Contacts of the helix formed by residues 186 - 203 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E LEU* 4.4 8.7 - - - -
185E TRP* 1.3 86.3 - - - +
187E GLU* 1.3 64.0 + - - +
188E ASP* 2.9 19.2 + - - +
189E GLU* 3.2 26.6 + - - +
190E GLU* 3.0 23.0 + - - +
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Residues in contact with GLU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LEU* 3.7 28.1 - - + +
186E SER* 1.3 75.5 - - - +
188E ASP* 1.3 62.0 + - - +
190E GLU* 3.4 3.5 - - - +
191E LYS* 3.1 23.6 + - - +
222E LEU* 6.0 5.8 - - + +
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Residues in contact with ASP 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E SER* 3.3 18.8 + - - +
187E GLU* 1.3 81.0 + - - +
189E GLU* 1.3 60.2 + - + +
190E GLU 2.9 1.3 - - - -
191E LYS* 2.5 30.8 + - - +
192E ASP* 2.8 22.4 + - - +
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Residues in contact with GLU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E HIS* 3.2 37.3 + - - -
157E PHE* 3.5 11.0 - - - -
184E PHE 3.8 18.5 - - - +
185E TRP* 3.6 28.7 - - + -
186E SER* 3.2 22.6 + - - +
188E ASP* 1.3 79.3 - - + +
190E GLU* 1.3 56.6 + - - +
192E ASP* 3.4 12.2 + - - +
193E LEU* 2.9 30.0 + - - +
303E SFG 4.9 1.2 + - - -
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Residues in contact with GLU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E PRO 4.5 0.2 - - - +
175E LEU* 3.8 13.3 + - + +
185E TRP* 3.0 29.3 + - - -
186E SER 3.0 13.5 + - - +
187E GLU 3.4 12.8 - - - +
188E ASP 2.8 0.4 + - - -
189E GLU* 1.3 76.2 - - - +
191E LYS* 1.3 62.0 + - - +
193E LEU* 3.2 8.8 + - - +
194E LEU* 3.0 46.3 + - + +
209E LEU* 5.8 0.9 - - - +
211E ASN* 3.9 21.5 + - - -
220E ASN* 3.8 33.9 + - - +
222E LEU* 4.8 7.6 - - + -
223E LEU* 4.4 5.7 - - - +
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Residues in contact with LYS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLU 3.1 11.4 + - - +
188E ASP* 2.5 16.0 + - - +
190E GLU* 1.3 74.2 - - - +
192E ASP* 1.3 64.9 + - - +
193E LEU 3.1 0.2 + - - -
194E LEU* 3.2 9.4 + - - +
195E ASN* 2.9 32.7 + - - +
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Residues in contact with ASP 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E HIS* 6.2 0.4 - - + -
157E PHE* 3.9 14.4 - - + -
158E LYS* 5.5 11.4 - - + +
188E ASP* 2.8 33.1 + - - +
189E GLU* 3.5 15.2 + - - +
191E LYS* 1.3 73.1 - - - +
193E LEU* 1.3 56.7 + - - +
195E ASN* 3.2 14.3 + - - +
196E LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 5.3 1.6 - - + -
32E PHE* 4.2 6.1 - - + -
157E PHE* 3.4 31.4 - - + -
170E VAL* 4.0 19.3 - - + -
172E PRO* 3.5 27.1 - - + -
185E TRP* 3.5 24.9 - - + -
189E GLU 2.9 13.2 + - - +
190E GLU* 3.2 14.8 - - - +
192E ASP* 1.3 72.5 - - - +
194E LEU* 1.3 62.2 + - + +
195E ASN 3.1 1.1 - - - -
196E LEU* 3.1 8.0 + - + +
197E LEU* 2.8 46.2 + - + +
209E LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E GLU* 3.0 34.4 + - + +
191E LYS* 3.8 9.0 - - - +
193E LEU* 1.3 77.9 - - + +
195E ASN* 1.3 57.2 + - - +
197E LEU* 3.3 14.2 + - + +
198E ASP* 2.8 33.6 + - - -
209E LEU* 4.7 5.2 - - + -
222E LEU* 4.2 11.2 - - + +
223E LEU* 3.7 20.9 - - + +
