Contacts of the helix formed by residues 186 - 203 (chain B) in PDB entry 1YFL
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 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.9 12.8 - - - +
185B TRP* 1.3 80.4 - - - +
187B GLU* 1.3 58.4 + - - +
188B ASP* 3.3 18.2 + - - +
189B GLU* 3.0 26.4 + - - +
190B GLU* 2.9 24.6 + - - +
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Residues in contact with GLU 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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175B LEU* 4.0 23.2 - - + +
186B SER* 1.3 68.9 - - - +
188B ASP* 1.3 59.5 + - - +
189B GLU 2.9 1.8 - - - -
190B GLU* 2.9 9.3 + - - +
191B LYS* 2.7 35.9 + - - +
222B LEU* 5.7 6.7 - - + +
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Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 3.4 14.8 + - - +
187B GLU* 1.3 79.7 + - - +
189B GLU* 1.3 60.2 + - + +
191B LYS* 3.5 7.8 - - - +
192B ASP* 2.8 33.2 + - - +
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Residues in contact with GLU 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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156B HIS* 2.9 27.9 + - - -
157B PHE* 3.5 20.4 - - - -
184B PHE 3.9 11.5 - - - +
185B TRP* 3.4 32.8 - - + -
186B SER* 3.0 27.1 + - - +
187B GLU 2.9 0.6 - - - -
188B ASP* 1.3 76.1 - - + +
190B GLU* 1.3 66.7 + - - +
191B LYS 3.0 1.8 - - - -
192B ASP* 3.3 10.7 + - - +
193B LEU* 3.0 25.5 + - - +
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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 PRO 4.5 0.3 - - - +
175B LEU* 3.7 29.6 + - + +
185B TRP* 3.3 28.4 + - - -
186B SER 2.9 9.3 + - - +
187B GLU* 3.3 9.2 - - - +
189B GLU* 1.3 75.2 - - - +
191B LYS* 1.3 57.8 + - - +
193B LEU* 3.6 6.2 - - - +
194B LEU* 2.9 67.1 + - + +
209B LEU* 5.4 1.2 - - - +
211B ASN* 4.1 20.9 + - - -
220B ASN* 4.1 13.1 + - - +
222B LEU* 4.9 8.3 - - + -
223B LEU* 4.3 6.4 - - - +
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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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187B GLU 2.7 16.3 + - - +
188B ASP* 3.5 9.9 - - - +
189B GLU 3.0 0.6 - - - -
190B GLU* 1.3 74.3 - - - +
192B ASP* 1.3 58.7 + - - +
194B LEU* 2.8 8.8 + - - +
195B ASN* 2.7 48.1 + - - +
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Residues in contact with ASP 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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156B HIS* 5.8 0.2 - - - -
157B PHE* 4.2 14.6 - - + -
158B LYS* 5.7 7.3 - - + +
188B ASP* 2.8 20.6 + - - +
189B GLU* 3.3 14.2 + - - +
191B LYS* 1.3 76.6 - - - +
193B LEU* 1.3 57.5 + - - +
195B ASN* 3.9 9.7 + - - +
196B LEU* 2.8 34.8 + - - +
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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
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31B LEU* 4.6 4.0 - - + -
32B PHE* 4.1 20.0 - - + -
157B PHE* 3.8 23.9 - - + -
170B VAL* 3.9 15.0 - - + -
172B PRO* 3.6 32.5 - - + -
185B TRP* 3.8 13.5 - - + -
189B GLU 3.0 17.9 + - - +
190B GLU* 3.6 11.0 - - - +
192B ASP* 1.3 77.2 - - - +
194B LEU* 1.3 54.0 + - + +
196B LEU* 3.7 4.3 - - + +
197B LEU* 2.7 56.9 + - + +
209B LEU* 4.4 6.7 - - + -
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Residues in contact with LEU 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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190B GLU* 2.9 55.0 + - + +
191B LYS* 2.8 8.0 + - - +
193B LEU* 1.3 75.8 - - + +
195B ASN* 1.3 64.2 + - - +
197B LEU* 3.3 10.7 + - + -
198B ASP* 3.1 16.3 + - - -
209B LEU* 5.1 7.9 - - + -
222B LEU* 4.6 5.6 - - + +
223B LEU* 4.3 18.4 - - + +
226B TRP* 3.3 72.2 + - + +
