Contacts of the helix formed by residues 323 - 332 (chain E) in PDB entry 5ZRV
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 323 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E SER 6.0 0.2 - - - -
319E GLY 4.5 4.2 + - - -
320E TYR 4.9 1.2 - - - -
321E LEU* 3.4 1.0 - - - +
322E CYS* 1.3 72.3 - - - +
324E SER* 1.3 58.5 + - - +
325E GLN 3.2 0.2 - - - -
326E LYS* 3.3 6.1 - - - +
327E PHE* 2.6 33.2 + - - +
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Residues in contact with SER 324 (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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117E THR* 4.3 23.1 - - - +
120E SER 5.1 10.2 + - - -
121E GLN* 5.7 2.5 - - - +
320E TYR 4.9 3.0 + - - -
321E LEU* 3.6 12.7 + - - +
322E CYS 3.1 1.2 - - - -
323E GLU* 1.3 78.1 - - - +
325E GLN* 1.3 57.3 + - - +
326E LYS 3.2 0.9 + - - -
328E GLY* 4.3 10.3 + - - +
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Residues in contact with GLN 325 (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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321E LEU 3.7 5.5 + - - -
322E CYS 2.8 14.4 + - - -
324E SER* 1.3 75.8 - - - +
326E LYS* 1.3 55.8 + - - +
328E GLY 5.0 1.1 - - - -
329E GLU* 4.9 4.8 + - - -
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Residues in contact with LYS 326 (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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322E CYS 3.2 4.2 + - - -
323E GLU* 2.9 8.8 + - - +
325E GLN* 1.3 80.2 - - - +
327E PHE* 1.3 62.0 + - - +
328E GLY 3.2 1.8 - - - -
329E GLU* 2.9 18.4 + - - +
330E LEU* 3.1 11.6 + - - -
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Residues in contact with PHE 327 (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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116E VAL 5.8 0.7 - - - -
179E LEU* 5.6 9.4 - - - +
323E GLU* 2.6 20.5 + - - +
326E LYS* 1.3 70.6 - - - +
328E GLY* 1.3 60.6 + - - +
330E LEU 4.2 0.4 - - - +
331E VAL* 3.2 21.3 + - - -
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Residues in contact with GLY 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E LEU* 5.3 9.8 - - - -
116E VAL* 5.2 6.0 + - - -
117E THR* 5.2 13.3 - - - +
324E SER* 4.3 11.1 + - - +
325E GLN 5.8 0.2 - - - -
326E LYS 3.2 0.8 - - - +
327E PHE* 1.3 74.1 - - - +
329E GLU* 1.3 64.9 + - - +
331E VAL* 5.5 0.2 - - - -
332E MET* 3.4 14.9 + - - -
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Residues in contact with GLU 329 (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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325E GLN 4.9 3.6 + - - -
326E LYS* 2.9 13.6 + - - +
328E GLY* 1.3 76.0 - - - +
330E LEU* 1.3 56.2 + - - +
331E VAL 3.2 0.9 - - - -
332E MET 3.1 19.2 + - - +
333E THR* 3.4 10.9 + - - -
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Residues in contact with LEU 330 (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 GLY 4.0 16.1 - - - +
178E ALA* 5.8 2.5 - - - -
326E LYS 3.1 12.0 + - - -
327E PHE* 4.2 0.7 - - - +
329E GLU* 1.3 73.6 - - - +
331E VAL* 1.3 58.4 + - - +
333E THR* 4.3 6.9 + - - +
336E SER* 5.1 10.7 + - - -
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Residues in contact with VAL 331 (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 GLY 5.5 1.1 - - - -
327E PHE 3.2 15.2 + - - -
329E GLU 3.2 0.8 - - - -
330E LEU* 1.3 77.5 - - - +
332E MET* 1.3 55.8 + - - +
333E THR 3.2 14.0 + - - +
336E SER 5.4 1.8 - - - -
337E LYS* 4.9 9.0 + - - -
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Residues in contact with MET 332 (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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328E GLY 3.4 12.7 + - - -
329E GLU 3.1 10.5 + - - -
331E VAL* 1.3 74.9 - - - +
333E THR* 1.3 56.3 + - - +
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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