Contacts of the helix formed by residues 195 - 215 (chain B) in PDB entry 5FN2
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 TYR 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ILE* 5.1 5.8 - - + +
237A GLN* 4.9 3.9 + - - -
240A PHE* 3.2 35.9 - + + +
241A SER* 3.5 18.2 + - - -
179B PHE* 5.1 9.4 - + - -
194B ASP* 1.3 71.3 - - - +
196B ILE* 1.3 63.3 + - + +
198B VAL* 3.7 3.1 - - + +
199B ALA* 2.9 32.1 + - - +
90D ASP 5.2 0.2 - - - -
91D TYR 3.3 19.1 - - - -
92D LEU* 2.8 15.0 + - - +
93D SER 3.0 31.4 - - - -
94D PHE* 3.3 34.7 - + + +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 2.8 9.2 + - + +
195B TYR* 1.3 83.6 - - + +
197B THR* 1.3 59.6 + - - +
199B ALA* 3.2 7.5 + - + +
200B LEU* 2.9 32.1 + - + +
74D TRP* 3.9 31.4 - - + +
92D LEU* 5.2 11.4 - - + -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 6.3 0.4 - - + -
193B VAL* 4.5 13.7 - - + -
194B ASP* 2.5 29.1 + - - -
196B ILE* 1.3 73.2 - - - +
198B VAL* 1.3 59.7 + - - +
200B LEU* 3.2 11.6 + - + +
201B LEU* 2.9 37.4 + - + +
71D LEU* 4.5 12.1 - - + +
74D TRP* 2.7 34.5 + - - +
75D ILE* 3.9 27.1 - - + +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.9 34.5 - - + -
182B LEU* 4.1 13.5 - - + -
186B PHE* 3.6 15.3 - - + -
193B VAL* 3.5 17.7 - - + -
194B ASP 3.3 18.1 + - - +
195B TYR* 3.7 5.2 - - + +
196B ILE 3.2 0.2 - - - -
197B THR* 1.3 81.6 - - - +
199B ALA* 1.3 58.7 + - - +
201B LEU* 3.2 9.3 + - - +
202B ILE* 2.9 29.2 + - + +
94D PHE* 3.5 27.4 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 6.4 0.4 - - - -
195B TYR 2.9 19.5 + - - +
196B ILE* 3.3 8.3 - - + +
198B VAL* 1.3 78.1 - - - +
200B LEU* 1.3 57.3 + - - +
202B ILE* 3.2 10.2 + - - +
203B TRP* 2.9 29.2 + - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 2.9 16.2 + - + +
197B THR* 3.3 13.2 - - + +
199B ALA* 1.3 75.0 - - - +
201B LEU* 1.3 66.8 + - + +
203B TRP* 3.2 7.9 + - - +
204B ASN* 2.7 52.6 + - - +
25D PHE* 5.8 4.3 - - + +
27D PRO* 5.2 4.5 - - + -
67D TRP* 3.8 31.6 - - + -
71D LEU* 3.4 45.1 - - + -
74D TRP* 6.1 0.7 - - + -
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.5 23.8 - - + -
186B PHE* 5.5 6.7 - - + -
197B THR* 2.9 21.3 + - + +
198B VAL* 3.2 12.1 + - - +
200B LEU* 1.3 87.4 - - + +
202B ILE* 1.3 54.3 + - + +
204B ASN* 3.2 8.5 + - + +
205B PHE* 2.6 53.7 + - + +
28D PHE* 6.0 5.8 - - + -
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Residues in contact with ILE 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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174B LEU 5.3 2.5 - - - +
175B PHE* 3.7 34.1 - - + +
178B SER* 5.0 4.3 - - - +
179B PHE* 4.0 35.9 - - + +
182B LEU* 3.5 34.5 - - + -
198B VAL* 2.9 15.4 + - + +
199B ALA* 3.2 11.0 + - - +
201B LEU* 1.3 78.3 - - + +
203B TRP* 1.3 58.8 + - + +
205B PHE* 4.5 7.2 - - + -
206B GLY* 2.5 37.5 + - - +
207B VAL 3.9 0.2 + - - -
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Residues in contact with TRP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 4.1 19.5 - + - -
199B ALA 2.9 13.6 + - - +
200B LEU* 3.4 12.1 - - - +
202B ILE* 1.3 78.2 - - + +
204B ASN* 1.3 65.3 + - - +
207B VAL* 3.1 51.8 + - + +
24D ALA* 3.0 22.9 + - + +
25D PHE* 3.1 29.4 - + + +
26D LEU* 3.7 15.1 - - + +
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Residues in contact with ASN 204 (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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200B LEU* 2.7 41.7 + - - +
201B LEU* 3.4 14.4 - - + +
203B TRP* 1.3 73.6 - - - +
205B PHE* 1.3 56.9 + - - +
208B VAL* 2.9 41.1 + - - +
25D PHE 3.3 18.8 + - - -
26D LEU* 3.6 12.0 - - - +
27D PRO* 3.0 18.5 - - - +
28D PHE* 2.7 39.9 + - + +
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Residues in contact with PHE 205 (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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174B LEU* 3.4 25.1 - - + +
178B SER* 3.2 25.1 - - - -
182B LEU* 6.6 0.2 - - + -
201B LEU* 2.6 35.1 + - + +
202B ILE* 4.1 8.7 - - + +
204B ASN* 1.3 73.2 - - - +
206B GLY* 1.3 60.7 + - - +
208B VAL* 4.0 0.7 - - - -
209B GLY 3.0 16.8 + - - -
225B TYR* 3.0 54.3 + + - -
228B MET* 3.5 39.9 - - + -
232B LEU* 5.5 0.9 - - + -
28D PHE* 5.5 5.4 - + - -
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.3 24.5 - - - +