226E TRP* 3.5 66.0 - - + +
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Residues in contact with ASN 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LYS* 2.9 29.7 + - - +
192E ASP* 3.2 14.8 + - - +
194E LEU* 1.3 74.0 - - - +
196E LEU* 1.3 67.8 + - - +
198E ASP* 3.1 10.1 + - - +
199E SER* 2.9 25.2 + - - -
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Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 4.2 16.8 - - + -
157E PHE* 3.8 37.5 - - + +
158E LYS* 5.5 7.4 - - - +
160E VAL 5.8 3.4 - - - +
162E ILE* 5.3 7.4 - - + -
192E ASP 2.9 9.9 + - - +
193E LEU* 3.4 11.2 - - + +
195E ASN* 1.3 79.5 - - - +
197E LEU* 1.3 55.0 + - + +
199E SER* 3.2 7.5 + - - -
200E LEU* 2.7 62.0 + - + +
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E VAL* 3.7 24.0 - - + -
193E LEU* 2.8 37.7 + - + +
194E LEU* 3.3 26.7 - - + +
195E ASN 3.0 0.2 - - - -
196E LEU* 1.3 74.4 - - + +
198E ASP* 1.3 68.9 + - - +
200E LEU* 3.3 15.6 + - + +
201E ASN 3.1 10.6 + - - -
207E PHE* 3.0 49.9 - - + -
209E LEU* 4.1 25.8 - - + -
226E TRP* 4.1 4.5 - - + -
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Residues in contact with ASP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E LEU 2.8 14.9 + - - +
195E ASN* 3.7 9.5 - - - +
197E LEU* 1.3 70.5 - - - +
199E SER* 1.3 56.5 + - - +
201E ASN* 2.6 33.4 + - - +
202E ASP* 2.9 12.8 + - - +
226E TRP* 3.0 22.2 + - - -
229E LYS* 2.7 25.2 + - - -
230E TYR* 2.3 45.3 + - - +
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Residues in contact with SER 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ASN 2.9 13.0 + - - -
196E LEU* 3.2 14.8 - - - -
198E ASP* 1.3 76.9 - - - +
200E LEU* 1.3 54.0 + - - -
202E ASP* 2.7 17.7 + - - +
203E ARG* 2.7 49.8 + - - +
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Residues in contact with LEU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ILE* 3.5 38.1 - - + -
168E VAL* 5.1 8.7 - - + -
196E LEU* 2.7 52.4 + - + +
197E LEU* 3.4 32.1 - - + +
199E SER* 1.3 72.5 + - - +
201E ASN* 1.3 54.0 + - - +
203E ARG* 3.4 14.6 + - - +
204E GLY 3.3 4.2 + - - -
205E ILE* 2.5 59.3 + - + +
207E PHE* 4.6 7.4 - - + -
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Residues in contact with ASN 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU 3.1 7.5 + - - +
198E ASP 2.6 21.1 + - - +
200E LEU* 1.3 68.2 - - - +
202E ASP* 1.3 56.7 + - - +
204E GLY* 2.6 29.0 + - - -
205E ILE 3.4 8.7 + - - +
230E TYR* 2.9 39.8 + - + +
259E ASN* 3.7 22.0 + - - +
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Residues in contact with ASP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ASP* 2.9 15.2 + - - +
199E SER* 2.7 24.8 + - - +
201E ASN* 1.3 70.4 - - - +
203E ARG* 1.3 54.9 + - + +
204E GLY* 2.4 19.6 + - - -
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Residues in contact with ARG 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ILE* 3.4 34.1 + - - +
164E ASP* 3.6 34.0 + - - +
199E SER* 2.7 32.2 + - - +
200E LEU* 3.6 18.5 - - - +
202E ASP* 1.3 70.6 - - + +
204E GLY* 1.3 60.1 + - - +
205E ILE* 3.3 22.9 + - + +
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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