Contacts of the helix formed by residues 188 - 198 (chain J) in PDB entry 1I43
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 188 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184J ILE* 3.4 23.1 - - - +
185J ASP* 3.1 29.9 + - + +
186J PRO 5.1 0.4 - - - -
187J ALA* 1.3 74.4 - - - +
189J VAL* 1.3 59.8 + - - +
190J GLY* 3.3 4.9 + - - -
191J ALA* 2.8 42.5 + - + +
192J LEU 3.6 2.3 + - - -
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Residues in contact with VAL 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J PRO 5.5 2.0 - - - +
187J ALA* 2.7 20.7 + - - +
188J ASP* 1.3 72.3 - - - +
190J GLY* 1.3 61.9 + - - +
192J LEU* 3.2 11.5 + - + +
193J GLU* 2.9 28.2 + - - +
218J ASP* 6.0 2.5 - - + -
221J LEU* 3.9 27.4 - - + -
222J VAL* 5.4 8.1 - - + -
225J LEU* 3.4 27.6 - - + -
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Residues in contact with GLY 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J ASP* 3.3 4.8 + - - -
189J VAL* 1.3 77.3 - - - +
191J ALA* 1.3 54.1 + - - +
193J GLU* 3.1 12.5 + - - +
194J LEU* 2.8 35.6 + - - +
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Residues in contact with ALA 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J ILE* 3.7 24.4 - - + +
188J ASP* 2.8 35.4 + - - +
190J GLY* 1.3 76.1 - - - +
192J LEU* 1.3 57.1 + - - +
194J LEU* 3.2 10.1 + - - +
195J ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J VAL* 3.9 14.1 - - + -
184J ILE* 3.6 16.7 - - + +
188J ASP 3.6 3.2 + - - +
189J VAL* 3.2 9.8 + - + +
190J GLY 3.2 0.2 - - - -
191J ALA* 1.3 80.1 - - - +
193J GLU* 1.3 57.4 + - - +
195J ALA* 3.5 4.5 + - - +
196J LEU* 2.9 54.8 + - + +
201J VAL* 6.3 0.2 - - + -
204J PHE* 3.9 36.1 - - + -
222J VAL* 3.7 39.5 - - + +
225J LEU* 4.1 20.9 - - + -
226J CYS* 4.4 2.9 - - - -
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Residues in contact with GLU 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J VAL* 2.9 15.1 + - - +
190J GLY* 3.1 15.0 + - - +
192J LEU* 1.3 76.2 - - - +
194J LEU* 1.3 63.4 + - - +
196J LEU* 3.3 15.7 - - + +
197J ASN* 3.2 31.4 + - - +
225J LEU* 4.6 23.4 - - + +
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Residues in contact with LEU 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J GLY 2.8 12.6 + - - +
191J ALA* 3.4 11.4 - - - +
193J GLU* 1.3 73.7 - - - +
195J ALA* 1.3 55.7 + - - +
196J LEU 3.0 1.1 - - - -
197J ASN* 2.7 29.8 + - + +
198J GLN* 2.9 48.7 + - + +
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Residues in contact with ALA 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J HIS* 5.5 0.2 - - - +
157J VAL* 4.5 12.3 - - + -
182J THR* 3.9 32.1 - - + +
191J ALA 2.9 19.0 + - - +
192J LEU* 3.9 4.9 - - - +
194J LEU* 1.3 74.3 - - - +
196J LEU* 1.3 62.0 + - - +
197J ASN 3.2 0.3 + - - -
198J GLN* 4.0 14.3 + - - +
199J LYS* 3.0 29.9 + - + +
201J VAL* 3.6 7.2 - - + +
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Residues in contact with LEU 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J LEU* 2.9 54.2 + - + +
193J GLU* 3.3 12.8 - - + +
194J LEU 3.0 0.2 - - - -
195J ALA* 1.3 75.3 - - - +
197J ASN* 1.3 59.2 + - - +
199J LYS 3.6 8.7 - - - +
200J LYS* 5.2 0.7 - - - -
201J VAL* 3.7 31.1 + - + +
225J LEU* 4.1 9.9 - - + +
226J CYS* 3.9 16.6 - - - +
229J LYS* 3.6 48.3 - - + +
231J ALA* 4.0 13.2 - - + -
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Residues in contact with ASN 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J GLU* 3.2 26.3 + - - +
194J LEU* 2.7 19.1 + - + +
196J LEU* 1.3 75.5 - - - +
198J GLN* 1.3 71.0 + - + +
199J LYS 3.8 2.1 - - - +
229J LYS* 3.4 30.0 + - - +
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Residues in contact with GLN 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194J LEU* 2.9 54.0 + - + +
195J ALA* 3.6 9.9 + - - +
197J ASN* 1.3 79.4 - - - +
199J LYS* 1.3 84.6 + - + +
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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