Contacts of the strand formed by residues 219 - 231 (chain E) in PDB entry 6D6U
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 ASP 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E PRO* 3.2 7.3 - - - +
176E ARG* 2.5 63.6 + - + +
177E GLU* 5.1 7.4 + - - +
212E VAL* 4.4 13.7 - - + -
213E VAL 3.5 4.0 - - - +
214E LYS* 3.3 30.8 + - - +
218E GLY* 1.3 81.3 - - - +
220E TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 220 (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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115A MET* 4.1 3.8 - - + +
117A ARG* 3.9 7.3 + - - -
114E ARG* 3.1 32.5 - - - +
170E SER* 4.9 0.7 - - - +
171E SER* 4.0 12.6 - - - +
172E TYR* 3.1 30.2 + + - -
173E GLY 4.5 0.2 - - - -
174E TYR 3.2 34.8 - - - +
175E PRO* 3.7 9.4 - - + -
176E ARG 4.6 0.7 - - - +
212E VAL* 3.8 3.1 - - - -
213E VAL 2.9 33.9 + - - +
215E THR* 3.8 20.0 - - + -
217E SER* 3.2 29.9 + - - -
218E GLY 5.0 0.7 - - - -
219E ASP* 1.3 83.3 - - - +
221E VAL* 1.3 64.8 + - - +
222E VAL* 3.4 6.5 + - + +
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Residues in contact with VAL 221 (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 SER* 3.3 17.2 - - - -
171E SER* 4.4 1.9 + - - +
175E PRO 5.7 0.2 - - - +
176E ARG* 3.7 32.9 - - + +
179E ILE* 3.5 25.6 - - + +
180E VAL* 3.9 21.5 - - + -
181E TYR* 3.9 22.4 - - + +
211E GLU 3.9 7.2 - - - +
212E VAL* 4.5 10.1 - - + -
219E ASP 4.3 0.8 + - - -
220E TYR* 1.3 70.2 - - - +
222E VAL* 1.3 60.3 + - - +
223E MET* 3.8 9.8 + - + -
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Residues in contact with VAL 222 (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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114E ARG* 3.7 33.0 - - - +
168E GLU* 4.2 22.0 - - + +
169E PHE 4.2 4.5 - - - +
170E SER* 3.7 9.6 - - - -
211E GLU* 3.3 36.5 + - + +
213E VAL* 3.6 29.8 - - + -
220E TYR 3.4 13.9 + - - +
221E VAL* 1.3 71.4 - - - +
223E MET* 1.3 74.7 + - - +
224E SER* 3.8 2.9 + - - -
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Residues in contact with MET 223 (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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55E THR* 5.4 1.1 - - - +
168E GLU* 3.3 7.4 - - - +
169E PHE* 3.0 53.3 + - + +
181E TYR* 3.5 47.1 - - + +
182E GLN* 4.3 4.9 - - - -
183E TRP* 3.3 30.5 - - + -
209E THR 4.2 1.3 - - - -
210E THR* 3.6 28.5 - - + -
211E GLU 5.3 0.7 - - - +
221E VAL* 3.8 12.2 + - + -
222E VAL* 1.3 91.3 - - - +
224E SER* 1.3 62.3 + - - +
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Residues in contact with SER 224 (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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166E PRO* 5.4 2.4 - - - +
167E LEU 3.7 7.7 + - - -
168E GLU* 4.0 18.8 + - - +
169E PHE* 5.6 0.4 - - - -
183E TRP* 4.8 1.5 - - - -
208E ASN* 4.3 0.3 - - - +
209E THR* 2.9 52.8 + - - +
211E GLU* 5.7 6.5 - - - -
222E VAL* 4.5 3.6 - - - -
223E MET* 1.3 79.3 - - - +
225E VAL* 1.3 66.3 + - - +
226E TYR* 3.6 21.4 - - - +
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Residues in contact with VAL 225 (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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57E MET* 4.9 14.8 - - + -
