Contacts of the helix formed by residues 176 - 194 (chain B) in PDB entry 3LXA
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 SER 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B CYS* 3.3 10.0 - - - -
175B ASP* 1.3 85.6 + - - +
177B LEU* 1.3 63.1 + - - +
178B GLU* 3.5 12.7 + - - +
179B ASN* 3.1 27.4 + - - +
180B LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 177 (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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176B SER* 1.3 73.2 - - - +
178B GLU* 1.3 60.9 + - - +
180B LEU* 3.4 13.1 - - + +
181B ALA* 2.9 31.4 + - - +
207B TYR 3.8 21.5 - - - +
208B MET* 3.8 26.8 - - + +
211B PHE* 3.1 56.5 - - + -
212B GLN* 3.4 18.4 - - + +
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Residues in contact with GLU 178 (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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176B SER* 3.5 11.4 + - - +
177B LEU* 1.3 79.6 - - - +
179B ASN* 1.3 67.5 + - - +
181B ALA* 3.5 4.6 + - - +
182B ASP* 3.0 35.2 + - - +
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Residues in contact with ASN 179 (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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137B VAL* 4.8 0.8 - - - +
149B PHE* 3.9 18.9 - - + -
152B TYR* 5.2 0.9 + - - -
174B CYS* 3.7 8.1 - - - -
175B ASP* 2.8 31.8 - - - +
176B SER* 3.1 16.4 + - - +
178B GLU* 1.3 81.7 - - - +
180B LEU* 1.3 69.2 + - - +
182B ASP* 2.8 11.2 + - - +
183B GLY* 2.8 24.4 + - - -
639B NAG 3.7 12.3 + - + +
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Residues in contact with LEU 180 (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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137B VAL* 3.9 16.8 - - + +
171B GLY* 4.0 17.3 - - - +
174B CYS* 3.2 13.6 - - + -
176B SER 3.0 15.1 + - - +
177B LEU* 3.4 27.4 - - + +
179B ASN* 1.3 76.4 - - - +
181B ALA* 1.3 62.5 + - - +
183B GLY* 3.4 0.5 + - - -
184B TYR* 3.2 51.7 + - + -
204B TRP* 3.8 35.9 - - + +
207B TYR* 4.1 17.0 - - + -
208B MET* 4.6 5.2 - - + +
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Residues in contact with ALA 181 (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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177B LEU 2.9 19.9 + - - +
178B GLU* 3.8 5.2 - - - +
180B LEU* 1.3 72.6 - - - +
182B ASP* 1.3 63.2 + - - +
184B TYR* 3.5 2.8 + - - +
185B LYS* 3.1 40.7 + - - +
204B TRP* 4.0 31.4 - - + +
208B MET* 5.7 3.1 - - + -
218B GLU* 5.1 1.3 - - - +
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Residues in contact with ASP 182 (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 TYR* 5.3 0.2 - - - -
178B GLU* 3.0 24.3 + - - +
179B ASN* 2.8 16.4 + - - +
181B ALA* 1.3 74.8 - - - +
183B GLY* 1.3 56.7 + - - +
185B LYS* 2.9 18.8 + - - +
186B HIS* 2.7 38.0 + - + +
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Residues in contact with GLY 183 (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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137B VAL* 3.4 14.4 - - - -
152B TYR* 3.3 36.5 - - - -
169B PHE* 4.0 1.2 - - - -
179B ASN 2.8 14.5 + - - -
182B ASP* 1.3 72.2 - - - +
184B TYR* 1.3 56.1 + - - +
186B HIS* 3.7 0.5 - - - +
187B MET* 2.9 33.1 + - - +
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Residues in contact with TYR 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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137B VAL* 3.6 8.0 - - + +
169B PHE* 2.6 41.3 + + - -
170B ASP 3.0 19.7 - - - -
171B GLY 3.3 2.8 + - - -
180B LEU* 3.2 47.6 + - + +
181B ALA 3.8 1.6 - - - +
182B ASP 3.1 0.6 - - - -
183B GLY* 1.3 75.3 - - - +
185B LYS* 1.3 61.2 + - - +
188B SER* 3.1 13.9 + - - -
200B TYR* 2.8 33.5 + - + -
202B CYS* 3.4 23.6 - - + -
203B SER 3.1 9.1 + - - -
204B TRP* 3.3 54.7 + + + -
222B TYR* 5.3 0.4 - - - -
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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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181B ALA* 3.1 33.0 + - - +
182B ASP* 2.9 19.6 + - - +
184B TYR* 1.3 70.4 - - - +
186B HIS* 1.3 65.3 + - - +
188B SER* 3.3 3.3 - - - -
189B LEU* 3.2 30.9 + - + +
204B TRP* 4.0 7.4 - - + -
218B GLU* 2.7 36.4 + - - -
222B TYR* 3.5 50.4 - - + +
