Contacts of the helix formed by residues 323 - 332 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319G GLY 4.5 4.4 + - - -
320G TYR 4.9 1.6 - - - -
321G LEU* 3.4 0.6 - - - +
322G CYS* 1.3 72.4 - - - +
324G SER* 1.3 59.4 + - - +
325G GLN 3.2 0.2 - - - -
326G LYS* 2.9 6.5 + - - +
327G PHE* 2.6 33.1 + - - +
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Residues in contact with SER 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G THR* 4.3 23.3 - - - +
120G SER 5.1 9.1 + - - -
121G GLN* 5.7 2.5 - - - +
320G TYR 4.9 2.2 + - - -
321G LEU* 3.6 12.9 + - - +
322G CYS 3.1 1.2 - - - -
323G GLU* 1.3 76.3 - - - +
325G GLN* 1.3 56.6 + - - +
326G LYS 3.2 0.6 + - - -
328G GLY* 4.3 10.8 + - - +
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Residues in contact with GLN 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321G LEU 3.7 4.6 + - - -
322G CYS 2.8 14.8 + - - -
324G SER* 1.3 75.0 - - - +
326G LYS* 1.3 55.5 - - - +
328G GLY* 5.0 1.1 - - - -
329G GLU* 4.9 5.2 + - - -
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Residues in contact with LYS 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322G CYS 3.2 4.6 + - - -
323G GLU* 2.9 8.8 + - - +
324G SER 3.2 0.2 - - - -
325G GLN* 1.3 81.1 - - - +
327G PHE* 1.3 60.7 + - - +
328G GLY 3.2 1.3 - - - -
329G GLU* 2.9 18.2 + - - +
330G LEU* 3.1 11.6 + - - -
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Residues in contact with PHE 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G VAL 5.8 0.9 - - - -
179G LEU* 5.6 9.6 - - - +
323G GLU* 2.6 20.5 + - - +
326G LYS* 1.3 70.3 - - - +
328G GLY* 1.3 60.6 + - - +
330G LEU* 4.8 0.4 - - - +
331G VAL* 3.2 21.8 + - - -
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Residues in contact with GLY 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LEU* 5.3 9.7 - - - -
116G VAL* 5.2 6.6 + - - -
117G THR* 5.2 13.1 - - - +
324G SER 4.3 11.3 + - - -
325G GLN 5.8 0.4 - - - -
326G LYS 3.2 0.6 - - - -
327G PHE* 1.3 73.7 - - - +
329G GLU* 1.3 66.2 + - - +
331G VAL* 5.5 0.2 - - - -
332G MET* 3.4 16.0 + - - -
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Residues in contact with GLU 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G GLN 4.9 3.3 + - - -
326G LYS* 2.9 13.6 + - - +
328G GLY* 1.3 76.4 - - - +
330G LEU* 1.3 57.3 + - - +
331G VAL 3.2 0.7 - - - -
332G MET 3.1 19.2 + - - -
333G THR* 3.4 10.9 + - - -
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Residues in contact with LEU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G GLY 4.0 15.9 - - - +
178G ALA* 5.8 2.9 - - - -
300G ALA* 6.6 0.2 - - - +
326G LYS 3.1 11.8 + - - -
327G PHE* 3.8 1.3 + - - +
329G GLU* 1.3 73.8 - - - +
331G VAL* 1.3 58.2 + - - +
333G THR* 4.3 7.4 + - - +
336G SER* 5.1 10.0 + - - -
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Residues in contact with VAL 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G GLY 5.5 1.3 - - - -
327G PHE 3.2 16.1 + - - -
329G GLU 3.2 0.6 - - - -
330G LEU* 1.3 77.5 - - - +
332G MET* 1.3 56.0 + - - +
333G THR 3.2 14.0 + - - +
336G SER 5.4 1.3 - - - -
337G LYS* 4.9 8.8 + - - -
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Residues in contact with MET 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328G GLY 3.4 12.6 + - - -
329G GLU 3.1 10.5 + - - -
331G VAL* 1.3 73.4 - - - +
333G 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