Contacts of the helix formed by residues 310 - 320 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ASP* 3.4 40.2 - - + +
251A HIS 3.4 4.7 - - - -
252A GLN* 4.2 11.4 - - + -
253A ILE* 4.4 6.5 - - - +
308A TYR* 5.4 3.8 - - + -
309A LEU* 1.3 80.6 - - - +
311A MET* 1.3 63.6 + - - +
312A ASP* 3.6 6.9 + - - +
313A ASP* 3.0 37.4 + - - +
314A LEU* 3.2 20.6 + - - +
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 5.0 0.2 - - - -
244A LEU* 3.9 14.6 - - - -
246A LEU* 3.8 19.7 - - + -
250A ASP 4.4 0.4 + - - -
251A HIS* 3.0 19.7 + - + +
253A ILE* 3.5 20.8 - - - +
310A THR* 1.3 73.1 - - - +
312A ASP* 1.3 61.5 + - - +
314A LEU* 3.2 21.1 + - + +
315A THR* 2.9 37.0 + - + +
341A ILE* 4.3 8.3 - - + -
343A TYR* 3.5 60.8 - - + +
348A ILE* 4.3 11.4 - - + -
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASP 5.2 4.4 + - - +
251A HIS* 6.2 1.6 - - - -
310A THR* 3.2 7.2 + - - +
311A MET* 1.3 78.6 - - - +
313A ASP* 1.3 65.1 + - - +
315A THR* 3.3 9.9 + - - +
316A THR* 2.9 34.8 + - - +
343A TYR* 5.5 4.0 + - - -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 6.4 0.4 - - + -
265A TRP* 3.7 18.8 - - + -
268A GLU* 4.2 15.2 - - - +
307A ARG* 3.7 13.3 + - - -
308A TYR 4.0 2.1 - - - +
309A LEU* 3.8 6.9 - - + -
310A THR* 3.0 42.2 + - - +
312A ASP* 1.3 74.9 - - - +
314A LEU* 1.3 61.6 + - - +
316A THR* 4.0 4.5 - - - -
317A ALA* 3.1 24.6 + - - +
322A ARG* 4.9 1.2 + - - -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ILE* 4.5 13.7 - - + -
263A LEU* 4.4 18.8 - - + -
265A TRP* 5.1 3.1 - - - -
310A THR 3.2 9.8 + - - +
311A MET* 3.3 27.1 - - + +
313A ASP* 1.3 77.7 - - - +
315A THR* 1.3 61.3 + - + +
317A ALA* 3.3 4.7 + - - +
318A LEU* 2.9 47.6 + - + +
323A VAL* 3.9 18.4 - - + -
326A MET* 4.2 11.2 - - + -
341A ILE* 3.6 31.0 - - + -
348A ILE* 6.0 0.9 - - + -
350A ILE* 4.4 9.4 - - + -
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A MET* 2.9 28.0 + - + +
312A ASP* 3.3 14.8 + - - +
314A LEU* 1.3 74.8 - - + +
316A THR* 1.3 63.6 + - - +
318A LEU* 3.4 12.3 + - + +
319A GLU* 3.0 32.8 + - - +
343A TYR* 5.3 4.7 - - + -
348A ILE* 4.2 26.7 - - + -
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ASP* 2.9 24.0 + - - +
313A ASP* 4.0 4.5 - - - -
315A THR* 1.3 77.6 + - - +
317A ALA* 1.3 59.9 + - - +
319A GLU* 3.2 16.8 + - + +
320A GLY* 3.2 18.0 + - - -
322A ARG* 4.2 14.6 + - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A TRP* 3.6 27.1 - - + -
313A ASP 3.1 20.0 + - - +
314A LEU 3.6 4.0 - - - +
316A THR* 1.3 76.2 - - - +
318A LEU* 1.3 58.2 + - - +
320A GLY 3.3 1.4 + - - -
321A ASN 3.2 4.2 + - - -
322A ARG* 2.7 57.7 + - + +
323A VAL* 3.7 10.3 - - + -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A LEU* 2.9 38.3 + - + +
315A THR* 3.7 8.5 - - - +
317A ALA* 1.3 73.0 - - - +
319A GLU* 1.3 66.2 + - - +
321A ASN* 3.2 19.0 + - - +
322A ARG 4.8 0.4 - - - +
323A VAL* 3.8 21.1 - - + -
348A ILE* 3.6 30.7 - - + -
349A HIS 3.6 17.5 - - - +
350A ILE* 3.9 8.7 - - + -
351A PRO* 3.7 23.1 - - + -
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A THR* 3.0 16.9 + - - +
316A THR* 3.2 21.3 + - - +
318A LEU* 1.3 77.3 - - - +
320A GLY* 1.3 56.1 + - - +
321A ASN* 3.3 8.7 + - - +
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A THR 3.2 9.6 + - - -
317A ALA 3.3 2.0 + - - -
318A LEU 3.2 0.6 - - - -
319A GLU* 1.3 79.2 - - - +
321A ASN* 1.3 70.0 + - - +
322A ARG* 3.2 18.2 + - - +
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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