Contacts of the helix formed by residues 332 - 346 (chain B) in PDB entry 5IY8
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 LYS 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B ASN* 5.5 7.2 - - - +
316B VAL* 6.2 1.9 - - - +
319B ASN* 3.3 32.6 + - + +
330B VAL 3.8 1.0 + - - +
331B THR* 1.3 76.6 + - - +
333B GLU* 1.3 69.6 + - + +
334B LYS 3.6 0.9 - - - -
335B ARG* 3.2 6.1 - - - +
336B ILE* 3.0 44.1 + - + +
158S GLU* 2.6 44.3 + - - -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 3.4 11.3 + - + +
332B LYS* 1.3 86.9 - - + +
334B LYS* 1.3 61.4 + - - +
336B ILE* 3.1 21.0 + - - +
337B LYS* 3.1 46.0 + - - +
53S ASN* 2.3 44.7 + - - +
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Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 4.1 17.6 - - + +
332B LYS 3.6 0.2 - - - -
333B GLU* 1.3 74.5 - - - +
335B ARG* 1.3 57.6 + - + +
337B LYS* 3.1 16.7 + - + +
338B TYR* 2.6 36.0 + - + +
36X T 5.0 9.5 + - - -
37X T 3.1 43.0 + - + +
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Residues in contact with ARG 335 (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 LEU 4.3 1.9 - - - +
319B ASN* 3.5 19.7 - - - +
322B GLY* 3.9 10.7 - - - -
323B SER* 2.8 43.5 + - - +
326B ALA* 3.2 32.7 + - - +
327B LYS 3.2 21.2 + - - -
328B PRO* 3.9 4.4 - - - +
329B GLY* 3.8 16.8 - - - +
330B VAL 6.1 0.9 - - - +
331B THR* 3.8 15.1 + - + +
332B LYS 3.2 15.7 - - - +
334B LYS* 1.3 81.0 - - + +
336B ILE* 1.3 55.5 + - - +
338B TYR* 4.0 9.5 - - - +
339B ALA* 3.0 30.5 + - - +
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Residues in contact with ILE 336 (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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315B ASN* 3.7 36.6 - - + +
318B LEU* 3.7 30.4 - - + +
319B ASN* 4.1 9.4 - - + +
332B LYS* 3.0 42.7 + - + +
333B GLU* 3.4 21.8 - - - +
334B LYS 3.1 0.4 - - - -
335B ARG* 1.3 76.6 - - - +
337B LYS* 1.3 55.2 + - + +
339B ALA* 3.6 2.4 + - - +
340B LYS* 2.8 35.6 + - + +
53S ASN* 5.5 7.0 - - - +
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLU* 3.1 44.0 + - - +
334B LYS* 3.1 19.9 + - + +
336B ILE* 1.3 76.8 - - + +
338B TYR* 1.3 59.6 + - - +
340B LYS* 3.2 14.4 + - + +
341B GLU* 3.0 32.1 + - - +
53S ASN* 3.7 23.5 + - - +
54S LYS* 4.8 17.9 - - + +
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Residues in contact with TYR 338 (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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263B ILE* 5.2 8.6 - - + +
322B GLY* 5.0 4.9 - - - -
325B GLY* 4.9 3.6 - - - -
326B ALA* 3.5 39.3 + - + +
334B LYS* 2.6 22.6 + - + +
335B ARG* 4.0 11.2 - - - +
337B LYS* 1.3 68.9 - - - +
339B ALA* 1.3 71.0 + - + +
341B GLU* 3.2 5.9 + - - +
342B VAL* 3.2 42.9 + - + +
37X T 4.0 31.0 - + + -
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Residues in contact with ALA 339 (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 LEU* 3.3 32.7 - - + +
321B ILE* 4.9 9.7 - - + +
322B GLY* 4.2 11.4 - - - +
335B ARG 3.0 20.5 + - - +
336B ILE 3.6 4.3 - - - +
338B TYR* 1.3 82.9 - - - +
340B LYS* 1.3 55.3 + - - +
