Contacts of the helix formed by residues 344 - 356 (chain G) in PDB entry 2R9R
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 SER 344 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341G PRO 4.8 0.8 + - - -
342G LYS 3.1 7.1 + - - -
343G LEU* 1.3 80.9 - - - +
345G SER* 1.3 64.8 + - - +
346G SER* 2.9 24.1 + - - -
347G ILE* 3.1 27.4 + - - +
348G VAL* 3.3 10.0 + - - +
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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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343G LEU 3.8 0.6 + - - -
344G SER* 1.3 73.8 - - - +
346G SER* 1.3 60.0 + - - +
348G VAL* 3.6 9.0 + - - +
349G HIS* 3.2 22.7 + - - +
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Residues in contact with SER 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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344G SER* 2.9 20.1 + - - -
345G SER* 1.3 77.4 - - - +
347G ILE* 1.3 59.9 + - - +
349G HIS* 3.5 5.7 + - - +
350G GLU* 2.9 32.0 + - - +
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Residues in contact with ILE 347 (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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295G ILE* 3.8 24.7 - - + -
298G ARG* 4.0 26.0 - - - +
299G LEU* 4.4 15.3 - - + -
342G LYS 4.2 8.3 - - - +
343G LEU* 4.0 15.0 - - + -
344G SER* 3.1 31.2 + - - +
346G SER* 1.3 75.6 - - - +
348G VAL* 1.3 60.7 + - - +
350G GLU* 3.1 10.5 + - - +
351G ILE* 2.8 47.9 + - + +
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Residues in contact with VAL 348 (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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310G TRP* 4.8 6.3 - - + +
313G ARG* 3.9 37.2 - - + +
343G LEU* 4.3 20.4 - - + +
344G SER 3.3 14.6 + - - +
345G SER* 3.8 9.4 - - - +
346G SER 3.3 0.2 - - - -
347G ILE* 1.3 75.9 - - - +
349G HIS* 1.3 63.4 + - - +
351G ILE* 3.2 11.5 + - - +
352G ASP* 3.0 33.7 + - - +
358G LYS* 6.3 0.2 - - - +
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Residues in contact with HIS 349 (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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345G SER 3.2 14.7 + - - +
346G SER* 3.8 7.2 - - - +
348G VAL* 1.3 79.4 - - - +
350G GLU* 1.3 65.2 + - - +
352G ASP* 3.3 13.9 + - + +
353G SER* 3.2 27.8 + - - -
358G LYS* 6.1 3.4 - - - -
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Residues in contact with GLU 350 (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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295G ILE* 3.7 16.3 - - + +
298G ARG* 2.8 45.9 + - - -
346G SER* 2.9 17.7 + - - +
347G ILE* 3.1 16.5 + - - +
349G HIS* 1.3 77.8 + - - +
351G ILE* 1.3 56.3 + - + +
353G SER* 2.8 34.8 + - - -
354G ILE* 3.2 13.5 + - + +
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Residues in contact with ILE 351 (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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219G MET* 3.7 22.7 - - + -
292G LEU* 3.8 21.1 - - + -
295G ILE* 4.8 9.2 - - + -
306G LEU* 4.4 16.8 - - + -
310G TRP* 4.0 26.9 - - + +
343G LEU* 4.6 2.7 - - + -
347G ILE* 2.8 42.4 + - + +
348G VAL* 3.2 9.2 + - - +
350G GLU* 1.3 70.9 - - - +
352G ASP* 1.3 57.5 + - - +
354G ILE* 3.3 4.8 + - - +
355G LEU* 2.9 49.7 + - + +
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Residues in contact with ASP 352 (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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222G ARG* 2.8 42.4 + - - +
310G TRP* 5.1 3.7 + - - -
348G VAL* 3.0 31.9 + - - +
349G HIS* 3.5 14.5 - - + +
350G GLU 3.2 0.2 - - - -
351G ILE* 1.3 76.2 - - - +
353G SER* 1.3 55.0 + - - +
355G LEU* 4.6 1.2 - - - +
356G GLY* 2.6 34.6 + - - +
357G ASN 4.2 0.3 + - - -
358G LYS* 3.6 38.3 + - + +
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Residues in contact with SER 353 (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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349G HIS* 3.2 25.8 + - - -
350G GLU* 2.8 15.2 + - - -
352G ASP* 1.3 80.7 - - - +
354G ILE* 1.3 63.3 + - - +
356G GLY* 3.6 6.9 + - - -
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Residues in contact with ILE 354 (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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288G LYS* 3.5 35.1 + - + +
291G GLU* 3.6 50.5 - - + +
292G LEU* 3.8 17.3 - - + -
295G ILE* 3.4 34.3 - - + -
350G GLU* 3.2 16.9 + - + +
351G ILE* 3.3 6.7 + - - +
353G SER* 1.3 80.3 - - - +
355G LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 355 (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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219G MET* 3.7 34.1 - - + +
220G PHE* 3.9 26.2 - - + -
222G ARG* 4.3 10.3 - - - +
288G LYS* 2.8 28.7 + - + -
292G LEU* 3.8 26.5 - - + -
310G TRP* 4.6 3.8 - - + -
351G ILE* 2.9 41.2 + - + +
352G ASP* 4.2 1.8 - - - +
354G ILE* 1.3 77.0 - - - +
356G GLY* 1.3 65.3 + - - +
357G ASN* 3.2 24.2 + - - +
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Residues in contact with GLY 356 (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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288G LYS* 5.1 0.2 - - - -
352G ASP 2.6 24.7 + - - -
353G SER* 4.1 6.7 - - - -
354G ILE 3.4 2.2 - - - -
355G LEU* 1.3 73.8 - - - +
357G ASN* 1.3 57.2 + - - +
358G LYS 3.7 2.0 - - - -
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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