Contacts of the helix formed by residues 183 - 199 (chain B) in PDB entry 1ADI
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ALA* 2.8 32.4 + - - +
161B LEU* 3.7 20.9 - - + -
162B LYS* 3.3 63.0 + - + -
165B MET* 3.8 26.9 - - + -
169B ASN* 5.6 1.8 - - - +
181B VAL 3.5 4.8 + - - +
182B ASP* 1.3 68.0 + - - +
184B GLN* 1.3 97.1 + - + +
185B LYS 3.0 2.0 - - - -
186B VAL* 3.0 4.3 + - - +
187B LEU* 3.0 35.1 + - + +
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Residues in contact with GLN 184 (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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182B ASP* 3.5 11.0 + - - +
183B TYR* 1.3 96.9 - - + +
185B LYS* 1.3 55.5 + - - +
187B LEU* 3.4 17.2 + - - +
188B ASP* 2.5 64.0 + - - +
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Residues in contact with LYS 185 (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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108B ASP* 2.8 27.2 + - - -
181B VAL* 6.0 2.2 - - - -
182B ASP* 3.3 26.8 + - + +
183B TYR 3.0 0.2 + - - -
184B GLN* 1.3 79.9 - - - +
186B VAL* 1.3 53.1 + - - +
188B ASP* 3.2 5.4 + - - +
189B ASP* 2.6 74.5 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.2 22.9 - - + -
108B ASP* 3.9 31.0 - - + +
109B TYR* 4.5 3.6 - - + -
161B LEU* 4.1 20.9 - - + -
165B MET* 4.3 10.8 - - - -
181B VAL* 4.0 10.8 - - + -
182B ASP 3.6 13.9 - - - +
183B TYR 3.0 6.4 + - - +
185B LYS* 1.3 73.2 - - + +
187B LEU* 1.3 58.9 + - - +
189B ASP* 3.9 6.6 - - - +
190B THR* 2.6 45.9 + - - +
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Residues in contact with LEU 187 (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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157B PHE* 3.3 34.8 - - + -
158B ALA* 3.6 26.7 - - + -
161B LEU* 3.5 19.4 - - + +
183B TYR* 3.0 23.3 + - + +
184B GLN* 3.7 24.5 - - - +
186B VAL* 1.3 76.3 - - - +
188B ASP* 1.3 54.3 + - - +
190B THR* 3.6 2.2 - - - -
191B MET* 2.7 54.5 + - + +
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Residues in contact with ASP 188 (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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184B GLN* 2.5 55.9 + - - +
185B LYS* 3.6 5.1 - - - +
187B LEU* 1.3 74.0 - - - +
189B ASP* 1.3 70.9 + - - +
191B MET* 3.6 5.8 + - - +
192B ALA* 3.3 19.4 + - - +
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Residues in contact with ASP 189 (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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108B ASP* 4.5 1.0 - - - +
185B LYS* 2.6 63.4 + - - +
186B VAL* 3.9 6.0 - - + +
188B ASP* 1.3 79.4 - - - +
190B THR* 1.3 63.0 + - - +
192B ALA* 3.2 18.7 + - - +
193B VAL* 3.8 8.7 + - - +
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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
----------------------------------------------------------
76B PRO* 5.2 12.8 - - + -
105B LEU* 5.4 3.1 - - + -
107B LEU* 3.7 26.9 - - + +
151B LEU* 3.8 19.7 - - + -
157B PHE* 3.5 30.1 - - + -
186B VAL* 2.6 27.2 + - - +
187B LEU 3.8 2.5 - - - -
189B ASP* 1.3 75.3 - - - +
191B MET* 1.3 64.9 + - - +
192B ALA 3.1 0.5 + - - -
193B VAL* 3.4 4.9 + - - +
194B ALA* 3.2 18.6 + - - +
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Residues in contact with MET 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 5.7 2.2 - - - -
154B LYS* 3.4 56.6 + - + +
157B PHE* 3.4 32.1 - - + -
158B ALA* 5.1 0.7 - - + -
187B LEU* 2.7 40.4 + - + +
