Contacts of the helix formed by residues 183 - 199 (chain B) in PDB entry 5LN3
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 GLU 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 4.2 5.0 - - - +
42B ASN* 4.8 9.1 + - - +
182B LEU* 1.3 74.3 - - - +
184B LEU* 1.3 82.0 + - - +
185B GLU* 2.9 34.6 + - - +
186B ASP* 3.3 23.4 + - - +
187B ALA* 2.9 28.2 + - - +
82Q LYS* 3.3 27.4 + - - -
120Q GLU 3.8 10.5 - - - +
121Q LYS* 3.4 28.6 - - - +
122Q ARG* 5.5 0.3 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 4.1 17.1 - - + +
42B ASN* 4.9 5.0 - - - +
43B GLY* 4.4 0.2 - - - -
44B VAL 4.1 9.0 - - - +
45B VAL* 3.8 13.5 - - + -
183B GLU* 1.3 81.6 + - - +
185B GLU* 1.4 67.7 + - + +
187B ALA* 3.5 1.9 + - - +
188B ILE* 3.4 40.0 + - + +
212B ILE* 3.7 37.2 - - + -
214B ASN* 3.6 28.9 - - + +
221B LEU* 6.1 1.6 - - + -
229B TYR* 5.2 4.5 - - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 2.9 16.3 + - - +
184B LEU* 1.4 76.6 - - + +
186B ASP* 1.3 64.2 + - - +
188B ILE* 3.3 11.9 + - - +
189B HIS* 3.1 41.5 + - + +
229B TYR* 3.7 24.3 - - + +
82Q LYS* 3.3 33.2 - - + +
83Q ALA* 3.4 27.2 + - - -
86Q ALA* 4.2 5.2 - - - +
120Q GLU* 4.6 0.3 - - - +
122Q ARG* 3.0 32.1 + - + +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.2 15.1 - - + -
183B GLU* 3.3 37.1 + - - +
185B GLU* 1.3 74.9 - - - +
187B ALA* 1.3 63.0 + - - +
189B HIS* 3.2 11.8 + - - -
190B THR* 3.1 24.4 + - - -
121Q LYS* 3.4 10.2 - - - +
122Q ARG* 3.8 23.7 - - - +
123Q THR* 3.9 16.7 + - - +
124Q PHE* 3.2 24.6 - - + +
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Residues in contact with ALA 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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38B ILE* 3.6 25.8 - - + +
40B ALA* 4.2 9.6 - - + -
45B VAL* 3.4 24.9 - - + -
182B LEU* 5.1 7.6 - - + +
183B GLU 2.9 15.8 + - - +
184B LEU 3.6 2.9 - - - +
186B ASP* 1.3 73.8 - - - +
188B ILE* 1.3 57.7 + - - +
190B THR* 3.3 8.8 + - - -
191B ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.9 19.1 - - + -
184B LEU* 3.4 33.9 - - + +
185B GLU 3.3 7.1 + - - +
187B ALA* 1.3 71.0 - - - +
189B HIS* 1.3 67.0 + - - +
191B ALA* 3.4 6.4 + - + +
192B ILE* 3.1 38.2 + - + +
210B VAL* 4.3 18.2 - - + -
212B ILE* 4.5 2.5 - - + -
221B LEU* 4.3 16.4 - - + -
226B VAL* 5.4 1.8 - - + -
229B TYR* 3.7 40.8 - - + -
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Residues in contact with HIS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU* 3.1 33.6 + - + +
186B ASP* 3.2 16.8 + - - +
188B ILE* 1.3 78.4 - - - +
190B THR* 1.3 63.4 + - - +
192B ILE* 3.4 7.5 + - - +
193B LEU* 3.1 20.4 + - - +
229B TYR* 3.2 43.4 + + + +
232B ALA* 4.3 14.4 - - + +
233B ILE* 3.6 21.7 - - + +
122Q ARG* 5.7 2.8 - - - +
124Q PHE* 3.6 41.5 - + + +
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Residues in contact with THR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.3 15.7 - - + -
174B LEU* 4.9 2.0 - - + -
177B ARG* 4.2 10.1 - - + -
178B TYR* 5.7 6.5 - - + -
182B LEU* 5.0 6.9 - - + +
186B ASP 3.1 15.8 + - - -
187B ALA* 3.4 9.9 + - - -
189B HIS* 1.3 74.9 - - - +
191B ALA* 1.3 65.6 + - - +
193B LEU* 3.0 7.7 + - - +
194B THR* 2.8 35.6 + - - +
124Q PHE* 3.3 16.8 - - - -
161Q ASP* 3.3 26.3 + - - +
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Residues in contact with ALA 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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36B VAL* 3.8 21.4 - - + +
38B ILE* 4.0 15.9 - - + +
45B VAL* 4.6 8.5 - - + -
47B ALA* 4.2 12.3 - - + -
187B ALA 2.9 13.4 + - - +
188B ILE* 3.4 4.7 + - + +
190B THR* 1.3 81.4 - - - +
192B ILE* 1.4 56.8 + - + +
194B THR* 3.3 8.1 + - - -
195B LEU* 2.9 33.6 + - - +
210B VAL* 6.2 0.4 - - + -
