Contacts of the helix formed by residues 183 - 200 (chain E) in PDB entry 5FWP
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 CYS 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147E LYS* 4.1 14.1 - - - +
151E PHE* 3.9 18.2 - - - -
180E HIS 4.0 8.5 - - - +
181E LEU 2.8 7.9 + - - -
182E VAL* 1.3 74.4 - - - +
184E GLU* 1.3 66.5 + - - +
185E GLU* 3.1 22.4 - - - +
186E THR* 3.4 28.4 + - - -
187E ALA 3.3 14.7 + - - -
216E MET* 3.7 10.2 - - - +
220E LEU* 4.0 14.1 - - - -
230E PRO* 5.4 0.7 - - - -
231E ARG* 6.1 1.1 - - - -
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Residues in contact with GLU 184 (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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144E ARG* 3.7 26.5 + - - -
183E CYS* 1.3 73.2 - - - +
185E GLU* 1.3 61.8 + - - +
187E ALA* 3.1 2.0 + - - +
188E ASN* 2.7 51.3 + - - +
220E LEU* 3.8 29.7 - - + +
224E LYS* 2.8 32.7 + - - +
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Residues in contact with GLU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E VAL* 5.4 0.5 - - - +
144E ARG* 3.4 27.4 - - + +
147E LYS* 3.4 31.2 + - + +
148E HIS* 3.8 42.8 - - + +
151E PHE* 4.3 6.1 - - + -
152E VAL* 3.7 19.9 - - + +
183E CYS* 3.1 21.4 - - - +
184E GLU* 1.3 74.8 + - - +
186E THR* 1.3 61.1 + - - +
188E ASN* 3.5 5.2 + - - +
189E TYR* 3.1 22.7 + - - +
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Residues in contact with THR 186 (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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151E PHE* 3.7 8.3 - - - -
159E ILE* 3.8 30.3 - - + +
162E PHE* 5.0 3.4 - - + -
181E LEU* 2.6 45.3 + - + +
183E CYS* 3.4 13.3 + - - -
184E GLU 3.2 0.4 - - - -
185E GLU* 1.3 75.6 - - - +
187E ALA* 1.3 65.7 + - - +
189E TYR* 3.2 5.4 + - - +
190E LEU* 3.0 30.7 + - + +
216E MET* 4.1 14.4 - - + -
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Residues in contact with ALA 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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183E CYS 3.3 4.5 + - - +
184E GLU* 3.1 7.5 + - - +
186E THR* 1.3 80.0 - - - +
188E ASN* 1.3 63.1 + - - +
190E LEU* 3.2 14.4 + - - +
191E VAL* 3.0 27.6 + - - +
213E THR* 4.0 2.2 - - - +
216E MET* 3.8 21.5 - - + -
217E GLN* 3.5 32.8 - - + +
220E LEU* 4.0 4.5 - - + -
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Residues in contact with ASN 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ARG* 5.4 8.1 - - - +
148E HIS* 4.0 17.8 + - + -
184E GLU* 2.7 36.3 + - - +
185E GLU* 3.7 8.5 - - - +
186E THR 3.2 0.2 - - - -
187E ALA* 1.3 70.7 - - - +
189E TYR* 1.3 65.2 + - - +
191E VAL* 3.3 10.0 + - - +
192E ILE* 3.1 31.3 + - + +
217E GLN* 4.6 8.8 + - - -
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Residues in contact with TYR 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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148E HIS* 4.8 2.4 - - + -
152E VAL* 3.5 26.7 - - + -
156E GLU* 2.7 42.1 + - + +
159E ILE* 3.4 24.0 - - + -
160E LYS* 3.5 30.3 + - + +
185E GLU 3.1 13.7 + - - +
186E THR 3.2 8.0 + - - +
188E ASN* 1.3 76.8 - - - +
190E LEU* 1.3 54.2 + - + +
192E ILE* 3.1 16.7 + - + +
193E TRP* 2.7 59.2 + + + -
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Residues in contact with LEU 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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159E ILE* 3.7 29.6 - - + +
162E PHE* 4.0 24.2 - - + -
163E GLY* 3.9 17.3 - - - -
186E THR* 3.0 25.6 + - + +
187E ALA* 3.2 12.8 + - - +
189E TYR* 1.3 78.4 - - - +
191E VAL* 1.3 56.8 + - - +
193E TRP* 3.4 12.6 + - + +
194E CYS* 2.9 33.8 + - - -
209E VAL* 3.5 10.8 - - + +
212E GLN 4.0 2.5 - - - +
213E THR* 3.2 35.9 - - - +
216E MET* 4.5 2.2 - - + -
