Contacts of the helix formed by residues 285 - 300 (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 285 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G TYR* 4.9 0.7 - - + -
282G HIS* 3.0 13.5 + - + +
284G LEU* 1.3 79.4 - - - +
286G SER* 1.3 65.5 + - - +
287G GLU 3.2 3.1 - - - -
288G ASN* 3.2 16.1 + - + +
289G MET* 3.0 28.0 + - + +
306G GLN 4.3 5.5 - - - +
307G TYR* 3.5 23.1 - - + -
308G ARG* 2.8 58.1 + - - +
318G TRP* 5.0 2.3 - - - -
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Residues in contact with SER 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G TYR* 4.4 11.4 + - - -
281G TYR* 3.7 21.2 + - - +
282G HIS 3.0 15.0 + - - -
283G ALA* 3.5 15.6 + - - -
285G ASP* 1.3 78.6 - - - +
287G GLU* 1.3 61.6 + - - +
289G MET* 3.6 3.1 + - - +
290G THR* 2.6 34.4 + - - -
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Residues in contact with GLU 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ALA 4.7 4.6 + - - +
284G LEU 4.9 4.2 + - - +
285G ASP 3.2 0.8 - - - -
286G SER* 1.3 83.7 - - - +
288G ASN* 1.3 64.8 + - - +
290G THR* 3.4 11.6 + - - +
291G LYS* 3.4 33.2 + - - +
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Residues in contact with ASN 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU 4.3 14.8 + - - -
285G ASP* 3.2 15.9 + - + +
287G GLU* 1.3 80.1 - - - +
289G MET* 1.3 61.9 + - + +
291G LYS* 3.4 20.0 + - - +
292G SER* 3.1 29.3 + - - -
304G SER 5.8 2.7 - - - +
307G TYR* 6.6 0.2 - - + -
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Residues in contact with MET 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252G MET* 6.0 0.9 - - + -
278G TYR* 3.6 4.8 + - + -
281G TYR* 3.5 56.8 - - + +
285G ASP* 3.0 20.5 + - + +
286G SER 4.1 2.0 - - - +
288G ASN* 1.3 75.9 - - + +
290G THR* 1.3 59.9 + - - +
291G LYS 3.3 0.2 - - - -
292G SER* 3.5 6.3 + - - -
293G HIS* 3.0 28.1 + - - +
304G SER* 3.7 33.9 - - - +
307G TYR* 3.6 42.2 - - + -
321G THR* 5.1 3.6 - - + +
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Residues in contact with THR 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G TYR* 3.6 23.1 - - + +
286G SER 2.6 20.9 + - - -
287G GLU* 3.5 15.4 + - - +
288G ASN 3.2 0.2 - - - -
289G MET* 1.3 77.6 - - - +
291G LYS* 1.3 62.3 + - + +
293G HIS* 3.5 2.6 + - - +
294G GLN* 3.3 40.4 + - + +
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Residues in contact with LYS 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G GLU* 3.4 22.5 + - - +
288G ASN* 3.4 18.8 + - - +
289G MET 3.3 0.2 - - - -
290G THR* 1.3 77.9 - - + +
292G SER* 1.3 60.8 + - - +
294G GLN* 3.7 14.0 + - - +
295G ASN* 3.0 34.4 + - - +
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Residues in contact with SER 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ASN 3.1 17.2 + - - -
289G MET* 3.7 10.7 - - - -
290G THR 3.3 0.2 - - - -
291G LYS* 1.3 77.3 - - - +
293G HIS* 1.3 59.9 + - - +
295G ASN* 3.4 8.5 + - - +
296G LEU 3.0 21.7 + - - -
302G VAL* 3.5 21.4 - - - +
303G VAL 4.6 1.7 + - - -
304G SER* 3.7 36.3 + - - -
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Residues in contact with HIS 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G MET 3.6 24.2 + - - -
251G ASP* 4.8 2.0 - - - -
252G MET* 3.9 26.6 - - + +
278G TYR* 3.1 35.5 + + + +
289G MET 3.0 10.1 + - - +
290G THR 3.8 3.4 - - - +
291G LYS 3.4 0.2 - - - -
292G SER* 1.3 78.3 - - - +
294G GLN* 1.3 60.6 + - + +
296G LEU* 3.4 12.8 + - + +
297G CYS* 3.2 36.0 + - - -
337G ILE* 3.8 17.5 - - + +
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Residues in contact with GLN 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G THR* 3.3 28.7 + - + +
291G LYS* 4.0 14.2 - - - +
292G SER 3.3 0.2 - - - -
293G HIS* 1.3 78.7 - - + +
295G ASN* 1.3 57.2 + - - +
297G CYS* 3.7 6.2 + - - +
298G THR* 2.4 38.7 + - - -
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Residues in contact with ASN 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G LYS* 3.0 23.9 + - - +
292G SER* 3.4 8.6 + - - +
293G HIS 3.3 0.2 - - - -
294G GLN* 1.3 76.5 - - - +
296G LEU* 1.3 59.6 + - - +
298G THR* 3.7 6.8 + - - +
299G LYS* 2.8 55.2 + - + +
301G GLN 4.2 1.6 - - - +
302G VAL* 4.3 17.0 - - + +
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Residues in contact with LEU 296 (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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252G MET* 5.2 6.5 - - + -
292G SER 3.0 14.6 + - - +
293G HIS* 3.5 17.7 - - + +
294G GLN 3.3 0.4 - - - -
295G ASN* 1.3 74.9 - - - +
297G CYS* 1.3 60.9 + - - +
300G GLY* 2.9 53.6 + - - +
301G GLN* 3.6 7.9 - - - -
302G VAL* 3.6 13.4 - - + +
323G GLY* 3.6 29.4 - - - -
324G THR 3.7 2.0 - - - +
325G VAL* 3.6 12.5 - - + +
337G ILE* 3.6 40.4 - - + -
339G CYS* 5.5 0.4 - - - -
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Residues in contact with CYS 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G MET* 4.6 20.9 - - + -
293G HIS* 3.2 39.5 + - - +
294G GLN* 3.7 6.3 + - - +
296G LEU* 1.3 79.8 - - - +
298G THR* 1.3 61.5 + - - +
300G GLY* 4.6 1.2 + - - -
325G VAL* 4.6 7.2 - - - +
337G ILE* 5.3 1.3 - - - -
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Residues in contact with THR 298 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G GLN* 2.4 25.9 + - - +
295G ASN* 3.9 8.2 + - - +
296G LEU 3.1 0.6 - - - -
297G CYS* 1.3 81.9 - - - +
299G LYS* 1.3 73.5 + - + +
300G GLY 3.6 0.2 - - - -
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Residues in contact with LYS 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G ASN* 2.8 43.3 + - + +
298G THR* 1.3 87.3 - - + +
300G GLY* 1.3 57.8 + - - +
301G GLN* 3.2 21.0 + - - +
302G VAL* 6.2 1.1 - - + -
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Residues in contact with GLY 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G LEU* 2.9 16.2 + - - -
297G CYS 4.6 1.5 - - - -
298G THR 3.6 1.6 - - - -
299G LYS* 1.3 76.0 - - - +
301G GLN* 1.3 59.8 + - - +
324G THR* 4.4 1.0 - - - +
325G VAL* 2.8 37.6 + - - +
327G TYR* 4.2 18.8 - - - -
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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