Contacts of the helix formed by residues 339 - 346 (chain G) in PDB entry 3DV0
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 LYS 339 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306F VAL* 4.8 4.3 - - - -
337G LYS* 4.6 5.8 - - + +
338G GLN* 1.3 79.0 - - - +
340G VAL* 1.3 64.8 + - - +
341G THR* 3.6 11.9 - - - +
342G ASP* 2.8 34.8 + - - +
343G LEU* 3.4 11.4 + - - +
366G GLU* 3.4 36.1 + - + +
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Residues in contact with VAL 340 (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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294F PRO* 3.8 20.2 - - + -
296F THR* 5.6 0.2 - - + -
306F VAL* 2.9 41.9 - - + +
307F TRP* 4.2 13.0 - - + -
339G LYS* 1.3 74.2 - - - +
341G THR* 1.3 58.0 + - - +
343G LEU* 3.4 8.8 + - + +
344G ILE* 3.0 36.2 + - + +
362G TYR* 3.4 41.3 - - + -
366G GLU* 3.4 4.2 + - - +
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Residues in contact with THR 341 (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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339G LYS* 3.6 12.5 - - - +
340G VAL* 1.3 76.4 - - - +
342G ASP* 1.3 68.5 + - - +
344G ILE* 4.0 2.9 - - - -
345G SER* 3.1 24.3 + - - -
359G TYR* 3.7 31.6 + - + +
362G TYR* 3.9 4.7 - - + -
363G LYS* 3.6 29.6 - - + +
366G GLU* 2.9 39.5 + - - +
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Residues in contact with ASP 342 (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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126G PHE* 3.7 31.1 - - + -
337G LYS 4.0 3.8 - - - +
338G GLN* 3.8 5.1 - - - -
339G LYS* 2.8 41.5 + - - +
340G VAL 3.1 0.2 - - - -
341G THR* 1.3 81.2 + - - +
343G LEU* 1.3 67.3 - - - +
345G SER* 2.9 17.1 + - - -
346G ILE* 3.2 19.0 + - + +
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Residues in contact with LEU 343 (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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296F THR* 3.8 10.3 - - + +
299F PRO* 3.8 16.2 - - + -
300F PHE* 4.2 7.2 - - + +
303F ALA* 4.1 13.7 - - + -
307F TRP* 3.6 31.0 - - + +
126G PHE* 4.8 4.9 - - + -
338G GLN* 4.0 21.5 - - + +
339G LYS 3.4 13.0 + - - +
340G VAL* 3.7 9.6 - - + +
342G ASP* 1.3 77.0 - - - +
344G ILE* 1.3 61.1 + - - +
346G ILE* 3.2 26.0 + - + +
347G MET* 3.5 11.3 - - - +
102H TYR* 3.7 30.4 - - + +
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Residues in contact with ILE 344 (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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294F PRO* 4.7 3.8 - - + -
296F THR* 3.5 22.7 - - + -
340G VAL* 3.0 33.5 + - + +
341G THR* 4.1 6.1 - - - +
343G LEU* 1.3 74.8 - - - +
345G SER* 1.3 64.3 + - - +
346G ILE 3.2 1.0 + - - -
347G MET* 3.2 17.1 + - - +
348G PHE 4.6 0.3 + - - -
351G LEU* 3.7 25.7 - - + +
355G LEU* 3.9 27.6 - - + +
358G GLN* 3.9 38.8 - - + +
359G TYR* 3.9 9.2 - - + +
362G TYR* 4.6 1.6 - - + -
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Residues in contact with SER 345 (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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341G THR 3.1 17.8 + - - -
342G ASP* 2.9 9.8 + - - -
344G ILE* 1.3 80.6 - - - +
346G ILE* 1.3 61.0 + - - +
347G MET 3.4 0.7 + - - -
348G PHE 3.7 13.5 - - - +
351G LEU* 4.7 15.0 - - - +
359G TYR* 4.8 8.0 - - - -
101H ARG* 5.4 0.2 - - - -
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Residues in contact with ILE 346 (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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300F PHE* 4.6 0.2 - - + -
126G PHE* 4.4 25.4 - - + -
130G GLN* 5.4 2.0 - - - +
342G ASP* 3.7 9.9 - - + +
343G LEU* 3.2 21.1 - - + +
345G SER* 1.3 81.2 - - - +
347G MET* 1.3 58.6 + - - +
348G PHE 3.6 2.0 - - - -
101H ARG* 3.4 19.4 - - - +
102H TYR* 3.1 68.0 + - + +
105H GLY* 4.1 23.3 - - - +
106H GLY* 4.4 2.9 - - - +
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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