Contacts of the helix formed by residues 316 - 327 (chain A) in PDB entry 5D0B
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 ALA 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LYS* 3.9 17.0 - - + -
276A LEU* 5.2 1.3 - - + -
308A LEU* 3.8 35.0 - - + -
313A ASP* 3.2 13.0 + - + +
314A ALA 3.0 1.2 - - - -
315A SER* 1.3 78.6 + - - +
317A LEU* 1.3 59.0 + - - +
318A PRO* 3.4 2.0 - - - -
319A GLU* 3.3 8.0 + - - +
320A LEU* 3.0 38.0 + - + +
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Residues in contact with LEU 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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314A ALA* 3.1 34.4 + - + +
316A ALA* 1.3 77.9 - - - +
318A PRO* 1.4 62.5 - - + +
320A LEU* 3.8 3.9 - - + +
321A THR* 2.7 35.8 + - - -
340A ILE* 4.1 33.2 - - + +
343A ILE* 3.9 27.8 - - + -
345A ASP* 3.7 23.3 - - + +
348A TYR* 3.6 36.3 - - + +
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Residues in contact with PRO 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 ALA 4.0 3.6 - - - +
315A SER* 3.7 12.6 - - - +
316A ALA 3.6 3.4 - - - -
317A LEU* 1.4 93.7 - - + +
319A GLU* 1.3 61.1 + - - +
321A THR* 3.2 8.0 + - - +
322A GLU* 3.1 23.5 + - - +
348A TYR* 4.1 13.0 - - + +
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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
----------------------------------------------------------
273A LYS* 4.9 8.7 - - + +
276A LEU* 3.8 35.9 - - + +
277A ALA* 4.1 18.2 - - - +
316A ALA* 3.3 10.3 + - - +
318A PRO* 1.3 79.4 - - - +
320A LEU* 1.3 57.2 + - - +
322A GLU* 3.4 17.9 + - - +
323A LEU* 3.0 47.1 + - + +
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Residues in contact with LEU 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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276A LEU* 4.3 12.6 - - + -
305A ILE* 3.8 39.5 - - + -
308A LEU* 4.9 6.7 - - + -
316A ALA* 3.0 31.8 + - + +
317A LEU* 3.8 5.4 - - - +
319A GLU* 1.3 77.3 - - - +
321A THR* 1.3 57.8 + - - +
323A LEU* 3.3 7.8 + - + +
324A MET* 2.9 25.5 + - - +
336A ALA* 3.5 18.2 - - + +
339A ALA* 4.3 11.4 - - + -
340A ILE* 3.9 16.8 - - + -
343A ILE* 3.7 29.6 - - + -
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Residues in contact with THR 321 (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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317A LEU 2.7 24.6 + - - -
318A PRO* 3.2 7.6 + - - -
320A LEU* 1.3 74.0 - - - +
322A GLU* 1.3 65.6 + - - +
324A MET* 3.2 5.5 + - + +
325A HIS* 3.2 29.1 + - + -
340A ILE* 3.8 14.2 - - - +
348A TYR* 3.3 23.8 - - + -
351A GLU* 3.6 33.4 - - + +
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Residues in contact with GLU 322 (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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318A PRO 3.1 13.5 + - - +
319A GLU* 3.8 22.0 - - - +
321A THR* 1.3 77.7 - - - +
323A LEU* 1.3 57.4 + - - +
325A HIS* 3.2 5.8 + - - +
326A LYS* 2.8 60.7 + - + +
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Residues in contact with LEU 323 (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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276A LEU* 4.0 44.4 - - + +
305A ILE* 4.4 15.7 - - + -
319A GLU* 3.0 35.7 + - - +
320A LEU* 3.5 13.7 - - + +
322A GLU* 1.3 77.6 - - - +
324A MET* 1.3 61.0 + - - +
326A LYS* 5.4 0.2 - - - -
327A ASP* 3.2 50.7 + - + +
329A ARG* 5.6 1.1 - - - +
332A ILE* 4.3 8.7 - - + -
333A ARG* 3.7 6.0 - - - +
336A ALA* 4.2 7.2 - - + -
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Residues in contact with MET 324 (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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320A LEU 2.9 13.4 + - - +
321A THR* 3.2 10.0 + - + +
323A LEU* 1.3 76.5 - - - +
325A HIS* 1.3 76.5 + - - +
333A ARG* 3.5 34.4 - - - +
336A ALA* 4.1 3.8 - - + +
337A ALA* 3.7 32.1 - - + +
340A ILE* 4.3 12.8 - - + -
351A GLU* 3.4 36.1 - - + +
352A LEU* 3.8 14.8 - - + +
355A ALA* 3.6 23.9 - - + +
359A GLU* 6.1 0.3 - - - +
368A ILE* 5.0 2.8 - - + +
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Residues in contact with HIS 325 (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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321A THR* 3.2 29.5 + - + -
322A GLU* 3.2 9.5 + - - +
324A MET* 1.3 86.1 - - + +
326A LYS* 1.3 66.2 + - + +
327A ASP 3.8 0.2 - - - -
333A ARG* 4.9 4.5 - - - -
351A GLU* 3.2 50.8 + - + +
354A LYS* 4.3 11.2 - - + -
355A ALA* 4.1 17.1 - - + +
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Residues in contact with LYS 326 (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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322A GLU* 2.8 48.7 + - + +
325A HIS* 1.3 80.8 - - + +
327A ASP* 1.3 67.5 + - - +
328A PRO* 3.4 6.4 - - - +
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Residues in contact with ASP 327 (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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322A GLU 4.2 0.2 + - - -
323A LEU* 3.2 34.4 + - + +
326A LYS* 1.3 78.0 - - - +
328A PRO* 1.3 61.6 - - - +
329A ARG* 2.7 65.9 + - - +
332A ILE* 3.7 19.8 - - + +
333A ARG* 2.6 39.0 + - + +
30F G 5.0 0.7 + - - -
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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