Contacts of the helix formed by residues 180 - 193 (chain B) in PDB entry 5FLZ
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 PRO 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B GLU* 1.4 66.1 + - - +
182B GLU* 3.2 12.1 - - - +
183B ASP* 2.9 37.5 - - - +
184B ILE* 3.1 21.9 + - + +
212B LYS* 4.4 20.4 - - - +
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Residues in contact with GLU 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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180B PRO* 1.4 74.6 - - - +
182B GLU* 1.3 63.2 + - + +
184B ILE* 3.6 9.7 - - + +
185B LEU* 2.8 35.3 + - - +
277B VAL* 3.2 22.2 - - + +
278B VAL 2.8 29.5 - - - +
279B SER* 3.8 13.0 - - - +
280B LEU* 3.5 29.3 - - + +
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Residues in contact with GLU 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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180B PRO* 3.2 21.1 - - - +
181B GLU* 1.3 79.0 + - + +
183B ASP* 1.4 79.3 + - - +
185B LEU* 3.0 23.0 + - - +
186B LYS* 3.1 28.6 + - - +
277B VAL* 5.2 11.8 - - + +
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Residues in contact with ASP 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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180B PRO* 2.9 33.3 - - - +
182B GLU* 1.4 96.1 - - - +
184B ILE* 1.4 79.7 + - - +
186B LYS* 3.0 29.4 - - + +
187B TYR* 3.0 39.1 - - + +
199B LEU* 4.8 3.6 - - - +
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Residues in contact with ILE 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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180B PRO* 3.1 34.2 + - + +
181B GLU* 3.7 8.7 - - + +
183B ASP* 1.4 84.7 + - - +
185B LEU* 1.4 59.8 + - - +
187B TYR* 3.3 11.7 + - + +
188B VAL* 3.0 35.6 + - + +
199B LEU* 5.4 5.8 - - + -
200B PHE* 4.8 11.0 - - + -
212B LYS* 6.3 1.8 - - + -
217B GLU* 4.5 20.4 - - + +
280B LEU* 4.6 17.0 - - + -
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Residues in contact with LEU 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 GLU* 2.8 28.2 + - - +
182B GLU* 3.0 14.3 + - - +
184B ILE* 1.4 72.8 - - - +
186B LYS* 1.3 58.7 + - - +
188B VAL* 3.3 7.5 + - + -
189B SER* 3.0 25.6 + - - +
277B VAL* 5.5 2.9 - - + -
278B VAL* 3.4 42.0 - - + +
279B SER 4.7 5.6 - - - +
280B LEU* 4.4 17.0 - - + -
283B LEU* 5.1 9.6 - - + -
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Residues in contact with LYS 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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182B GLU* 3.1 37.8 + - - +
183B ASP* 3.0 28.6 - - + +
185B LEU* 1.3 73.4 - - - +
187B TYR* 1.3 71.5 + - + +
189B SER* 2.7 24.1 + - - +
190B TYR* 2.9 36.5 - - + +
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Residues in contact with TYR 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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183B ASP* 3.0 41.3 + - + +
184B ILE* 3.4 10.3 - - - +
185B LEU 3.3 0.2 - - - -
186B LYS* 1.3 88.2 - - + +
188B VAL* 1.4 49.4 + - - +
190B TYR* 3.4 12.1 + + - +
191B THR* 2.8 35.9 + - - -
197B SER* 3.0 23.8 + - - +
198B ALA* 5.4 8.7 - - + +
199B LEU* 3.4 34.6 - - + +
200B PHE* 3.4 21.8 - + + -
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Residues in contact with VAL 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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184B ILE* 3.0 34.7 + - + +
185B LEU* 3.7 8.1 - - + +
187B TYR* 1.4 58.5 - - - +
189B SER* 1.3 63.1 + - - +
191B THR* 3.0 14.4 + - - -
192B LEU* 3.0 25.7 + - + +
200B PHE* 4.1 13.9 - - + -
224B ILE* 3.2 37.0 - - + -
280B LEU* 4.0 21.5 - - + -
283B LEU* 5.3 4.5 - - + -
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Residues in contact with SER 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 LEU* 3.0 18.4 + - - +
186B LYS* 2.7 24.0 + - - +
188B VAL* 1.3 76.0 - - - +
190B TYR* 1.3 73.2 + - - +
191B THR 3.4 0.2 + - - -
192B LEU* 3.4 16.8 + - - +
193B LEU* 3.0 26.5 + - - +
268B VAL* 5.4 9.5 - - - +
272B VAL* 6.0 5.6 - - - -
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Residues in contact with TYR 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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186B LYS* 2.9 42.9 + - + +
187B TYR* 3.5 15.7 - + - +
188B VAL 3.2 0.2 - - - -
189B SER* 1.3 88.6 + - - +
191B THR* 1.3 60.7 + - - +
193B LEU* 3.2 19.5 + - + +
194B ALA 3.5 0.3 + - - -
195B THR* 3.1 36.4 + - - +
196B THR 5.4 0.9 - - - +
197B SER* 4.7 4.0 - - - +
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Residues in contact with THR 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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187B TYR 2.8 16.2 + - - -
188B VAL* 3.0 13.8 + - - -
190B TYR* 1.3 76.8 - - - +
192B LEU* 1.3 55.3 - - + +
194B ALA* 2.8 25.3 + - - -
195B THR 3.3 13.6 + - - +
196B THR* 4.1 5.6 - - - -
197B SER* 3.4 1.6 + - - -
200B PHE* 3.3 27.0 - - + -
202B PHE* 5.2 16.5 - - + -
207B ILE* 5.0 13.0 - - + -
224B ILE* 5.3 11.0 - - + -
228B GLY* 5.0 11.3 - - - -
231B TYR* 5.5 0.2 - - - +
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Residues in contact with LEU 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 VAL* 3.0 22.3 + - + +
189B SER* 3.9 11.9 - - - +
190B TYR 3.4 0.4 - - - -
191B THR* 1.3 78.0 - - + +
193B LEU* 1.3 59.1 + - + +
194B ALA 3.2 0.8 + - - -
224B ILE* 4.3 19.5 - - + -
227B ALA* 4.3 25.4 - - + -
228B GLY* 5.3 4.3 - - - +
231B TYR* 3.1 34.6 - - - +
264B TYR* 3.7 28.0 + - + +
271B LEU* 5.3 4.9 - - + -
283B LEU* 3.9 40.2 - - + -
287B ILE* 5.4 2.7 - - + -
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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
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189B SER* 3.0 29.6 - - - +
190B TYR* 3.2 13.9 + - + +
191B THR 3.2 1.2 - - - -
192B LEU* 1.3 78.2 - - + +
194B ALA* 1.4 65.0 + - - +
195B THR* 3.6 9.2 - - + +
231B TYR* 3.4 35.9 - - + +
264B TYR* 4.5 2.5 - - + -
265B THR* 5.9 4.7 - - + +
268B VAL* 4.0 38.6 - - + -
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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