175B PHE* 3.7 20.4 - - - -
202B ILE* 2.5 22.5 + - - -
205B PHE* 1.3 73.6 - - - +
207B VAL* 1.3 59.2 + - - -
209B GLY 3.2 1.6 + - - -
210B MET* 2.9 28.0 + - - +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 3.9 9.8 - - + -
203B TRP* 3.1 61.5 + - + +
206B GLY* 1.3 74.0 - - - +
208B VAL* 1.3 57.4 + - - +
210B MET* 3.2 8.7 + - + +
211B ILE* 2.9 39.5 + - + +
26D LEU* 3.5 19.7 - - + -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASN 2.9 31.7 + - - +
205B PHE 3.4 0.2 - - - +
207B VAL* 1.3 76.5 - - - +
209B GLY* 1.3 55.3 + - - +
211B ILE* 3.1 14.5 - - + +
212B SER* 2.9 31.7 + - - +
221B LEU* 5.7 0.4 - - + -
225B TYR* 3.0 33.0 - - + +
26D LEU* 4.1 4.7 - - + -
28D PHE* 3.7 16.2 - - + -
29D LEU* 3.4 51.8 - - + +
32D VAL* 5.1 5.8 - - + -
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Residues in contact with GLY 209 (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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174B LEU* 3.6 8.5 - - - -
205B PHE 3.0 10.7 + - - -
206B GLY 3.6 3.8 - - - -
208B VAL* 1.3 77.5 - - - +
210B MET* 1.3 55.6 + - - +
212B SER* 3.2 2.9 + - - -
213B ILE* 2.9 34.7 + - - +
225B TYR* 3.3 37.2 - - - -
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Residues in contact with MET 210 (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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167B ILE* 3.4 27.6 - - + +
170B SER* 3.1 32.3 - - - +
171B LEU* 3.6 28.5 - - + -
174B LEU* 3.5 10.3 - - + +
175B PHE* 5.4 5.6 - - + -
206B GLY 2.9 19.1 + - - +
207B VAL* 3.2 12.5 + - + +
209B GLY* 1.3 74.7 - - - +
211B ILE* 1.3 65.6 + - + +
213B ILE* 3.2 4.9 + - - -
214B HIS* 3.0 53.0 + - + +
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Residues in contact with ILE 211 (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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207B VAL* 2.9 30.1 + - + +
208B VAL* 3.1 23.8 + - + +
210B MET* 1.3 79.4 - - + +
212B SER* 1.3 68.0 + - - +
214B HIS* 5.3 0.2 - - - -
215B TRP* 2.8 50.7 + - + +
216B LYS 3.8 0.2 - - - +
217B GLY* 5.0 0.2 - - - -
221B LEU* 5.6 0.2 - - + -
18D TYR* 3.1 38.4 - - + +
29D LEU* 3.7 18.6 - - + -
32D VAL* 5.4 3.4 - - + -
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Residues in contact with SER 212 (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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208B VAL 2.9 15.0 + - - -
209B GLY* 3.4 12.1 - - - -
211B ILE* 1.3 80.8 - - - +
213B ILE* 1.3 62.8 + - - +
214B HIS 3.4 0.2 + - - -
216B LYS* 3.0 25.1 + - - +
217B GLY* 5.1 1.6 - - - -
218B PRO 5.3 0.4 + - - -
221B LEU* 3.3 29.6 - - - +
222B GLN* 3.2 37.9 - - - +
225B TYR* 4.2 8.4 - - - -
281B THR* 4.5 0.2 + - - -
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Residues in contact with ILE 213 (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 SER* 5.3 1.8 - - - +
174B LEU* 5.0 1.6 - - + -
209B GLY 2.9 29.6 + - - +
210B MET* 3.4 11.9 - - - +
212B SER* 1.3 79.0 - - - +
214B HIS* 1.3 77.7 + - + +
222B GLN* 4.4 3.1 - - - +
225B TYR* 4.2 15.9 - - + -
226B LEU* 3.4 28.0 - - + +
229B ILE* 4.7 17.5 - - + -
281B THR* 2.3 43.4 + - - +
282B LEU* 3.4 32.1 - - + -
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Residues in contact with HIS 214 (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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167B ILE* 3.1 33.7 - - + +
170B SER* 3.9 5.4 - - - -
210B MET* 3.0 51.0 + - + +
211B ILE* 3.2 0.4 + - - -
213B ILE* 1.3 99.6 - - + +
215B TRP* 1.3 65.6 + - + +
216B LYS 3.4 7.2 + - - -
280B GLU* 3.8 7.4 - - - -
281B THR* 3.5 25.7 - - + +
282B LEU* 3.8 8.7 - - + +
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Residues in contact with TRP 215 (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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211B ILE* 2.8 30.7 + - + +
214B HIS* 1.3 78.9 - - + +
216B LYS* 1.3 66.1 + - - +
217B GLY 3.7 1.6 + - - -
14D LEU* 4.3 11.3 - - + +
17D LYS* 3.7 38.0 - - + +
18D TYR* 4.1 12.2 + + - -
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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
------------------------------------------------------------
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