Contacts of the helix formed by residues 338 - 347 (chain E) in PDB entry 2VUU
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 VAL 338 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329E ARG* 3.3 46.7 - - - +
333E GLU 4.5 0.4 - - - +
334E TYR* 2.7 41.8 + - + +
336E ARG 3.6 0.2 - - - -
337E GLU* 1.3 78.1 - - + +
339E PHE* 1.3 68.2 + - - +
340E PRO* 3.2 2.7 - - - -
341E ILE* 2.7 20.8 + - + +
342E GLU* 3.0 28.8 + - + +
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Residues in contact with PHE 339 (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 PHE 4.1 5.2 - - - -
158E THR* 3.9 16.6 - - - -
159E SER 4.4 2.5 - - - -
167E MET* 4.0 20.2 - - + -
175E PHE* 4.4 9.0 - + - -
232E PHE* 3.8 21.8 - + - -
236E LEU* 4.0 21.1 - - + -
334E TYR* 2.8 34.6 + + + +
335E ALA* 3.0 26.9 - - - +
338E VAL* 1.3 73.3 - - - +
340E PRO* 1.3 63.7 - - + +
342E GLU* 3.1 5.2 + - + +
343E GLU* 3.0 52.9 + - + +
350E TRP* 3.5 27.8 - + - -
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Residues in contact with PRO 340 (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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236E LEU* 4.1 13.9 - - + -
335E ALA 2.8 25.6 - - - +
336E ARG 3.3 21.5 - - - +
337E GLU 4.4 0.2 - - - -
338E VAL 3.3 4.9 - - - +
339E PHE* 1.3 82.4 - - + +
341E ILE* 1.3 61.7 + - + +
343E GLU* 3.2 7.1 + - + +
344E GLU* 3.0 30.1 + - - +
350E TRP* 4.3 7.9 - - + -
351E MET* 4.0 26.0 - - + +
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Residues in contact with ILE 341 (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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337E GLU 3.3 26.9 - - - +
338E VAL* 2.7 13.5 + - + +
340E PRO* 1.3 76.7 - - + +
342E GLU* 1.3 61.6 + - + +
344E GLU* 3.5 15.0 + - - +
345E ALA* 3.1 22.4 + - + +
711M LEU* 5.4 12.3 - - + -
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Residues in contact with GLU 342 (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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155E ASN* 3.1 32.6 + - - +
157E PHE 3.8 9.7 - - - +
193E GLU* 5.7 1.7 - - - +
334E TYR* 2.5 27.2 + - - -
338E VAL* 3.0 28.8 + - + +
339E PHE* 3.6 5.4 - - + +
341E ILE* 1.3 73.7 - - + +
343E GLU* 1.3 68.6 + - + +
345E ALA* 2.9 9.0 + - - +
346E ASN* 2.9 37.9 + - - +
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Residues in contact with GLU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E THR* 3.2 17.2 + - - -
159E SER* 3.0 30.8 + - - -
160E LEU* 5.5 0.5 - - - +
339E PHE* 3.0 30.2 + - + +
340E PRO 3.3 9.0 - - - +
342E GLU* 1.3 78.2 - - - +
344E GLU* 1.3 62.7 + - - +
346E ASN* 3.2 6.5 + - - +
347E GLY 3.0 7.4 + - - -
348E LEU* 2.6 57.2 + - + +
350E TRP* 3.1 33.0 + - + +
351E MET* 4.1 2.5 - - + -
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Residues in contact with GLU 344 (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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340E PRO 3.0 15.5 + - - +
341E ILE* 3.8 15.2 - - - +
343E GLU* 1.3 76.2 - - - +
345E ALA* 1.3 60.3 + - - +
347E GLY* 3.5 9.5 + - - -
348E LEU 3.4 14.0 - - - +
351E MET* 3.9 10.0 - - - +
352E LEU* 3.6 33.3 - - + +
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Residues in contact with ALA 345 (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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341E ILE* 3.1 14.5 + - + +
342E GLU* 2.9 13.1 + - - +
344E GLU* 1.3 76.9 - - - +
346E ASN* 1.3 65.0 + - - +
347E GLY* 3.6 0.3 + - - -
711M LEU* 6.5 0.4 - - + -
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Residues in contact with ASN 346 (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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158E THR* 4.7 7.7 + - - +
160E LEU* 3.6 35.9 - - + +
162E TYR* 5.7 1.4 + - - -
342E GLU* 2.9 35.1 + - - +
343E GLU* 3.9 6.4 - - - +
345E ALA* 1.3 79.7 - - - +
347E GLY* 1.3 57.3 + - - +
348E LEU* 3.9 2.5 - - + +
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Residues in contact with GLY 347 (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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343E GLU 3.0 2.0 + - - -
344E GLU 3.5 6.0 + - - -
345E ALA 3.3 3.4 - - - -
346E ASN* 1.3 81.1 - - - +
348E LEU* 1.3 71.8 + - - +
349E ASP* 3.9 4.5 + - - +
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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