Contacts of the helix formed by residues 259 - 265 (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 ASP 259 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603B LEU* 5.6 0.7 - - - +
606B THR* 5.2 6.0 + - + -
610B LYS* 5.2 10.3 + - - +
607C LEU* 3.3 31.3 - - + +
257G CYS 5.3 0.4 - - - -
258G ASP* 1.3 71.7 - - - +
260G ARG* 1.3 62.2 + - - +
261G ILE 3.2 1.8 - - - -
262G THR* 3.3 22.3 + - - +
263G GLU* 4.0 9.5 + - - +
269G PRO* 3.4 25.1 - - - +
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Residues in contact with ARG 260 (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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602B SER* 2.6 46.3 + - - -
605B MET* 3.3 31.7 - - - +
606B THR* 3.3 25.1 + - + +
609B GLN* 5.1 5.3 - - - +
239G LEU* 4.8 2.2 - - - +
240G ASP 3.7 12.3 + - - -
241G SER* 4.9 9.6 - - - +
243G THR* 2.6 42.5 + - - +
244G PHE* 3.8 14.4 - - + +
245G LEU* 4.3 7.7 - - - +
258G ASP* 3.1 7.4 + - + -
259G ASP* 1.3 76.6 - - - +
261G ILE* 1.3 65.0 + - - +
262G THR 3.2 0.4 - - - -
263G GLU* 3.2 23.7 + - - +
264G LEU* 3.2 29.7 + - + +
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Residues in contact with ILE 261 (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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244G PHE* 3.9 27.0 - - + +
254G PHE* 5.3 1.3 - - + -
257G CYS* 3.6 22.0 - - - -
258G ASP 3.3 17.6 + - - +
260G ARG* 1.3 76.5 - - - +
262G THR* 1.3 66.8 + - - +
264G LEU* 4.3 1.3 - - - +
265G ILE* 2.6 57.5 + - + -
266G GLY 3.1 2.9 + - - -
267G TYR* 3.4 18.4 - - + +
269G PRO* 4.6 5.4 - - + -
272G LEU* 3.5 28.7 - - + -
309G MET* 4.3 12.3 - - + -
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Residues in contact with THR 262 (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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381A VAL* 5.1 2.6 - - - +
259G ASP* 3.4 14.7 + - - +
260G ARG 3.2 0.6 - - - -
261G ILE* 1.3 79.4 - - - +
263G GLU* 1.3 63.1 + - + +
266G GLY* 3.2 29.0 + - - +
267G TYR 2.8 21.9 + - - +
268G HIS* 4.0 23.0 + - + +
269G PRO* 3.7 17.0 - - - +
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Residues in contact with GLU 263 (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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378A HIS* 6.3 3.4 - - + -
381A VAL* 3.3 24.3 - - + +
387A GLN* 3.0 40.4 + - - +
606B THR* 4.5 8.0 - - - +
609B GLN* 3.6 26.8 + - - -
610B LYS* 5.4 5.4 + - - -
241G SER 5.1 6.2 - - - +
259G ASP* 4.2 7.6 - - - +
260G ARG* 3.2 24.1 + - - +
261G ILE 3.2 0.4 - - - -
262G THR* 1.3 80.5 - - + +
264G LEU* 1.3 60.6 + - + +
265G ILE 5.4 0.2 - - - -
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Residues in contact with LEU 264 (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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387A GLN* 4.4 18.6 - - + +
241G SER 4.4 7.6 - - - +
242G LYS* 3.9 34.8 - - + -
243G THR 4.2 3.8 - - - +
244G PHE* 3.6 26.0 - - + -
260G ARG* 3.2 20.4 + - + +
261G ILE* 3.2 2.5 + - - +
263G GLU* 1.3 82.4 - - + +
265G ILE* 1.3 72.7 + - + +
317G VAL* 4.1 14.7 - - - +
343G VAL* 3.7 31.3 - - + +
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Residues in contact with ILE 265 (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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244G PHE* 4.1 22.4 - - + -
261G ILE* 2.6 40.1 + - + +
263G GLU 5.4 0.2 - - - -
264G LEU* 1.3 89.0 - - + +
266G GLY* 1.3 56.6 + - - +
267G TYR* 3.3 30.3 - - + -
309G MET* 4.4 15.0 - - + -
310G LEU 3.8 4.0 - - - +
311G ALA* 3.5 24.3 - - + +
312G LYS 3.4 14.4 + - - -
313G HIS* 4.7 1.7 + - - -
317G VAL* 3.4 24.9 - - + -
319G LEU* 4.4 4.5 - - + -
343G VAL* 4.7 0.4 - - + -
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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