Contacts of the helix formed by residues 189 - 200 (chain B) in PDB entry 1LK7
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
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Residue Dist Surf HB Arom Phob DC
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187B ILE* 3.1 4.8 - - - +
188B ASP* 1.3 93.4 - - + +
190B PRO* 1.3 64.1 - - - +
191B LEU 3.4 3.2 + - - -
192B ASP* 2.7 32.6 + - + +
193B MET* 3.1 22.0 + - - +
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Residues in contact with PRO 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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91B ASP* 3.8 15.3 - - - +
95B ASN* 3.9 17.5 - - - +
130B LEU* 3.7 29.6 - - + -
187B ILE* 3.2 26.0 - - + +
188B ASP 3.1 11.9 - - - +
189B ASP* 1.3 83.3 - - - +
191B LEU* 1.3 59.1 + - - +
193B MET* 3.4 1.7 + - - +
194B GLU* 2.9 30.3 + - - +
208B ILE* 3.5 6.1 - - + +
210B ALA* 4.0 9.6 - - + -
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Residues in contact with LEU 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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95B ASN* 5.5 0.2 - - - +
189B ASP 3.4 0.8 - - - -
190B PRO* 1.3 80.1 - - - +
192B ASP* 1.3 65.7 + - - +
194B GLU* 3.4 13.1 + - - +
195B ILE* 3.1 40.9 + - + +
210B ALA* 3.7 29.8 - - + +
211B ASP* 4.0 23.8 - - + +
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Residues in contact with ASP 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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189B ASP* 2.7 38.2 + - + +
190B PRO 3.3 0.4 - - - -
191B LEU* 1.3 82.3 - - - +
193B MET* 1.3 56.5 - - - +
195B ILE* 3.4 10.2 + - - +
196B GLU* 3.0 27.8 + - - +
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Residues in contact with MET 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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155B PHE* 6.2 2.2 - - + -
184B PHE* 4.1 37.0 - - + -
186B ARG 6.1 0.9 - - - +
187B ILE* 4.2 15.0 - - + -
189B ASP 3.1 14.2 + - - +
190B PRO 3.9 2.9 - - - +
192B ASP* 1.3 77.2 - - - +
194B GLU* 1.3 62.0 + - - +
196B GLU* 3.8 12.7 - - - +
197B LEU* 2.9 46.5 + - + +
208B ILE* 3.7 19.5 - - + -
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Residues in contact with GLU 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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108B LYS* 3.0 30.5 + - - +
190B PRO 2.9 16.7 + - - +
191B LEU* 3.5 14.7 - - + +
193B MET* 1.3 77.2 - - - +
195B ILE* 1.3 62.3 + - + +
198B ASN* 3.3 14.5 + - - +
206B ASN* 2.8 32.1 - - - +
208B ILE* 2.9 26.1 - - + +
209B PHE* 4.4 0.3 - - - -
210B ALA* 2.7 41.2 + - - +
212B ILE* 6.0 0.3 - - - +
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Residues in contact with ILE 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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195A ILE* 4.3 9.4 - - + -
199A THR* 3.9 32.0 - - + +
191B LEU* 3.1 38.7 + - + +
192B ASP* 3.7 11.4 - - - +
194B GLU* 1.3 75.1 - - + +
196B GLU* 1.3 66.4 + - - +
198B ASN* 3.2 8.8 + - - +
199B THR* 3.0 35.6 + - + +
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Residues in contact with GLU 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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192B ASP 3.0 17.7 + - - +
193B MET* 3.3 15.5 + - - +
195B ILE* 1.3 78.4 - - - +
197B LEU* 1.3 65.3 + - + +
199B THR* 2.7 30.7 + - - +
200B ILE* 3.5 16.1 + - + +
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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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136B VAL* 4.4 5.4 - - + -
138B ILE* 4.1 16.4 - - + -
152B LEU* 3.5 31.9 - - + -
184B PHE* 4.5 7.2 - - + -
193B MET* 2.9 45.1 + - + +
196B GLU* 1.3 76.9 - - + +
198B ASN* 1.3 63.0 + - - +
200B ILE* 3.2 22.8 + - + +
203B VAL* 3.3 24.5 - - + +
206B ASN* 3.6 38.8 - - + +
208B ILE* 4.1 5.4 - - + -
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Residues in contact with ASN 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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198A ASN* 4.2 32.3 - - - +
199A THR* 5.2 7.6 - - + +
108B LYS* 4.5 2.4 + - - +
194B GLU* 3.3 7.7 + - - +
195B ILE* 3.2 10.8 + - - +
197B LEU* 1.3 79.8 - - - +
199B THR* 1.3 60.3 + - + +
200B ILE 3.3 6.5 + - - +
203B VAL* 3.7 15.5 - - - +
204B ILE 4.2 4.2 - - - -
205B GLU* 2.9 48.2 - - - +
206B ASN* 2.9 23.2 + - - +
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Residues in contact with THR 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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108A LYS* 6.0 0.2 - - - +
112A TYR* 5.4 1.4 - - - -
195A ILE* 4.0 43.7 - - + +
198A ASN* 4.9 13.3 - - + +
199A THR* 5.3 1.6 - - + -
195B ILE* 3.0 19.0 + - + +
196B GLU* 2.7 31.2 + - - +
198B ASN* 1.3 75.0 - - - +
200B ILE* 1.3 62.7 + - - +
201B PRO* 3.4 10.2 - - - +
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Residues in contact with ILE 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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112A TYR* 4.4 12.6 - - + +
113A ARG* 3.5 24.0 - - - +
148B ILE* 4.3 5.8 - - + -
151B GLU* 3.9 17.5 - - + +
152B LEU* 4.6 11.2 - - + -
196B GLU* 3.7 17.3 - - + +
197B LEU* 3.2 32.2 + - + +
198B ASN 3.8 1.6 - - - +
199B THR* 1.3 78.7 - - - +
201B PRO* 1.3 74.1 - - + +
202B GLY 3.2 0.5 + - - -
203B VAL* 3.0 38.8 + - + +
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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