Contacts of the helix formed by residues 189 - 209 (chain B) in PDB entry 3LOC
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLY 5.0 1.1 - - - +
185B ALA* 3.7 10.0 - - + -
186B THR* 2.9 39.8 + - - +
187B LEU 3.8 0.7 - - - +
188B ARG* 1.3 75.8 - - - +
190B GLU* 1.3 67.8 + - - +
191B VAL* 3.2 2.7 - - + +
192B PHE* 3.1 13.8 + - + +
193B PHE* 2.9 21.5 + - - +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU 5.2 0.2 - - - -
188B ARG 3.5 8.6 + - - +
189B ASP* 1.3 70.1 - - - +
191B VAL* 1.3 63.8 + - + +
193B PHE* 3.3 10.3 + - - +
194B ASN* 3.1 22.9 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 3.2 3.3 - - + -
190B GLU* 1.3 76.6 - - + +
192B PHE* 1.3 59.1 + - - +
194B ASN* 3.2 7.8 + - - +
195B GLN* 2.9 53.8 + - + +
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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
----------------------------------------------------------
159A GLN* 5.7 0.7 - - - -
160A HIS* 3.8 23.8 - + - -
163A PHE* 5.2 0.2 - + - -
172B TYR* 4.3 2.9 - + - -
179B VAL* 3.5 32.3 - - + -
183B THR* 3.8 24.5 - - + -
185B ALA* 3.7 22.9 - - + -
186B THR* 3.5 27.4 - - - +
187B LEU* 4.1 11.7 - - + -
189B ASP* 3.1 12.1 + - + +
191B VAL* 1.3 76.8 - - - +
193B PHE* 1.3 65.9 + - - +
195B GLN* 3.4 19.9 + - - +
196B THR* 2.7 46.1 + - - -
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 4.4 16.2 - - - -
101B LEU* 3.6 31.9 - - + -
102B GLU* 3.9 25.6 - - + -
105B ARG* 3.8 32.5 - - + +
187B LEU* 3.6 34.1 + - + +
189B ASP 2.9 7.8 + - - +
190B GLU* 3.4 12.8 - - - +
192B PHE* 1.3 79.2 - - - +
194B ASN* 1.3 62.1 + - + +
196B THR* 2.9 9.6 + - - -
197B VAL* 2.8 52.0 + - + +
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Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 4.0 20.6 - - - +
190B GLU 3.1 10.0 + - - +
191B VAL* 3.2 9.4 + - - +
193B PHE* 1.3 83.0 - - + +
195B GLN* 1.3 66.6 + - + +
197B VAL* 3.0 4.8 + - - +
198B GLU* 2.8 49.0 + - - +
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Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 5.2 4.9 - - - +
160A HIS* 4.4 11.5 + - - +
191B VAL* 2.9 42.2 + - + +
192B PHE* 3.7 22.1 - - - +
193B PHE 3.4 0.2 - - - -
194B ASN* 1.3 75.6 + - + +
196B THR* 1.3 62.2 + - - +
198B GLU* 3.4 5.0 + - - +
199B ASN* 2.8 36.2 + - - +
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Residues in contact with THR 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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160A HIS* 3.3 19.7 - - - -
101B LEU* 4.0 14.1 - - + -
172B TYR* 3.3 48.0 - - + +
187B LEU* 5.1 3.3 - - + +
192B PHE* 2.7 33.3 + - - -
193B PHE* 2.9 10.4 + - - -
195B GLN* 1.3 75.3 - - - +
197B VAL* 1.3 64.7 + - - +
199B ASN* 3.2 1.2 + - - +
200B VAL* 3.0 25.3 + - + +
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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
----------------------------------------------------------
98B ARG* 3.8 32.3 - - + +
101B LEU* 3.8 21.3 - - + -
193B PHE* 2.8 55.7 + - + +
194B ASN* 3.0 6.5 + - - +
196B THR* 1.3 76.4 - - - +
198B GLU* 1.3 64.8 + - + +
201B GLN* 3.0 54.5 + - + +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 5.6 3.9 + - - -
194B ASN* 2.8 41.0 + - - +
195B GLN* 3.8 6.1 - - - +
197B VAL* 1.3 78.2 - - - +
199B ASN* 1.3 58.8 + - - +
201B GLN* 3.9 12.0 - - - +
202B ARG* 3.0 31.4 + - - +
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Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.9 11.3 - - - +
157A ASP* 2.8 53.7 + - - +
160A HIS* 3.6 33.3 - - + +
164A MSE 4.6 1.6 - - - -
195B GLN* 2.8 31.1 + - - +
196B THR 3.2 1.5 + - - +
198B GLU* 1.3 78.9 - - - +
200B VAL* 1.3 67.9 + - - +
202B ARG* 3.4 3.2 + - - +
203B ILE* 3.1 30.7 + - + +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 5.8 0.2 - - + -
164A MSE 3.6 19.3 - - + -
97B ILE* 3.6 22.4 - - + -
101B LEU* 4.2 11.7 - - + -
168B SER* 3.7 25.1 - - - +
169B THR* 4.6 2.0 - - + -
172B TYR* 4.1 28.5 - - + +
196B THR* 3.0 23.7 + - + +
197B VAL 4.3 0.2 - - - +
199B ASN* 1.3 75.5 - - + +
201B GLN* 1.3 62.8 + - - +
203B ILE* 4.2 0.7 - - - +
204B ILE* 3.1 32.2 + - + +