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Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E ALA 3.0 20.2 + - - +
188E ASN* 3.5 11.9 - - - +
190E LEU* 1.3 72.8 - - - +
192E ILE* 1.3 66.6 + - + +
194E CYS* 3.2 10.9 + - - +
195E ILE* 3.1 35.6 + - + +
213E THR* 3.6 19.7 + - + -
217E GLN* 4.7 5.8 - - - +
260E LYS* 4.6 16.4 - - + +
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Residues in contact with ILE 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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148E HIS* 4.9 14.8 - - + +
188E ASN* 3.1 20.3 + - + +
189E TYR* 3.5 16.4 - - + +
191E VAL* 1.3 76.5 - - + +
193E TRP* 1.3 62.3 + - - +
195E ILE* 3.1 16.9 + - + +
196E ASP* 2.9 41.7 + - - +
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Residues in contact with TRP 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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160E LYS* 3.5 65.3 - - + +
163E GLY* 4.1 5.2 - - - -
164E MET* 3.9 15.9 - - + -
189E TYR* 2.7 40.6 + + + +
190E LEU* 3.5 14.1 - - + +
192E ILE* 1.3 73.9 - - - +
194E CYS* 1.3 51.1 + - - +
196E ASP* 3.1 14.1 + - + -
197E LEU* 2.7 55.7 + - + +
205E LEU* 3.8 19.5 - - + -
209E VAL* 3.4 32.5 - - + -
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Residues in contact with CYS 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 LEU 2.9 24.5 + - - -
191E VAL* 3.4 10.3 - - - +
193E TRP* 1.3 75.2 - - - +
195E ILE* 1.3 57.8 + - + +
197E LEU* 3.2 5.1 + - - +
198E GLU 2.9 24.4 + - - -
206E MET* 3.4 34.0 - - + +
209E VAL* 3.4 20.0 - - - -
210E ALA* 3.4 28.3 - - + -
213E THR* 3.9 3.6 - - - -
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Residues in contact with ILE 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 VAL* 3.4 24.9 - - + +
192E ILE* 3.1 19.2 + - + +
194E CYS* 1.3 77.6 - - + +
196E ASP* 1.3 67.5 + - - +
198E GLU* 3.2 17.3 + - - +
199E VAL* 3.1 28.1 + - + +
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Residues in contact with ASP 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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192E ILE* 2.9 30.7 + - - +
193E TRP* 3.1 17.7 + - + +
195E ILE* 1.3 80.7 - - - +
197E LEU* 1.3 58.1 + - + +
199E VAL* 3.2 11.1 + - - +
200E GLU* 2.9 41.7 + - + +
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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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193E TRP* 2.7 48.2 + - + +
194E CYS* 3.5 4.5 - - - +
196E ASP* 1.3 68.9 - - - +
198E GLU* 1.3 64.3 + - - +
200E GLU* 3.2 8.3 + - - +
201E GLU 3.0 4.3 + - - -
202E LYS* 2.8 70.1 + - + +
205E LEU* 3.7 22.2 - - + -
206E MET* 3.6 28.0 - - + +
209E VAL* 3.7 16.4 - - + -
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Residues in contact with GLU 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 CYS 2.9 7.7 + - - +
195E ILE* 3.3 19.7 - - - +
197E LEU* 1.3 77.1 - - - +
199E VAL* 1.3 64.5 + - + +
201E GLU* 3.0 16.8 + - - +
202E LYS 5.0 0.7 - - - +
203E CYS* 5.0 10.0 - - - -
206E MET* 3.6 27.1 - - + +
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Residues in contact with VAL 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E ILE* 3.1 22.3 + - + +
196E ASP* 3.3 12.6 - - - +
198E GLU* 1.3 79.7 - - + +
200E GLU* 1.3 62.9 - - + +
201E GLU* 3.2 10.8 + - - +
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Residues in contact with GLU 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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193E TRP* 5.8 0.2 + - - -
196E ASP* 2.9 26.4 + - - +
197E LEU* 3.2 10.0 + - - +
199E VAL* 1.3 79.2 - - + +
201E GLU* 1.3 70.3 + - - +
202E LYS* 2.7 47.2 + - + +
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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