342B VAL* 3.6 6.4 + - - +
343B LEU* 2.9 30.7 + - - +
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 4.0 20.6 - - + +
336B ILE* 2.8 24.6 + - + +
337B LYS* 3.3 15.3 - - + +
338B TYR 3.1 0.4 - - - -
339B ALA* 1.3 74.5 - - - +
341B GLU* 1.3 62.4 + - - +
343B LEU* 3.3 4.2 + - + +
344B GLN* 2.6 69.1 + - + +
355B ASP* 3.3 15.8 + - - -
358B GLU* 5.7 2.5 - - - +
54S LYS* 3.5 33.0 - - + +
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Residues in contact with GLU 341 (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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337B LYS 3.0 15.4 + - - +
338B TYR* 3.2 5.3 + - + +
340B LYS* 1.3 78.3 + - - +
342B VAL* 1.3 58.5 + - + +
344B GLN* 3.9 20.8 + - - +
345B LYS* 2.7 51.2 + - + +
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Residues in contact with VAL 342 (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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260B LEU* 4.9 11.7 - - + -
261B PRO* 5.8 2.7 - - + -
263B ILE* 4.6 20.6 - - + -
321B ILE* 6.4 0.9 - - + -
338B TYR* 3.2 43.7 + - + +
339B ALA* 3.8 6.1 - - - +
341B GLU* 1.3 73.8 - - + +
343B LEU* 1.3 68.9 + - - +
346B GLU* 2.9 43.0 + - + +
347B MET* 3.3 6.2 + - - +
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Residues in contact with LEU 343 (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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260B LEU* 4.6 10.5 - - + -
272B VAL* 4.2 24.5 - - + -
275B ALA* 3.5 46.2 - - + +
276B LEU* 3.7 21.2 - - + +
318B LEU* 4.2 7.4 - - + -
321B ILE* 5.3 5.8 - - + -
339B ALA 2.9 19.4 + - - +
340B LYS* 3.3 5.8 + - - +
342B VAL* 1.3 78.0 - - - +
344B GLN* 1.3 58.5 + - + +
347B MET* 3.0 37.7 - - + +
358B GLU* 4.3 7.0 - - - +
361B LYS* 4.2 6.1 - - - +
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Residues in contact with GLN 344 (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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340B LYS* 2.6 58.3 + - + +
341B GLU* 3.7 23.9 + - + +
343B LEU* 1.3 78.6 - - + +
345B LYS* 1.3 62.3 + - + +
347B MET 4.2 0.4 - - - +
352B GLY 3.8 5.2 - - - +
353B VAL* 4.5 7.7 + - - +
354B SER* 4.8 10.9 + - - +
355B ASP* 2.7 35.8 + - - +
358B GLU* 4.2 21.8 - - + +
361B LYS* 3.5 26.7 + - - +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 2.7 32.8 + - + +
344B GLN* 1.3 76.9 - - + +
346B GLU* 1.3 75.1 + - + +
347B MET 3.5 0.4 - - - -
349B PRO* 3.3 28.5 - - + +
353B VAL* 4.5 35.7 + - + +
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Residues in contact with GLU 346 (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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231B PRO* 5.5 6.8 - - - +
232B THR* 4.4 9.7 - - - +
233B SER* 2.9 43.7 + - - -
235B ILE* 4.6 1.0 - - - +
260B LEU* 6.1 0.2 - - - -
261B PRO* 3.8 21.9 - - + +
262B TYR* 5.3 6.2 + - - +
342B VAL* 2.9 34.2 + - + +
345B LYS* 1.3 97.0 - - + +
347B MET* 1.3 60.3 + - - +
348B LEU 3.4 6.1 + - - -
349B PRO* 3.8 4.7 - - - +
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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