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Residues in contact with GLN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.0 49.9 + - + +
97B ILE* 4.0 26.2 - - + -
98B ARG* 4.0 16.7 + - - +
197B VAL* 3.0 41.0 + - - +
198B GLU* 3.9 13.2 - - - +
200B VAL* 1.3 75.7 - - - +
202B ARG* 1.3 57.3 + - - +
205B ILE* 2.7 43.4 + - + +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 3.2 29.1 - - - +
155A PRO* 4.2 19.7 + - - +
156A ILE* 3.3 26.4 - - + +
206A GLU 5.1 0.2 + - - -
207A GLY 2.6 29.7 + - - -
209A ARG 4.2 6.5 + - - -
211A ARG* 4.6 11.5 - - - +
198B GLU 3.0 20.5 + - - +
199B ASN* 3.9 3.8 - - - +
201B GLN* 1.3 76.5 - - - +
203B ILE* 1.3 64.4 + - - +
205B ILE* 4.9 1.6 - - - -
206B GLU* 2.8 67.5 + - + +
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Residues in contact with ILE 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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156A ILE* 3.9 23.3 - - + -
160A HIS 4.9 0.7 - - - -
161A LEU* 3.7 37.9 - - + +
164A MSE 3.7 36.3 - - + -
203A ILE* 3.8 2.4 - - + +
204A ILE* 4.0 31.6 - - + +
207A GLY* 3.2 16.1 - - - -
208A ILE* 4.1 8.1 - - + -
199B ASN* 3.1 16.8 + - + +
202B ARG* 1.3 77.8 - - - +
204B ILE* 1.3 66.3 + - - +
207B GLY* 3.0 18.5 + - - -
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Residues in contact with ILE 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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164A MSE 4.2 11.0 - - - -
203A ILE* 4.0 9.8 - - + +
93B ILE* 4.6 2.0 - - + -
97B ILE* 4.1 15.9 - - + -
161B LEU* 3.9 26.7 - - + -
164B MSE 3.7 28.7 - - + -
165B ILE* 4.0 16.4 - - + -
168B SER* 3.7 19.7 - - - +
200B VAL* 3.1 26.3 + - + +
201B GLN 4.1 0.4 - - - +
203B ILE* 1.3 77.4 - - - +
205B ILE* 1.3 64.3 + - - +
207B GLY* 3.0 11.3 + - - -
208B ILE* 3.1 20.2 + - + +
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Residues in contact with ILE 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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90B LEU* 3.6 41.5 - - + +
93B ILE* 3.6 33.7 - - + -
94B LYS* 3.8 29.2 - - + -
97B ILE* 4.7 2.5 - - + -
201B GLN* 2.7 28.3 + - - +
202B ARG* 4.9 1.3 - - - -
204B ILE* 1.3 70.5 - - - +
206B GLU* 1.3 60.8 + - + +
208B ILE* 2.8 22.4 + - + +
209B ARG* 2.9 35.5 + - - +
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Residues in contact with GLU 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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206A GLU* 3.8 6.8 - - - +
207A GLY* 4.0 6.3 - - - +
211A ARG* 4.7 3.3 - - - +
202B ARG* 2.8 65.6 + - + +
205B ILE* 1.3 75.6 - - + +
207B GLY* 1.3 59.4 + - - +
208B ILE 3.3 0.7 + - - -
209B ARG* 2.9 41.3 + - - +
211B ARG* 2.7 53.7 + - - +
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Residues in contact with GLY 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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202A ARG* 4.3 7.1 - - - +
203A ILE* 3.4 30.8 - - - +
206A GLU* 3.9 14.2 - - - +
207A GLY* 3.5 7.4 - - - -
154B ALA* 4.7 5.4 - - - +
156B ILE* 5.4 0.2 - - - +
203B ILE 3.0 8.1 + - - -
204B ILE 3.0 9.8 + - - -
206B GLU* 1.3 78.8 - - - +
208B ILE* 1.3 66.0 + - - +
209B ARG 5.2 0.7 - - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 4.2 24.2 - - + -
90B LEU* 4.0 11.0 - - + -
93B ILE* 3.5 31.6 - - + -
153B LEU* 3.4 18.3 - - + +
154B ALA* 2.9 29.9 + - + +
156B ILE* 4.6 17.5 - - + -
161B LEU* 4.1 20.9 - - + -
204B ILE* 3.5 14.1 - - + +
205B ILE* 2.8 20.6 + - + +
207B GLY* 1.3 84.4 - - - +
209B ARG* 1.3 63.4 + - - +
210B PRO 3.5 0.2 - - - -
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.4 27.0 - - + +
94B LYS* 5.3 7.7 - - - +
154B ALA* 3.4 10.4 - - - +
205B ILE* 2.9 25.9 + - - +
206B GLU* 2.9 33.2 + - - +
207B GLY 5.2 0.2 - - - -
208B ILE* 1.3 78.6 - - - +
210B PRO* 1.3 84.2 - - + +
211B ARG* 3.5 41.0 + - - +
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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
------------------------------------------------------------
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