Contacts of the strand formed by residues 336 - 343 (chain G) in PDB entry 4PKY
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 CYS 336 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B LYS* 4.0 15.9 - - - -
247G GLU* 3.9 32.8 - - + +
248G HIS 3.2 15.7 - - - +
249G SER* 4.7 1.8 - - - +
250G MET* 4.1 7.7 - - - -
255G THR* 5.4 0.9 - - - +
325G VAL* 3.8 6.2 - - - +
326G ILE* 3.0 38.7 + - - +
335G GLN* 1.3 93.5 - - + +
337G ILE* 1.3 65.1 + - - +
338G MET* 5.7 0.4 - - - -
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Residues in contact with ILE 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G GLU* 3.4 5.2 - - - +
248G HIS* 2.7 46.2 + - + +
249G SER 4.1 10.8 - - - +
250G MET* 4.2 24.5 - - + +
252G MET* 4.0 13.5 - - - -
293G HIS* 3.8 21.8 - - + +
296G LEU* 3.6 34.5 - - + -
297G CYS* 5.3 0.9 - - - -
324G THR 3.5 10.5 - - - +
325G VAL* 4.5 6.3 - - + -
336G CYS* 1.3 80.3 - - - +
338G MET* 1.3 62.3 + - - +
339G CYS* 3.8 22.9 + - - -
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Residues in contact with MET 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LYS* 4.1 15.5 - - + -
598B MET* 3.6 33.2 - - + -
599B GLN* 3.5 30.1 - - - +
245G LEU* 3.8 28.5 - - + -
246G SER 3.8 13.5 - - - +
247G GLU* 4.4 11.2 - - + +
256G TYR* 5.4 0.2 - - + -
322G GLN 3.5 4.5 - - - +
324G THR* 2.8 44.8 + - - +
326G ILE* 4.1 18.1 - - + +
336G CYS* 4.2 0.8 - - - -
337G ILE* 1.3 71.4 - - - +
339G CYS* 1.3 63.9 + - - +
340G VAL* 4.9 3.0 - - + +
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Residues in contact with CYS 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G LEU* 3.8 2.4 - - - -
246G SER* 2.9 45.4 + - - +
248G HIS* 3.7 22.0 - - + +
252G MET* 4.2 14.1 - - - -
296G LEU* 5.5 0.4 - - - -
321G THR* 3.6 26.5 - - + -
322G GLN 3.5 3.6 - - - -
323G GLY* 4.1 5.6 - - - -
337G ILE* 3.8 18.1 + - - -
338G MET* 1.3 79.3 - - - +
340G VAL* 1.3 67.0 + - - +
341G ASN* 4.0 4.7 - - - +
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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
----------------------------------------------------------
598B MET* 4.5 24.9 - - + -
239G LEU* 3.6 19.1 - - + -
243G THR* 3.6 26.0 - - + -
244G PHE 4.1 2.9 - - - -
245G LEU* 4.4 11.4 - - + +
322G GLN* 3.0 50.3 + - + +
338G MET* 4.9 4.3 - - + +
339G CYS* 1.3 78.9 - - - +
341G ASN* 1.3 59.4 + - - +
342G TYR* 3.4 23.4 - - + +
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Residues in contact with ASN 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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243G THR* 3.3 5.5 - - - +
244G PHE* 3.0 75.0 + - + +
246G SER* 3.1 27.1 + - - +
248G HIS* 5.7 0.3 + - - -
307G TYR* 3.7 8.2 + - - +
319G LEU* 4.9 4.3 - - + -
320G GLU 3.5 4.5 - - - +
321G THR* 2.8 31.3 + - - +
339G CYS* 4.0 5.1 - - - +
340G VAL* 1.3 73.9 - - - +
342G TYR* 1.3 62.8 - - - +
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Residues in contact with TYR 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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239G LEU* 4.0 19.2 - - + +
240G ASP* 4.5 10.1 - - - +
242G LYS 3.8 3.6 - - - +
243G THR* 3.3 29.8 - - + +
319G LEU* 3.1 8.2 - - - -
320G GLU* 2.8 72.6 + - + +
322G GLN* 3.6 28.1 + - + -
340G VAL* 3.4 29.5 - - + +
341G ASN* 1.3 72.5 - - - +
343G VAL* 1.3 66.3 + - - +
344G LEU* 3.9 2.8 + - + +
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Residues in contact with VAL 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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240G ASP* 5.8 0.3 - - - +
242G LYS* 2.9 49.7 + - + +
244G PHE* 4.3 6.5 - - + -
264G LEU* 3.7 38.8 - - + +
265G ILE* 4.7 2.2 - - + -
317G VAL* 4.6 14.6 - - + -
318G TRP 4.3 2.2 - - - +
319G LEU* 3.6 23.3 - - + -
342G TYR* 1.3 77.0 - - - +
344G LEU* 1.3 70.8 + - - +
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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