 1.3 73.7 - - - +
205B GLU* 1.3 63.9 + - - +
206B TYR 3.2 0.9 + - - -
207B TYR* 3.5 3.1 + - - +
208B GLY* 3.4 17.5 + - - -
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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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121B GLU* 5.3 0.9 - - - +
125B LEU* 3.4 26.7 - - + +
129B LYS* 2.6 38.3 + - - +
201B GLU 2.8 20.6 + - - +
202B ALA 3.7 2.9 - - - +
204B ALA* 1.3 73.5 - - - +
206B TYR* 1.3 62.7 + - - +
207B TYR 3.7 0.2 + - - -
208B GLY* 3.7 8.2 + - - -
209B LEU* 3.9 5.2 + - - +
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Residues in contact with TYR 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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98B ASP* 3.5 30.2 + - - -
119B ASN* 3.1 31.6 + - - -
121B GLU* 3.5 35.1 - - + +
122B LEU* 4.0 20.9 - - + -
125B LEU* 3.7 15.9 - - + +
160B LYS* 4.4 6.1 + - - -
202B ALA 2.8 16.8 + - - +
203B GLU* 3.0 10.5 + - - +
205B GLU* 1.3 73.3 - - - +
207B TYR* 1.3 86.2 + + - +
209B LEU* 3.1 24.7 - - + +
210B GLU* 3.4 24.0 + - - +
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Residues in contact with TYR 207 (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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33B SER* 3.3 39.7 + - - -
34B MET* 3.5 6.7 - - + +
97B THR* 5.8 1.1 - - + -
98B ASP* 2.7 34.5 + - - +
203B GLU* 3.2 55.5 + - + +
204B ALA* 4.5 2.5 - - - +
206B TYR* 1.3 89.6 - + - +
208B GLY* 1.3 54.2 + - - +
209B LEU 2.8 6.4 + - - -
210B GLU* 2.7 52.8 + - + +
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Residues in contact with GLY 208 (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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204B ALA 3.4 11.5 + - - -
205B GLU 4.0 6.5 - - - -
206B TYR 3.3 1.2 - - - -
207B TYR* 1.3 75.2 - - - +
209B LEU* 1.3 59.7 - - - +
210B GLU 4.4 2.2 - - - +
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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