Contacts of the strand formed by residues 238 - 249 (chain E) in PDB entry 2VIG
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 THR 238 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185E TRP* 3.4 40.4 - - + +
186E ILE 3.5 4.7 - - - -
187E THR* 4.5 2.1 + - - -
227E LYS* 3.5 3.9 - - - +
228E GLU* 2.8 44.3 + - + +
230E LYS* 3.0 35.4 + - - +
233E ILE* 5.6 0.3 - - - +
236E SER* 4.2 2.6 + - - -
237E SER* 1.3 75.4 + - - +
239E ALA* 1.3 60.4 + - - +
501E FAD 4.0 22.8 - - + +
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Residues in contact with ALA 239 (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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185E TRP 4.4 1.1 - - - -
186E ILE* 3.1 34.6 + - - +
189E ALA* 3.8 8.2 - - + +
190E TRP* 3.4 35.7 - - + +
224E LEU* 5.2 0.2 - - + -
225E GLY 3.5 11.4 - - - +
226E LYS 3.6 9.0 - - - +
228E GLU* 4.7 5.2 - - - -
238E THR* 1.3 78.6 - - - +
240E ASN* 1.3 68.6 + - - +
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Residues in contact with ASN 240 (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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157E PRO* 4.7 6.9 - - - +
182E THR* 3.7 19.1 - - + +
183E LYS 3.1 13.7 - - - +
184E ALA* 3.2 23.3 - - - +
185E TRP 3.8 2.3 + - - -
224E LEU* 3.4 6.1 - - - +
225E GLY* 2.8 39.4 + - - +
226E LYS 4.7 0.6 + - - -
228E GLU* 4.4 11.3 + - - +
239E ALA* 1.3 75.6 - - - +
241E LEU* 1.3 63.4 + - - +
242E ILE* 4.4 7.4 - - + +
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Residues in contact with LEU 241 (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 CYS* 4.5 0.2 - - - -
153E ALA* 4.2 22.4 - - + -
181E GLY 3.8 1.6 - - - +
182E THR* 3.4 2.8 - - - -
183E LYS* 2.9 40.8 + - + +
186E ILE* 4.1 11.2 - - + +
189E ALA* 3.8 18.6 - - + -
195E ALA* 4.3 15.5 - - + -
217E MET* 4.2 17.5 - - + -
222E LEU* 3.8 17.7 - - + -
223E THR 3.8 2.9 - - - -
224E LEU* 3.7 17.3 - - + -
239E ALA 3.8 2.9 + - - +
240E ASN* 1.3 80.5 - - - +
242E ILE* 1.3 61.1 + - - +
243E PHE* 3.9 21.5 - - + -
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Residues in contact with ILE 242 (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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181E GLY 3.8 3.1 - - - +
182E THR* 4.1 25.4 - - + +
221E GLY 3.3 5.4 - - - +
222E LEU* 3.4 3.0 - - - +
223E THR* 2.9 58.6 + - - +
224E LEU 4.1 3.1 - - - +
225E GLY* 4.0 22.7 - - - +
240E ASN* 4.4 5.8 - - + +
241E LEU* 1.3 75.0 - - - +
243E PHE* 1.3 68.7 + - - +
244E GLU* 4.0 12.9 + - + +
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Residues in contact with PHE 243 (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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168E THR* 4.7 7.9 - - + -
179E LEU* 3.6 33.4 - - + +
180E ASN* 3.6 2.8 - - - +
181E GLY* 2.9 41.6 + - - +
183E LYS* 4.0 9.9 - - + -
197E VAL* 3.9 39.3 - - + -
215E VAL* 4.0 22.7 - - + -
221E GLY 3.3 1.8 - - - -
222E LEU* 3.6 24.5 - - + -
241E LEU* 3.9 25.1 - - + -
242E ILE* 1.3 75.4 - - - +
244E GLU* 1.3 61.3 + - - +
246E CYS* 3.7 21.8 - - + -
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Residues in contact with GLU 244 (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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180E ASN* 3.8 5.8 - - - +
221E GLY* 2.7 27.3 + - - +
223E THR* 5.7 0.3 + - - -
242E ILE* 4.8 12.7 - - + +
243E PHE* 1.3 74.6 - - - +
245E ASP* 1.3 74.5 + - + +
246E CYS 3.1 0.7 + - - +
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Residues in contact with ASP 245 (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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178E VAL* 3.9 20.2 - - + -
179E LEU 3.6 1.3 + - - -
180E ASN* 3.1 17.6 + - - +
220E PRO 4.9 0.5 - - - +
221E GLY* 4.7 1.9 - - - -
244E GLU* 1.3 76.1 - - + +
246E CYS* 1.3 61.5 + - - +
247E ARG* 3.5 11.5 + - + +
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Residues in contact with CYS 246 (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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177E TRP 3.4 1.9 - - - +
178E VAL* 3.3 3.2 - - - -
179E LEU* 2.8 45.5 + - + +
215E VAL* 5.0 0.2 - - - -
219E THR* 3.8 20.4 - - - -
220E PRO 3.4 20.9 - - - -
221E GLY 3.8 17.7 - - - +
243E PHE* 3.7 27.4 - - + -
244E GLU 3.8 1.3 - - - -
245E ASP* 1.3 73.9 - - - +
247E ARG* 1.3 59.0 + - - +
248E ILE* 3.9 13.1 + - - +
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Residues in contact with ARG 247 (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 GLU* 3.6 29.5 + - - +
174E GLY* 5.6 0.6 - - - -
175E ASP 5.4 1.2 - - - +
176E SER* 2.7 42.1 + - - +
177E TRP 3.3 4.3 - - - -
178E VAL* 4.2 15.8 - - + +
219E THR* 4.8 6.2 + - - -
220E PRO* 4.4 6.3 + - - +
245E ASP* 3.5 12.4 + - + +
246E CYS* 1.3 73.5 - - - +
248E ILE* 1.3 68.2 + - - +
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Residues in contact with ILE 248 (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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176E SER* 3.1 6.5 - - - -
177E TRP* 2.8 45.0 + - + +
179E LEU* 4.3 8.7 - - + -
213E PHE* 4.0 25.8 - - + -
214E LEU 3.7 10.5 - - - +
215E VAL* 4.1 21.5 - - + -
216E PRO* 4.7 9.9 - - + -
219E THR* 5.1 3.6 - - - +
246E CYS* 4.3 19.7 - - - +
247E ARG* 1.3 80.1 - - - +
249E PRO* 1.3 70.8 - - + +
252E SER* 3.2 27.8 - - - +
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Residues in contact with PRO 249 (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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139E TRP* 6.5 0.7 - - + -
175E ASP 3.9 8.7 - - - +
176E SER* 4.4 1.1 - - - -
177E TRP* 3.6 4.0 - - - -
216E PRO* 6.0 4.7 - - + -
248E ILE* 1.3 88.8 - - + +
250E LYS* 1.3 60.7 + - - +
251E ASP* 3.2 17.0 - - - +
252E SER* 2.8 41.6 + - - +
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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