Contacts of the helix formed by residues 316 - 327 (chain B) in PDB entry 5T8Y
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B LYS* 4.1 17.9 - - + -
276B LEU* 5.0 1.8 - - + -
308B LEU* 3.7 35.2 - - + -
313B ASP* 3.1 13.1 + - + +
315B SER* 1.3 76.2 + - - +
317B LEU* 1.3 60.2 + - - +
318B PRO* 3.3 3.4 - - - -
319B GLU* 3.0 9.7 + - + +
320B LEU* 2.8 36.1 + - + +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ASP 4.0 0.4 + - - -
314B ALA* 3.3 37.7 - - + +
316B ALA* 1.3 77.1 - - - +
318B PRO* 1.3 64.2 - - + +
320B LEU* 4.0 4.1 - - - +
321B THR* 2.7 32.2 + - - -
340B ILE* 3.8 36.8 - - + +
343B ILE* 3.7 27.1 - - + -
345B ASP* 3.8 22.0 - - + +
348B TYR* 3.6 33.2 - - + +
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Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA 4.0 2.7 - - - +
315B SER* 3.3 19.5 - - - +
316B ALA 3.4 0.9 - - - -
317B LEU* 1.3 95.2 - - + +
319B GLU* 1.3 55.4 - - - +
321B THR* 3.4 6.0 + - - +
322B GLU* 3.1 27.0 + - - +
348B TYR* 3.9 14.8 - - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LYS* 5.0 5.8 - - + +
276B LEU* 3.6 48.2 - - + +
277B ALA* 3.6 18.3 - - - +
315B SER 5.2 0.4 + - - +
316B ALA* 3.0 10.8 + - + +
318B PRO* 1.3 77.4 - - - +
320B LEU* 1.3 66.2 + - - +
322B GLU* 3.3 20.0 + - - +
323B LEU* 3.0 35.3 + - + +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.7 23.3 - - + -
305B ILE* 3.8 30.5 - - + -
308B LEU* 4.5 8.1 - - + -
316B ALA* 2.8 30.2 + - + +
317B LEU* 4.0 3.1 - - - +
319B GLU* 1.3 75.6 - - - +
321B THR* 1.3 61.4 + - - +
323B LEU* 3.5 2.5 + - + -
324B MET* 3.1 19.6 + - - +
336B ALA* 3.4 21.3 - - + +
339B ALA* 4.0 15.5 - - + -
340B ILE* 4.0 18.1 - - + +
343B ILE* 3.8 29.6 - - + -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B LEU 2.7 25.0 + - - -
318B PRO* 3.5 7.4 - - - +
320B LEU* 1.3 75.4 - - - +
322B GLU* 1.3 64.9 + - - +
324B MET* 3.1 13.8 + - + +
325B HIS* 3.2 22.0 - - + -
340B ILE* 3.6 15.4 - - - +
348B TYR* 3.2 23.8 - - + -
351B GLU* 3.6 31.4 - - + -
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B PRO 3.1 12.6 + - - +
319B GLU* 3.3 26.3 + - - +
321B THR* 1.3 77.8 - - - +
323B LEU* 1.3 53.4 + - + +
325B HIS* 3.1 5.9 + - - +
326B LYS* 2.7 71.4 + - + +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 4.0 47.1 - - + +
305B ILE* 4.3 9.0 - - + -
319B GLU* 3.0 28.9 + - - +
320B LEU* 3.7 7.4 - - - +
322B GLU* 1.3 77.8 - - + +
324B MET* 1.3 63.0 + - - +
326B LYS* 5.0 0.9 - - + -
327B ASP* 3.2 53.5 + - + +
329B ARG* 5.4 1.3 - - - +
332B ILE* 4.1 20.6 - - + -
333B ARG* 3.4 10.3 - - - +
336B ALA* 4.3 3.6 - - + -
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU 3.1 13.7 + - - +
321B THR* 3.1 9.4 + - + +
323B LEU* 1.3 77.6 - - - +
325B HIS* 1.3 74.5 + - + +
333B ARG* 3.5 35.0 - - + +
336B ALA* 4.5 0.4 - - - +
337B ALA* 3.7 24.7 - - + +
340B ILE* 4.2 13.9 - - + -
351B GLU* 3.3 34.3 - - + +
352B LEU* 3.5 28.3 - - + +
355B ALA* 3.9 21.8 - - + +
359B GLU* 4.8 2.6 - - - +
368B ILE* 5.1 3.0 - - + +
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Residues in contact with HIS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B THR* 3.2 30.0 + - + -
322B GLU* 3.1 7.2 + - - +
324B MET* 1.3 88.4 - - + +
326B LYS* 1.3 61.8 + - + +
333B ARG* 4.9 5.1 - - - -
351B GLU* 3.2 50.0 + - - +
354B LYS* 4.0 17.9 - - + +
355B ALA* 3.8 25.8 - - + +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B GLU* 2.7 50.4 + - + +
323B LEU* 5.0 0.7 - - + -
325B HIS* 1.3 76.0 - - + +
327B ASP* 1.3 66.4 + - - +
328B PRO* 3.4 5.8 - - - +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B GLU 4.1 0.2 + - - -
323B LEU* 3.2 42.9 + - + +
326B LYS* 1.3 79.0 - - - +
328B PRO* 1.3 62.6 - - - +
329B ARG* 2.8 61.4 + - - +
332B ILE* 3.3 18.0 - - + +
333B ARG* 2.8 36.7 + - + +
31X A 4.9 0.3 + - - -
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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