Contacts of the helix formed by residues 189 - 203 (chain B) in PDB entry 1LEI
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B LEU* 5.8 2.4 - - - +
187B THR* 2.9 18.7 - - + +
188B ASP* 1.3 81.5 - - - +
190B GLU* 1.3 83.1 + - - +
192B GLU* 4.1 11.3 - - - +
193B ILE* 4.1 23.0 - - - +
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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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173B LEU* 4.9 7.1 - - + +
176B LEU* 4.6 22.6 - - - +
184B ARG* 5.4 0.9 + - - -
186B LEU* 3.5 20.7 - - + +
187B THR* 2.9 48.3 + - + +
189B ARG* 1.3 97.8 + - - +
191B LYS* 1.3 61.0 + - - +
192B GLU 3.1 2.2 - - - -
193B ILE* 2.7 38.9 - - + +
194B ILE* 3.1 11.6 - - + +
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Residues in contact with LYS 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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152B GLU* 6.2 0.2 - - - +
156B THR* 5.6 8.7 - - + -
185B GLN* 4.2 17.6 - - - +
186B LEU* 3.3 44.9 + - + +
187B THR 2.6 17.9 + - - +
188B ASP* 3.9 23.1 + - - +
189B ARG 3.5 0.2 - - - -
190B GLU* 1.3 73.7 - - - +
192B GLU* 1.3 61.2 + - - +
194B ILE* 3.1 25.8 - - + +
195B ARG* 3.3 8.7 + - - +
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Residues in contact with GLU 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 3.9 14.5 + - - +
189B ARG* 4.1 9.5 - - - +
190B GLU 3.1 0.6 - - - -
191B LYS* 1.3 74.9 - - - +
193B ILE* 1.3 64.6 + - - +
194B ILE 2.9 4.9 - - - -
195B ARG* 2.9 24.1 + - - +
196B GLN* 2.9 49.3 + - + +
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Residues in contact with ILE 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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170B HIS* 4.8 18.1 + - + +
172B ASP* 5.7 2.5 - - + -
173B LEU* 3.3 36.6 - - + -
189B ARG* 4.1 21.5 - - - +
190B GLU* 2.7 33.6 + - + +
192B GLU* 1.3 79.0 - - - +
194B ILE* 1.3 60.9 + - + +
196B GLN* 3.3 23.4 - - + +
197B ALA* 2.8 28.8 + - - +
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Residues in contact with ILE 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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152B GLU* 4.2 3.8 - - + -
155B MET* 2.9 41.7 - - + +
156B THR* 3.5 38.6 - - + +
159B CYS* 3.7 21.1 - - - -
169B VAL* 5.1 6.3 - - + +
173B LEU* 3.5 32.1 - - + -
186B LEU* 5.3 6.5 - - + -
190B GLU* 3.1 16.6 - - + +
191B LYS* 3.1 15.9 - - + +
192B GLU 2.9 0.6 - - - -
193B ILE* 1.3 73.9 - - - +
195B ARG* 1.3 59.1 + - - +
196B GLN 2.9 8.6 + - - -
197B ALA* 3.2 3.1 + - + -
198B ALA 3.2 3.3 + - - -
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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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148B PHE* 4.1 9.5 - - + -
152B GLU* 2.8 35.2 - - - +
191B LYS 3.3 7.2 + - - +
192B GLU* 2.9 26.6 + - - +
194B ILE* 1.3 78.9 - - - +
196B GLN* 1.3 63.4 + - - +
198B ALA* 4.1 3.7 - - - +
199B VAL* 3.2 34.8 + - - +
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Residues in contact with GLN 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 GLU* 2.9 54.8 + - + +
193B ILE* 3.3 26.8 - - + +
194B ILE 2.9 0.2 - - - -
195B ARG* 1.3 87.9 - - - +
197B ALA* 1.3 65.0 + - - +
198B ALA 3.2 1.3 - - - -
199B VAL* 3.4 5.6 + - - +
200B GLN* 3.0 32.1 + - + +
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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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155B MET* 3.9 4.3 - - + -
169B VAL 3.5 15.7 - - - +
170B HIS* 4.9 8.1 - - + +
193B ILE 2.8 16.5 + - - +
194B ILE* 3.8 7.2 - - + +
196B GLN* 1.3 72.8 - - - +
198B ALA* 1.3 61.9 + - - +
200B GLN* 3.2 5.4 + - - +
201B GLN* 2.8 57.5 + - - +
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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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148B PHE* 3.5 24.7 - - + -
151B LEU* 3.4 10.3 - - + +
152B GLU* 3.7 16.8 - - + +
155B MET* 3.2 25.4 - - + +
194B ILE 3.7 5.4 - - - +
195B ARG 4.1 2.7 - - - +
197B ALA* 1.3 78.6 - - - +
199B VAL* 1.3 55.5 + - - +
201B GLN 3.0 0.9 + - - -
202B THR* 2.5 38.7 + - - -
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Residues in contact with VAL 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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148B PHE* 3.6 22.0 - - + -
195B ARG* 3.2 28.2 + - - +
196B GLN* 3.4 9.1 + - - +
197B ALA 3.4 0.4 - - - -
198B ALA* 1.3 76.6 - - - +
200B GLN* 1.3 70.1 + - - +
201B GLN 3.6 0.2 + - - -
202B THR* 4.2 4.9 - - - -
203B LYS* 3.0 35.9 + - + +
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Residues in contact with GLN 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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196B GLN* 3.0 22.4 + - + +
197B ALA* 3.5 6.1 - - - +
198B ALA 3.2 0.4 - - - -
199B VAL* 1.3 93.6 - - - +
201B GLN* 1.3 61.1 + - + +
202B THR 3.6 0.4 - - - -
203B LYS* 3.7 26.4 + - - +
204B GLU* 5.1 4.0 + - - +
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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
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105B HIS* 2.9 54.2 + - + +
106B LEU 4.6 2.2 + - - +
151B LEU* 4.1 11.4 - - + +
155B MET* 3.7 13.0 - - - +
168B LEU 3.9 2.9 - - - +
169B VAL 3.4 13.1 + - - -
197B ALA* 2.8 49.0 + - - +
198B ALA 3.5 1.3 - - - +
200B GLN* 1.3 81.4 - - + +
202B THR* 1.3 63.3 + - - +
203B LYS 3.4 0.7 - - - -
204B GLU 4.3 3.3 + - - +
205B MET* 3.6 27.0 + - + +
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Residues in contact with THR 202 (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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147B VAL* 3.2 40.7 - - + +
148B PHE* 3.5 21.9 - - + +
151B LEU* 3.2 15.1 - - - +
198B ALA 2.5 24.9 + - - -
199B VAL* 4.2 6.1 - - - -
200B GLN 3.6 0.2 - - - -
201B GLN* 1.3 79.9 - - - +
203B LYS* 1.3 66.9 + - + +
204B GLU 3.1 1.7 + - - -
205B MET* 3.4 15.6 + - - +
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Residues in contact with LYS 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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199B VAL* 3.0 28.5 - - + +
200B GLN* 3.7 25.8 + - - +
201B GLN 3.4 0.2 - - - -
202B THR* 1.3 79.2 - - - +
204B GLU* 1.3 82.5 + - + +
205B MET 3.7 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