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.1 34.1 + - + +
189B HIS* 3.8 7.6 - - - +
191B ALA* 1.4 73.9 - - + +
193B LEU* 1.3 64.9 + - - +
195B LEU* 3.3 8.9 + - + +
196B LYS* 2.8 23.6 + - + +
203B MET* 4.2 12.5 - - + +
208B ILE* 3.8 26.2 - - + -
210B VAL* 5.3 3.4 - - + -
226B VAL* 4.7 6.1 - - + -
229B TYR* 4.5 15.5 - - + +
230B LEU* 3.8 35.9 - - + +
233B ILE 5.8 2.0 - - - +
234B ALA 5.9 3.8 - - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 3.2 33.9 - - - +
189B HIS 3.1 13.4 + - - +
190B THR* 3.0 8.8 + - - +
192B ILE* 1.3 74.9 - - - +
194B THR* 1.4 62.4 + - - +
196B LYS* 3.0 34.4 + - + +
197B GLU* 3.0 21.1 + - + +
233B ILE* 6.1 0.2 - - + -
234B ALA* 4.9 10.5 - - - +
124Q PHE* 5.6 0.4 - - + -
161Q ASP* 4.5 8.1 - - + +
162Q ASP* 3.5 43.5 - - - +
163Q LYS* 5.5 1.3 - - - +
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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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36B VAL* 4.1 21.5 - - + -
162B ALA* 5.7 2.5 - - + -
170B GLY* 4.5 10.9 - - - +
173B PHE* 5.5 3.0 - - + +
174B LEU* 4.2 26.1 - - + +
177B ARG* 3.8 22.3 - - - +
190B THR* 2.8 19.6 + - - +
191B ALA* 3.4 10.4 - - - -
193B LEU* 1.4 72.9 - - - +
195B LEU* 1.4 62.9 + - + +
197B GLU* 3.3 8.9 + - - +
198B SER* 3.2 25.8 + - - +
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Residues in contact with LEU 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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34B PRO* 3.6 42.6 - - + +
35B SER 3.8 15.9 - - - +
36B VAL* 3.9 7.2 - - + -
47B ALA* 3.9 26.7 - - + -
48B THR 4.1 18.8 - - - +
49B GLU* 4.5 5.8 - - + +
191B ALA 2.9 19.0 + - - +
192B ILE* 3.8 7.4 - - + +
194B THR* 1.4 75.0 - - + +
196B LYS* 1.3 54.8 + - - +
198B SER* 3.3 7.6 + - - +
199B PHE 2.7 30.8 + - - +
203B MET* 3.9 15.0 - - + -
208B ILE* 5.8 6.1 - - + -
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Residues in contact with LYS 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 ILE* 2.8 15.6 + - + +
193B LEU* 3.2 25.1 - - + +
195B LEU* 1.3 76.2 - - - +
197B GLU* 1.4 85.3 + - - +
199B PHE* 3.1 23.7 + - - -
200B GLU* 3.4 32.6 + - + +
203B MET* 3.6 14.3 - - + +
234B ALA 4.6 15.0 - - - +
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Residues in contact with GLU 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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173B PHE* 3.9 37.2 - - + -
177B ARG* 4.9 2.5 - - - +
193B LEU* 3.0 16.6 + - + +
194B THR* 3.6 12.6 - - - +
195B LEU 3.3 0.2 - - - -
196B LYS* 1.4 93.3 + - - +
198B SER* 1.4 64.1 + - - +
199B PHE* 3.3 0.6 - - - -
163Q LYS* 3.0 33.3 + - - +
200Q ILE* 5.0 10.0 - - - +
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Residues in contact with SER 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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34B PRO* 4.7 18.4 - - - -
165B LYS 5.0 8.7 + - - -
166B ASN* 4.8 17.7 + - - +
170B GLY* 4.0 22.5 + - - -
173B PHE* 5.7 1.7 - - - -
194B THR* 3.2 14.9 + - - +
195B LEU* 3.6 12.5 - - - +
196B LYS 3.3 0.4 - - - -
197B GLU* 1.4 77.1 - - - +
199B PHE* 1.3 63.7 - - - +
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Residues in contact with PHE 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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34B PRO* 4.9 11.1 - - + +
49B GLU* 3.7 14.8 - - - +
51B LYS* 3.3 30.5 - - - -
165B LYS* 6.5 1.3 - - + -
195B LEU 2.7 18.0 - - - +
196B LYS* 3.1 10.7 + - - +
197B GLU 4.5 0.4 - - - -
198B SER* 1.3 82.8 - - - +
200B GLU* 1.3 81.3 + - - +
201B GLY* 3.4 20.0 - - - -
203B MET* 4.4 0.3 - - - +
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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