Contacts of the helix formed by residues 310 - 320 (chain G) in PDB entry 2ABJ
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 THR 310 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250G ASP* 3.3 44.9 - - + +
251G HIS 3.5 4.5 - - - -
252G GLN* 4.2 6.1 - - + +
253G ILE* 3.6 11.1 - - - +
308G TYR* 5.3 3.6 - - + -
309G LEU* 1.3 80.2 - - - +
311G MET* 1.3 65.0 + - - +
312G ASP* 3.5 8.2 + - - +
313G ASP* 3.1 36.6 + - - +
314G LEU* 3.1 17.7 + - - +
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Residues in contact with MET 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ALA* 5.1 0.2 - - - -
244G LEU* 4.0 9.0 - - - -
246G LEU* 3.8 18.2 - - + -
250G ASP 4.4 0.4 + - - -
251G HIS* 3.1 23.3 + - + +
253G ILE* 3.6 25.5 - - + +
310G THR* 1.3 73.4 - - - +
312G ASP* 1.3 55.5 + - - +
314G LEU* 3.3 14.7 + - + +
315G THR* 2.7 39.1 + - - +
341G ILE* 4.0 14.6 - - + -
343G TYR* 3.6 61.9 - - + +
348G ILE* 4.2 10.1 - - + -
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Residues in contact with ASP 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G ASP 5.3 3.6 + - - +
251G HIS* 6.4 1.8 - - - -
310G THR* 3.2 7.9 + - - +
311G MET* 1.3 79.0 - - - +
313G ASP* 1.3 59.1 + - - +
315G THR* 4.0 11.2 - - - +
316G THR* 2.9 42.5 + - + +
343G TYR* 5.7 2.9 + - - -
344G LYS* 5.6 3.5 + - - -
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Residues in contact with ASP 313 (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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263G LEU* 6.2 0.4 - - + -
265G TRP* 3.7 17.7 - - + -
268G GLU* 4.1 16.0 - - - +
307G ARG* 3.6 15.3 + - - -
308G TYR 3.9 1.7 - - - +
309G LEU* 3.7 7.6 - - + -
310G THR* 3.1 45.4 + - - +
312G ASP* 1.3 75.2 - - - +
314G LEU* 1.3 62.2 + - - +
316G THR* 4.0 5.2 + - - -
317G ALA* 3.1 25.3 + - - +
322G ARG* 4.9 1.0 + - - -
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Residues in contact with LEU 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G ILE* 4.1 17.0 - - + -
263G LEU* 4.5 14.6 - - + -
265G TRP* 5.0 2.7 - - - -
310G THR 3.1 9.7 + - - +
311G MET* 3.4 16.6 - - + +
313G ASP* 1.3 75.5 - - - +
315G THR* 1.3 57.0 + - - +
317G ALA* 3.2 5.7 + - - +
318G LEU* 2.8 53.0 + - + +
323G VAL* 3.9 21.1 - - + -
326G MET* 3.7 24.9 - - + -
341G ILE* 3.6 31.6 - - + -
348G ILE* 5.5 1.8 - - + -
350G ILE* 4.4 5.6 - - + -
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Residues in contact with THR 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G MET* 2.7 23.2 + - - +
312G ASP* 3.7 14.8 - - - +
314G LEU* 1.3 74.5 - - - +
316G THR* 1.3 65.6 + - + +
318G LEU* 3.4 9.7 + - - +
319G GLU* 3.2 44.0 + - - +
343G TYR* 5.7 2.3 - - - -
348G ILE* 4.4 19.6 - - - +
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Residues in contact with THR 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G ASP* 2.9 27.4 + - + +
313G ASP* 4.0 4.9 + - - -
315G THR* 1.3 79.7 - - + +
317G ALA* 1.3 64.4 + - - +
319G GLU* 3.6 18.2 + - - +
320G GLY* 3.2 17.8 + - - -
322G ARG* 4.0 12.7 + - - -
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Residues in contact with ALA 317 (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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265G TRP* 3.5 29.8 - - + -
313G ASP 3.1 20.0 + - - +
314G LEU 3.2 4.5 + - - +
316G THR* 1.3 76.6 + - - +
318G LEU* 1.3 60.2 + - - +
320G GLY 3.3 1.4 + - - -
321G ASN 3.1 4.2 + - - -
322G ARG* 2.7 51.8 + - + +
323G VAL* 3.8 9.9 - - + -
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G LEU* 2.8 36.3 + - + +
315G THR* 3.7 7.4 - - - +
316G THR 3.4 0.2 - - - -
317G ALA* 1.3 74.5 - - - +
319G GLU* 1.3 64.5 + - - +
321G ASN* 3.1 18.0 + - - +
322G ARG 4.8 0.9 - - - +
323G VAL* 3.8 21.8 - - + +
348G ILE* 3.4 32.8 - - + -
349G HIS 3.5 19.1 - - - +
350G ILE* 4.0 6.1 - - + -
351G PRO* 3.7 23.3 - - + -
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Residues in contact with GLU 319 (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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315G THR* 3.2 34.0 + - - +
316G THR* 3.7 22.8 - - - +
318G LEU* 1.3 76.6 - - - +
320G GLY* 1.3 57.0 + - - +
321G ASN* 3.3 12.3 + - - -
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Residues in contact with GLY 320 (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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316G THR 3.2 11.7 + - - -
317G ALA 3.3 2.9 + - - -
318G LEU 3.2 0.6 - - - -
319G GLU* 1.3 76.0 - - - +
321G ASN* 1.3 71.1 + - - +
322G ARG* 3.2 20.6 + - - +
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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