715B NAG 5.6 0.7 - - - -
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Residues in contact with HIS 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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152B TYR* 3.6 32.7 - + + +
153B ASP* 3.1 26.0 + - - -
182B ASP* 2.7 21.5 + - + +
183B GLY 3.7 4.0 - - - +
185B LYS* 1.3 70.7 - - - +
187B MET* 1.3 53.9 + - - +
189B LEU* 3.0 11.2 + - + +
190B ALA* 2.7 33.8 + - + -
193B ARG* 3.8 17.9 + - - -
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Residues in contact with MET 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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148B SER* 4.5 2.5 - - - +
152B TYR* 3.7 35.6 - - + +
155B ASP* 4.1 17.7 - - + -
156B ALA* 4.0 14.6 - - - +
159B PHE* 4.2 6.7 - - + -
167B LEU* 3.9 15.7 - - + -
169B PHE* 3.5 44.6 - - + -
183B GLY 2.9 7.9 + - - +
186B HIS* 1.3 76.6 - - - +
188B SER* 1.3 54.9 + - - +
190B ALA* 4.0 2.5 - - - -
191B LEU* 2.8 45.9 + - + +
200B TYR* 3.4 27.1 - - + +
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Residues in contact with SER 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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32B LEU* 4.1 10.9 - - - +
184B TYR 3.1 15.3 + - - -
185B LYS 3.3 11.4 - - - -
187B MET* 1.3 77.6 - - - +
189B LEU* 1.3 61.4 + - - +
191B LEU* 3.8 4.2 - - - +
192B ASN* 3.2 20.8 + - - +
200B TYR* 3.6 17.6 + - - -
222B TYR* 2.6 43.4 + - - +
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Residues in contact with LEU 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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185B LYS* 3.2 20.9 - - + +
186B HIS* 3.0 9.0 + - + +
188B SER* 1.3 74.2 - - - +
190B ALA* 1.3 56.2 + - - +
192B ASN* 2.9 12.6 + - + +
193B ARG* 2.7 58.8 + - + +
222B TYR* 4.2 21.1 - - + +
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Residues in contact with ALA 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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152B TYR 4.0 10.3 - - - +
153B ASP* 3.6 20.4 - - - +
156B ALA* 3.7 18.9 - - + +
186B HIS* 2.7 22.8 + - + +
187B MET* 3.7 8.1 - - - +
189B LEU* 1.3 72.1 - - - +
191B LEU* 1.3 62.9 + - - +
193B ARG* 3.2 16.6 + - - +
194B THR* 3.2 23.6 + - - +
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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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156B ALA* 3.7 23.3 - - + +
159B PHE* 4.9 5.2 - - + -
167B LEU* 4.1 11.2 - - + -
187B MET* 2.8 33.1 + - + +
188B SER* 3.8 4.7 - - - +
190B ALA* 1.3 72.9 - - - +
192B ASN* 1.3 60.6 + - - +
194B THR* 2.7 25.7 + - - -
195B GLY 3.8 0.7 + - - -
196B ARG 4.1 7.7 - - - +
198B ILE* 3.6 43.6 - - + +
200B TYR* 3.3 44.2 - - + -
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Residues in contact with ASN 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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32B LEU* 6.1 3.6 - - + +
34B ASN* 5.3 1.4 - - - +
188B SER 3.2 12.5 + - - +
189B LEU* 2.9 15.6 + - + +
191B LEU* 1.3 78.9 - - - +
193B ARG* 1.3 62.4 + - - +
195B GLY* 3.0 21.8 + - - -
1E NAG 1.4 77.7 + - - +
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Residues in contact with ARG 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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153B ASP* 2.7 33.3 + - - -
157B GLN* 4.7 2.4 - - - +
186B HIS* 3.8 14.8 + - - -
189B LEU* 2.7 45.8 + - + +
190B ALA* 3.6 16.5 - - - +
191B LEU 3.2 0.2 - - - -
192B ASN* 1.3 74.4 - - - +
194B THR* 1.3 60.9 + - - +
195B GLY* 3.0 7.6 + - - -
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Residues in contact with THR 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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156B ALA* 3.6 32.5 - - + +
157B GLN* 3.6 27.5 + - + +
160B ALA* 3.4 22.5 - - + +
190B ALA 3.2 16.5 + - - +
191B LEU* 2.7 17.9 + - + +
193B ARG* 1.3 75.0 - - - +
195B GLY* 1.3 56.2 + - - +
196B ARG* 3.2 16.7 + - - +
198B ILE* 4.3 2.6 - - - +
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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
------------------------------------------------------------
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