Contacts of the helix formed by residues 318 - 328 (chain B) in PDB entry 6A5T
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 ASP 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B ARG* 5.1 2.8 - - - +
284B VAL* 4.2 15.7 - - - +
316B ILE* 3.5 7.3 + - - +
317B GLN* 1.3 80.3 + - - +
319B LYS* 1.3 65.5 + - - +
320B GLU 4.8 3.1 - - - -
321B VAL* 3.1 29.0 - - - +
322B ALA* 3.6 13.9 + - - +
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Residues in contact with LYS 319 (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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279B ARG 4.7 3.8 - - - +
280B ALA* 4.4 16.1 - - - +
281B LEU 6.2 0.2 - - - -
282B GLY* 6.0 5.2 - - - +
284B VAL* 4.2 14.3 - - + +
318B ASP* 1.3 77.7 - - - +
320B GLU* 1.3 73.6 + - + +
322B ALA* 2.8 23.4 + - - +
323B LEU* 3.0 38.0 + - + +
346B LYS* 4.8 16.9 - - - +
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Residues in contact with GLU 320 (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 ASP* 4.7 2.2 + - - -
319B LYS* 1.3 96.3 + - + +
321B VAL* 1.3 58.1 + - - +
323B LEU* 3.4 5.8 + - + +
324B ASP* 2.9 23.7 + - - +
338B ARG* 4.4 15.3 + - - +
339B GLU* 6.1 1.8 - - - +
342B ILE* 3.3 45.4 - - + +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 3.4 30.0 - - + +
317B GLN 5.0 0.2 - - - +
318B ASP* 3.1 28.2 + - - +
320B GLU* 1.3 75.5 - - - +
322B ALA* 1.3 60.6 + - - +
324B ASP* 3.6 8.2 - - + +
325B PHE* 2.8 27.7 + - - +
328B ARG* 5.6 4.9 - - - +
338B ARG* 3.5 23.3 - - - +
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Residues in contact with ALA 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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276B ILE* 4.3 12.2 - - + +
279B ARG* 4.9 2.7 - - + -
280B ALA* 4.0 23.8 - - + +
316B ILE* 3.7 14.6 - - + -
318B ASP 3.6 11.0 - - - +
319B LYS 2.8 13.9 + - - +
321B VAL* 1.3 79.5 - - - +
323B LEU* 1.3 62.6 + - - +
325B PHE* 2.9 15.8 + - - +
326B ILE* 2.9 19.1 + - - +
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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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280B ALA* 4.5 14.4 - - + +
281B LEU* 6.1 0.9 - - + -
319B LYS* 3.0 48.8 + - + +
320B GLU* 3.7 9.2 - - + +
322B ALA* 1.3 75.0 - - - +
324B ASP* 1.3 58.1 + - - +
326B ILE* 3.2 17.9 + - + +
327B GLY* 2.9 22.9 + - - -
341B ARG 5.0 0.5 - - - +
342B ILE* 4.0 28.5 - - + -
345B ALA* 3.4 32.6 - - + +
346B LYS* 4.2 19.7 - - + +
349B LEU* 5.1 6.3 - - + -
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Residues in contact with ASP 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 GLU 2.9 17.6 + - - +
321B VAL* 3.6 9.0 - - + +
322B ALA 3.1 0.2 - - - -
323B LEU* 1.3 73.4 - - - +
325B PHE* 1.3 60.2 + - - +
326B ILE 3.0 1.8 - - - -
327B GLY 3.2 0.2 + - - -
328B ARG* 2.3 78.6 + - - +
338B ARG* 4.3 21.7 - - - +
341B ARG* 3.0 32.7 + - - +
342B ILE* 4.1 10.5 - - + +
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Residues in contact with PHE 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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272B ILE* 4.6 4.3 - - + -
273B PRO* 4.7 3.4 - - + -
276B ILE* 3.5 43.1 - - + -
316B ILE* 5.2 14.4 - - + -
321B VAL 2.8 21.0 + - - +
322B ALA* 2.9 7.6 + - - +
324B ASP* 1.3 74.2 + - - +
326B ILE* 1.3 63.6 + - - +
328B ARG* 3.7 29.4 - - + +
329B ARG* 3.2 63.3 - - - -
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Residues in contact with ILE 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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265B LEU* 5.7 0.9 - - + -
268B VAL* 5.7 2.9 - - + -
272B ILE* 4.1 30.1 - - + -
276B ILE* 4.5 12.3 - - + -
277B VAL* 5.0 4.5 - - + -
280B ALA* 3.8 26.2 - - + -
322B ALA 2.9 13.2 + - - +
323B LEU* 3.3 15.7 - - + +
325B PHE* 1.3 77.0 - - - +
327B GLY* 1.3 54.5 + - - +
329B ARG* 2.6 13.7 + - - +
330B GLY* 2.6 35.6 + - - -
345B ALA* 4.5 11.4 - - + -
348B ILE* 5.8 2.5 - - + -
349B LEU* 4.2 29.8 - - + -
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Residues in contact with GLY 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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323B LEU 2.9 12.4 + - - -
324B ASP 3.2 3.1 + - - -
326B ILE* 1.3 76.8 - - - +
328B ARG* 1.3 56.8 + - - +
329B ARG 2.9 6.6 + - - -
330B GLY* 3.2 13.7 + - - -
332B ALA* 3.2 16.4 + - - +
341B ARG* 3.1 37.0 + - - -
344B TYR* 5.6 0.9 - - - -
345B ALA* 4.6 3.6 - - - +
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Residues in contact with ARG 328 (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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270B GLN* 4.8 1.7 - - - +
316B ILE* 6.4 0.4 - - - +
321B VAL* 5.6 5.3 + - - +
324B ASP* 2.3 51.8 + - - +
325B PHE* 3.7 32.1 - - + +
326B ILE 3.0 0.4 + - - -
327B GLY* 1.3 73.2 - - - +
329B ARG* 1.3 65.5 + - - +
334B LEU* 6.2 0.8 - - - +
341B ARG* 3.6 13.9 - - - +
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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