Contacts of the strand formed by residues 292 - 301 (chain E) in PDB entry 3VBB
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 ILE 292 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E ILE* 5.7 3.8 - - + -
280E HIS* 4.2 13.7 - - + +
285E LEU* 3.9 31.0 - - + -
289E ASP* 3.4 29.6 - - + +
290E LEU* 3.7 7.8 - - + +
291E PRO* 1.3 71.2 - - - +
293E LYS* 1.3 62.0 + - - +
294E TYR* 3.8 36.1 - - + +
327E PHE 3.8 1.2 - - - +
328E VAL* 3.3 2.9 - - - -
329E TYR* 2.8 44.6 + - + +
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Residues in contact with LYS 293 (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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218E ARG* 3.6 24.3 + - - +
219E GLY* 4.1 16.8 + - - +
220E TYR* 3.7 31.2 - - + -
221E ILE* 3.1 26.7 + - - +
291E PRO* 3.9 20.0 + - + +
292E ILE* 1.3 79.7 - - - +
294E TYR* 1.3 70.5 + - - +
327E PHE 3.7 3.4 - - - -
328E VAL* 4.1 11.4 - - + +
340E MET* 3.4 22.4 - - + +
343E GLU* 3.4 24.5 + - - -
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Residues in contact with TYR 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E TYR* 3.6 6.0 - - - -
221E ILE* 3.5 34.5 - - + +
223E ILE* 4.6 14.8 - - + -
276E ILE* 3.8 29.6 - - + -
279E LEU* 3.4 25.8 - - + +
280E HIS* 2.9 32.5 + - - -
292E ILE* 3.8 14.9 - - + +
293E LYS* 1.3 85.8 - - - +
295E ALA* 1.3 59.9 + - - +
325E GLU 3.4 1.0 - - - +
326E GLN* 3.3 4.9 - - - -
327E PHE* 2.8 46.8 + - + +
329E TYR* 4.0 13.5 - + - -
197F LYS* 5.0 9.7 + - + -
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Residues in contact with ALA 295 (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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212E LEU* 4.5 11.7 - - + +
215E LEU* 3.5 33.0 - - + -
216E GLY 5.7 0.2 - - - +
220E TYR* 4.0 12.6 - - + +
221E ILE 2.9 8.5 + - - -
222E PRO* 3.2 14.1 - - + +
223E ILE* 2.7 29.0 + - - +
294E TYR* 1.3 70.4 - - - +
296E GLY* 1.3 63.1 + - - +
297E LEU* 4.8 1.4 - - - +
324E ILE* 4.7 0.9 - - + -
325E GLU 3.5 4.5 - - - -
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Residues in contact with GLY 296 (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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223E ILE* 3.3 15.9 - - - -
272E SER* 3.8 16.6 - - - -
276E ILE* 3.9 8.7 - - - +
294E TYR 3.7 2.2 - - - -
295E ALA* 1.3 73.0 - - - +
297E LEU* 1.3 60.8 + - - +
323E LYS 3.6 0.2 - - - +
324E ILE* 3.1 9.4 - - - +
325E GLU 2.6 38.7 + - - -
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Residues in contact with LEU 297 (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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208E ILE* 4.1 27.6 - - + -
212E LEU* 4.3 16.4 - - + -
223E ILE 2.9 12.4 + - - +
224E TYR* 3.5 20.8 - - + -
225E THR* 3.5 19.3 + - - +
272E SER* 4.0 1.2 + - - -
295E ALA 4.8 1.8 - - - +
296E GLY* 1.3 74.6 - - - +
298E SER* 1.3 65.5 + - - +
322E GLU* 5.3 7.9 - - + -
323E LYS 3.5 4.3 - - - +
324E ILE* 4.1 16.8 - - + -
201F VAL* 4.0 26.9 - - + -
205F GLN* 4.0 18.2 - - - +
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Residues in contact with SER 298 (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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225E THR* 3.8 7.2 - - - -
227E PHE* 3.3 16.8 - - - -
269E ILE* 3.9 9.2 - - - -
272E SER* 2.9 39.1 + - - -
297E LEU* 1.3 78.9 - - - +
299E THR* 1.3 63.2 + - - +
300E CYS* 3.5 9.5 + - - -
322E GLU* 3.5 7.0 - - - +
323E LYS* 3.0 31.3 + - - +
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Residues in contact with THR 299 (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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227E PHE* 3.0 37.7 - - - -
269E ILE* 3.9 10.0 - - - +
298E SER* 1.3 75.5 - - - +
300E CYS* 1.3 62.0 + - - +
301E PHE* 3.7 15.9 - - + -
320E GLN* 3.9 16.6 - - + -
321E PHE 3.4 10.8 - - - +
322E GLU* 2.5 29.9 + - - +
227F PHE* 3.5 32.1 - - + -
299F THR* 4.2 1.6 + - - -
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Residues in contact with CYS 300 (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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269E ILE* 3.8 4.0 - - - -
270E ALA 3.3 24.7 - - - +
271E THR* 3.7 10.1 - - - -
298E SER* 3.5 25.6 - - - -
299E THR* 1.3 74.3 - - - +
301E PHE* 1.3 66.0 - - - +
302E ARG 4.2 0.7 - - - -
319E HIS 3.3 5.1 - - - +
320E GLN* 3.4 3.6 - - - +
321E PHE* 2.7 49.6 + - + +
323E LYS* 3.7 26.0 - - - -
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Residues in contact with PHE 301 (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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227E PHE* 4.5 13.2 - - + -
247E LEU* 4.1 13.7 - - - +
248E TYR* 3.8 17.4 - - + -
268E LEU* 3.9 35.4 - - + -
269E ILE 3.1 21.0 + - - +
270E ALA* 3.8 12.0 - - - +
299E THR* 3.7 22.0 - - + -
300E CYS* 1.3 80.2 - - - +
302E ARG* 1.3 60.6 + - - +
319E HIS 3.2 4.9 - - - +
320E GLN* 4.0 27.6 - - + -
321E PHE* 5.3 0.2 - - - -
227F PHE* 4.0 27.8 - + + -
228F PHE* 3.7 30.7 - + - -
268F LEU* 5.1 1.8 - - + -
301F PHE* 5.0 6.1 - + - -
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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