165E CYS 4.6 0.2 - - - +
167E LEU* 2.9 40.7 + - + +
169E PHE* 5.1 1.7 - - + -
183E TRP* 3.3 39.5 - - + -
188E VAL* 4.4 18.8 - - + -
206E LEU* 5.0 7.0 - - + -
207E ARG 3.7 12.6 - - - +
208E ASN* 4.1 12.1 - - + -
224E SER* 1.3 74.3 - - - +
226E TYR* 1.3 64.3 + - - +
227E PHE* 4.9 13.0 - - + -
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Residues in contact with TYR 226 (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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164E SER* 4.4 19.5 - - - -
165E CYS 3.5 7.4 - - - +
166E PRO* 3.4 29.8 - - + -
207E ARG* 2.9 73.1 + - + +
208E ASN 5.6 0.7 - - - -
209E THR* 3.7 32.1 - - + +
224E SER* 3.6 17.0 - - - -
225E VAL* 1.3 77.7 - - - +
227E PHE* 1.3 58.7 + - - +
228E ASP* 4.8 1.4 - - - +
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Residues in contact with PHE 227 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59E VAL* 5.3 7.2 - - + -
62E ILE* 3.6 33.7 - - + -
72E TYR* 4.5 16.8 - + - -
74E ILE* 4.0 24.5 - - + -
164E SER* 4.8 0.2 - - - -
165E CYS* 3.4 32.1 + - + +
167E LEU* 5.8 4.0 - - + -
203E PHE* 3.7 20.0 - + + -
205E GLY 3.2 15.3 - - - +
206E LEU* 3.8 26.5 - - + +
225E VAL* 4.9 11.0 - - + -
226E TYR* 1.3 76.6 - - - +
228E ASP* 1.3 66.9 + - - +
229E LEU* 4.6 15.1 - - + +
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Residues in contact with ASP 228 (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 GLU* 5.3 11.7 - - + +
163E HIS 3.4 5.5 - - - +
164E SER* 3.1 26.9 - - - -
203E PHE* 4.4 0.7 - - - -
204E VAL* 3.6 17.2 + - + -
205E GLY* 3.2 25.0 + - - +
206E LEU 4.5 0.8 + - - +
207E ARG* 3.9 27.0 + - - -
226E TYR* 4.8 1.7 - - - -
227E PHE* 1.3 79.9 - - - +
229E LEU* 1.3 74.2 + - - +
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E ILE* 5.6 2.9 - - + -
65E VAL* 5.0 7.9 - - + -
72E TYR* 6.6 0.4 - - + -
162E GLU* 3.3 8.9 - - - +
163E HIS* 2.7 38.8 + - + +
165E CYS* 4.2 23.1 - - - -
198E LEU* 4.2 17.5 - - + -
201E PHE* 4.3 28.5 - - + -
202E SER 3.6 7.6 - - - +
203E PHE* 3.6 33.9 - - + +
204E VAL* 4.6 3.6 - - - +
227E PHE* 4.6 17.9 - - + +
228E ASP* 1.3 83.7 - - - +
230E SER* 1.3 59.6 + - - +
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Residues in contact with SER 230 (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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161E ASP 3.9 11.4 - - - -
162E GLU* 4.8 6.3 - - - +
163E HIS* 5.1 0.7 - - - +
201E PHE* 3.1 8.1 - - - -
202E SER* 2.6 56.2 + - - -
204E VAL* 3.3 19.2 - - - +
229E LEU* 1.3 75.6 - - - +
231E ARG* 1.3 63.3 + - - +
232E ARG* 5.6 0.2 - - - +
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Residues in contact with ARG 231 (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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67E ALA* 4.9 10.3 - - - +
155E LEU* 3.4 28.0 - - - +
158E PHE* 3.8 21.8 - - + -
159E PRO 4.8 5.7 - - - +
161E ASP* 3.2 40.2 + - - +
163E HIS* 5.3 0.6 + - + -
200E GLN* 3.7 33.4 + - - +
201E PHE* 3.1 37.5 - - + -
230E SER* 1.3 79.1 + - - +
232E ARG* 1.3 70.4 + - - +
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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