Contacts of the strand formed by residues 343 - 347 (chain E) in PDB entry 3VZC
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 GLU 343 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E GLY* 3.7 25.9 - - - +
85E HIS* 4.2 24.0 - - + +
86E GLU* 5.2 6.0 - - + +
339E ALA* 3.2 4.9 - - - -
340E VAL* 2.8 44.3 + - + +
341E ASP 4.3 4.2 - - - +
342E GLY* 1.3 88.6 - - - +
344E LEU* 1.3 66.6 + - - +
345E MET* 3.5 0.7 + - - +
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Residues in contact with LEU 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E LEU* 4.0 34.1 - - + -
337E VAL* 3.7 31.9 - - + -
338E PHE 3.5 4.0 - - - -
339E ALA* 4.7 1.1 - - - +
342E GLY 4.0 2.2 + - - -
343E GLU* 1.3 76.2 - - - +
345E MET* 1.3 76.6 + - - +
346E VAL* 4.5 10.8 - - + +
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Residues in contact with MET 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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155E LEU* 5.7 0.7 - - + -
157E THR* 4.1 14.1 - - + -
161E LEU* 5.1 9.4 - - + -
163E LEU* 3.9 29.4 - - + -
169E LEU* 4.6 4.0 - - + -
337E VAL* 3.5 1.0 - - - -
338E PHE* 2.6 56.9 + - + +
340E VAL* 3.9 31.6 - - + -
343E GLU 4.4 0.2 - - - +
344E LEU* 1.3 80.4 - - - +
346E VAL* 1.3 67.9 + - - +
347E SER* 4.7 2.5 - - - -
350E VAL* 4.0 29.2 - - + -
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Residues in contact with VAL 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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159E SER* 6.1 1.0 - - - -
335E LYS* 5.7 12.1 - - + -
336E GLY 3.3 12.6 - - - +
337E VAL* 4.0 14.8 - - + -
344E LEU* 4.5 11.7 - - + -
345E MET* 1.3 82.0 - - - +
347E SER* 1.3 65.4 + - - +
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Residues in contact with SER 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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157E THR* 3.7 17.2 + - - -
158E ALA* 4.0 4.0 + - - +
159E SER* 5.0 2.2 + - - -
331E PRO* 4.2 1.4 - - - +
335E LYS* 4.7 6.8 - - - +
336E GLY* 2.9 32.4 + - - +
338E PHE* 3.6 12.5 - - - -
345E MET* 4.7 2.7 - - - -
346E VAL* 1.3 76.7 - - - +
348E GLU* 1.3 70.6 + - - +
349E ALA 3.0 22.9 + - - -
350E VAL* 4.0 18.4 - - - -
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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