Contacts of the helix formed by residues 185 - 198 (chain B) in PDB entry 1TU8
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 ARG 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.0 45.7 + - - +
24B GLN* 4.7 2.6 - - - +
141B LEU* 4.1 16.9 - - - +
147B ILE* 3.5 30.1 - - - +
181B ARG* 3.3 15.3 + - + +
182B MET* 3.2 37.1 + - - +
184B ASP* 1.3 75.1 - - - +
186B PRO* 1.3 75.9 - - + +
187B LYS 3.3 1.8 - - - -
188B LEU* 3.1 9.1 + - + -
189B LYS 2.8 19.1 + - - -
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Residues in contact with PRO 186 (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 ASP 3.2 7.4 - - - +
185B ARG* 1.3 83.9 - - + +
187B LYS* 1.3 68.0 + - + +
189B LYS* 3.4 7.9 + - + +
190B GLU* 3.3 23.0 + - - +
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Residues in contact with LYS 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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22B VAL* 3.5 28.7 - - + +
23B ASP* 3.1 32.9 + - - +
24B GLN* 4.2 3.2 + - - +
25B ASP* 3.7 29.0 - - + +
185B ARG* 3.3 1.4 - - - +
186B PRO* 1.3 81.6 - - + +
188B LEU* 1.3 57.5 + - - +
190B GLU* 3.8 10.5 + - - +
191B TYR* 3.2 26.7 + - - +
194B LYS* 5.7 0.2 + - - -
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Residues in contact with LEU 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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19B LEU* 3.7 41.1 - - + +
22B VAL* 4.1 9.2 - - + -
23B ASP* 3.7 32.7 + - + +
152B TYR* 4.4 3.4 - - + -
155B PHE* 4.2 12.3 - - + -
182B MET* 3.5 50.3 - - + +
183B LYS* 4.0 2.2 - - - +
185B ARG* 3.1 5.2 + - - +
187B LYS* 1.3 76.3 - - - +
189B LYS* 1.3 58.2 + - - +
191B TYR* 4.2 2.7 - - + -
192B CYS* 2.8 41.5 + - - -
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Residues in contact with LYS 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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183B LYS* 3.2 22.6 + - + +
184B ASP* 4.4 19.3 + - - +
185B ARG 2.8 14.2 + - - +
186B PRO* 3.4 9.4 + - + +
188B LEU* 1.3 75.6 - - - +
190B GLU* 1.3 62.2 + - - +
192B CYS* 3.9 3.9 - - - +
193B GLU* 3.1 49.6 + - + +
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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
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186B PRO 3.3 13.3 + - - +
187B LYS* 3.9 8.9 - - - +
189B LYS* 1.3 80.5 - - - +
191B TYR* 1.3 61.4 + - - +
193B GLU* 3.3 15.6 + - - +
194B LYS* 3.2 49.3 + - + +
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Residues in contact with TYR 191 (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 GLU* 2.7 35.9 + - - -
18B ARG* 3.7 17.8 - - + +
19B LEU* 3.8 27.8 - - + -
22B VAL* 3.8 35.9 - - + -
28B PHE* 6.3 0.7 - + - -
30B ASP* 5.6 3.1 - - - -
32B ARG* 4.7 5.9 + - - -
187B LYS 3.2 17.6 + - - +
188B LEU* 3.8 3.6 - - + +
189B LYS 3.4 0.2 - - - -
190B GLU* 1.3 78.7 - - - +
192B CYS* 1.3 63.3 + - - +
194B LYS* 3.3 22.9 + - + +
195B ARG* 2.9 41.9 + - + +
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Residues in contact with CYS 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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19B LEU* 4.7 2.0 - - - -
155B PHE* 4.0 27.1 - - - -
183B LYS* 4.6 22.7 - - + -
188B LEU 2.8 28.1 + - - +
189B LYS 3.9 2.7 - - - +
191B TYR* 1.3 77.8 - - - +
193B GLU* 1.3 60.2 + - - +
195B ARG* 3.5 36.0 + - - +
196B ASP* 3.0 35.2 + - - +
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Residues in contact with GLU 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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189B LYS* 3.1 46.0 + - + +
190B GLU* 3.6 15.4 - - - +
191B TYR 3.3 0.2 - - - -
192B CYS* 1.3 77.0 - - - +
194B LYS* 1.3 57.7 + - + +
196B ASP* 3.4 6.1 + - - +
197B ALA* 3.0 29.0 + - - +
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Residues in contact with LYS 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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22B VAL* 6.3 0.2 - - - +
190B GLU* 3.2 45.8 + - + +
191B TYR* 3.7 23.5 - - + +
193B GLU* 1.3 76.5 - - + +
195B ARG* 1.3 66.1 + - - +
197B ALA* 3.4 7.4 + - - +
198B ALA* 3.2 24.6 + - - +
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Residues in contact with ARG 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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11B ARG* 3.4 40.5 - - - +
15B GLU* 2.9 33.3 + - - +
19B LEU* 4.1 6.5 - - - +
155B PHE* 5.0 3.4 - - - -
156B GLU* 3.3 20.6 + - - -
159B ASP* 3.5 15.6 + - - -
191B TYR* 2.9 32.4 + - + +
192B CYS* 3.5 32.7 + - - +
194B LYS* 1.3 77.2 - - - +
196B ASP* 1.3 61.6 + - - +
198B ALA 3.5 0.5 + - - -
199B LYS 3.1 19.8 + - - -
200B VAL* 3.2 40.3 + - + +
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Residues in contact with ASP 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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11B ARG* 5.9 1.9 + - - -
183B LYS* 5.4 7.3 + - - -
192B CYS* 3.0 21.5 + - - +
193B GLU* 3.6 6.7 - - - +
195B ARG* 1.3 78.7 + - - +
197B ALA* 1.3 64.9 + - - +
199B LYS* 3.0 24.3 + - - +
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Residues in contact with ALA 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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193B GLU 3.0 16.5 + - - +
194B LYS* 3.4 8.7 + - - +
196B ASP* 1.3 77.3 - - - +
198B ALA* 1.3 58.5 + - - +
199B LYS* 3.6 5.4 + - - +
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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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194B LYS 3.2 13.9 + - - +
195B ARG* 4.0 3.6 - - - +
196B ASP 3.2 0.6 - - - -
197B ALA* 1.3 76.4 - - - +
199B LYS* 1.3 71.0 + - - +
200B VAL* 3.3 14.1 + - + +
201B PRO* 5.5 0.2 - - - +
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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