188B ASP* 4.1 5.6 - - - +
189B ASP 3.5 0.2 - - - -
190B THR* 1.3 73.2 - - - +
192B ALA* 1.3 62.5 + - - +
194B ALA* 3.5 18.3 + - - +
195B ASP* 4.8 1.4 + - - +
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Residues in contact with ALA 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 ASP 3.3 10.9 + - - +
189B ASP* 3.2 14.7 + - - +
190B THR 3.1 0.8 - - - -
191B MET* 1.3 77.4 - - - +
193B VAL* 1.3 62.2 + - + +
194B ALA 3.3 0.2 - - - -
195B ASP* 3.0 17.8 - - - +
196B ILE* 4.6 3.5 - - - +
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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
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76B PRO* 5.0 12.1 - - + -
80B MET* 3.1 56.1 - - + -
189B ASP 3.8 9.1 + - - +
190B THR* 3.4 7.7 + - - +
192B ALA* 1.3 78.5 - - + +
194B ALA* 1.3 63.9 + - - +
195B ASP* 3.4 4.0 - - - -
196B ILE* 3.1 14.8 + - + -
197B LEU* 3.0 32.1 + - + +
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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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151B LEU* 4.7 27.6 - - + +
154B LYS* 5.0 9.6 - - + -
190B THR 3.2 12.6 + - - +
191B MET* 3.6 27.4 - - - +
192B ALA 3.3 2.6 - - - -
193B VAL* 1.3 77.4 - - - +
195B ASP* 1.3 64.6 + - - +
196B ILE 3.2 0.7 + - - -
197B LEU* 3.2 1.7 + - - +
198B THR* 3.1 29.3 + - - +
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Residues in contact with ASP 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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94B ARG* 4.9 1.6 - - - -
191B MET 4.8 1.0 + - - -
192B ALA 3.0 22.6 - - - +
194B ALA* 1.3 74.7 - - - +
196B ILE* 1.3 80.3 + - - +
198B THR* 3.5 6.3 + - - -
199B SER* 3.4 21.5 + - - -
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Residues in contact with ILE 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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80B MET* 3.5 31.4 - - + -
83B MET* 4.9 9.6 - - + -
94B ARG* 3.1 46.0 - - - +
192B ALA 4.6 2.2 - - - +
193B VAL* 3.4 21.3 - - + +
194B ALA 3.1 0.6 - - - -
195B ASP* 1.3 94.7 - - - +
197B LEU* 1.3 63.3 + - + +
199B SER* 2.6 22.3 + - - -
200B MET* 3.3 9.9 - - - +
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Residues in contact with LEU 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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74B LEU* 3.7 28.0 - - + -
76B PRO* 4.3 21.1 - - + -
79B LEU* 4.0 26.2 - - + -
80B MET* 5.0 1.1 - - - -
99B LEU* 4.3 12.0 - - + +
105B LEU* 4.3 2.7 - - + -
148B VAL* 4.3 8.5 - - + -
151B LEU* 4.1 25.4 - - + -
193B VAL* 3.0 36.7 + - + +
194B ALA 3.2 2.6 + - - +
196B ILE* 1.3 76.0 - - + +
198B THR* 1.3 60.6 + - - +
200B MET* 2.8 29.5 + - - +
201B VAL* 3.5 11.4 + - - +
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Residues in contact with THR 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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148B VAL* 4.6 4.9 - - + +
151B LEU* 4.1 26.5 - - + -
152B PHE* 3.6 48.4 - - + +
194B ALA 3.1 15.0 + - - +
195B ASP* 3.5 8.7 + - - -
197B LEU* 1.3 76.9 - - - +
199B SER* 1.3 60.9 + - - +
200B MET 3.2 0.7 + - - -
201B VAL* 3.3 22.3 + - + +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 3.4 19.4 + - - -
98B LEU* 5.7 1.0 - - - +
195B ASP 3.4 13.6 + - - -
196B ILE 2.6 21.7 + - - -
197B LEU 3.0 1.0 + - - -
198B THR* 1.3 76.8 + - - +
200B MET* 1.3 64.2 + - - +
201B VAL 3.6 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