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Residues in contact with ASN 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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191B LYS* 2.7 38.2 + - - +
192B ASP* 3.9 8.8 + - - +
194B LEU* 1.3 72.0 - - - +
196B LEU* 1.3 55.1 + - - +
198B ASP* 2.7 43.0 + - - +
199B SER* 3.1 7.1 + - - -
226B TRP* 5.5 2.1 + - - -
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Residues in contact with LEU 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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31B LEU* 5.6 6.1 - - + -
157B PHE* 5.2 9.6 - - + +
158B LYS* 4.7 24.9 - - + +
160B VAL 5.9 2.5 - - - +
162B ILE* 5.6 4.5 - - + -
192B ASP 2.8 21.7 + - - +
193B LEU* 4.0 10.5 - - + +
195B ASN* 1.3 70.3 - - - +
197B LEU* 1.3 72.7 - - + +
199B SER* 3.0 14.2 + - - -
200B LEU* 2.9 45.8 + - + -
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Residues in contact with LEU 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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31B LEU* 6.2 0.2 - - + -
168B VAL* 5.8 0.2 - - + -
170B VAL* 4.4 14.8 - - + -
193B LEU* 2.7 41.3 + - + +
194B LEU* 3.4 11.0 - - + +
196B LEU* 1.3 76.6 - - + +
198B ASP* 1.3 63.1 + - - +
200B LEU* 3.5 12.4 + - + +
201B ASN 3.4 4.0 + - - -
207B PHE* 2.9 62.1 - - + -
209B LEU* 4.1 32.5 - - + -
226B TRP* 3.8 24.5 - - + -
230B TYR* 4.4 0.2 - - - -
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU 3.1 12.0 + - - +
195B ASN* 2.7 23.3 + - - +
197B LEU* 1.3 74.6 - - - +
199B SER* 1.3 54.1 + - - +
201B ASN* 2.5 34.7 + - - +
202B ASP* 3.1 12.3 - - - +
226B TRP* 3.5 7.3 + - - -
229B LYS* 2.6 35.9 + - - -
230B TYR* 2.4 33.7 + - - +
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Residues in contact with SER 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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195B ASN 3.5 9.4 + - - -
196B LEU* 3.2 19.0 - - - +
198B ASP* 1.3 77.7 - - - +
200B LEU* 1.3 63.1 + - - -
201B ASN 3.1 0.2 + - - -
202B ASP* 3.2 11.4 + - - +
203B ARG* 3.1 32.4 + - - +
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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
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31B LEU* 6.0 4.0 - - + -
162B ILE* 3.8 32.8 - - + -
168B VAL* 4.5 17.7 - - + -
196B LEU* 2.9 36.6 + - + +
197B LEU* 3.7 21.5 - - + +
199B SER* 1.3 77.5 - - - +
201B ASN* 1.3 53.2 + - - +
203B ARG* 3.4 32.4 + - - +
205B ILE* 2.8 56.4 + - + +
207B PHE* 4.5 4.5 - - + -
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Residues in contact with ASN 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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197B LEU 3.4 4.2 + - - +
198B ASP 2.5 19.3 + - - +
200B LEU* 1.3 70.1 - - - +
202B ASP* 1.3 57.8 + - - +
203B ARG 3.1 1.8 - - - -
204B GLY* 2.7 26.3 + - - -
205B ILE 4.0 7.4 + - - -
206B LYS* 6.2 0.2 - - - +
207B PHE* 4.6 0.2 - - - -
230B TYR* 3.0 39.1 + - + +
259B ASN* 3.5 21.1 - - - +
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Residues in contact with ASP 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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198B ASP* 3.1 21.6 - - - +
199B SER* 3.6 11.0 - - - +
201B ASN* 1.3 75.0 - - - +
203B ARG* 1.3 59.5 + - + +
204B GLY* 2.9 9.6 + - - -
230B TYR* 5.2 0.5 + - - -
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Residues in contact with ARG 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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162B ILE* 3.0 29.1 + - - +
164B ASP* 3.2 37.6 + - - +
199B SER* 3.1 21.6 + - - +
200B LEU* 3.6 28.4 - - - +
201B ASN 3.1 0.8 - - - -
202B ASP* 1.3 76.6 - - + +
204B GLY* 1.3 63.1 + - - +
205B ILE* 3.1 27.2 + - + +
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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