Contacts of the helix formed by residues 329 - 344 (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 ARG 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B LEU 5.6 0.8 + - - -
297B LYS* 3.7 18.0 - - - +
298B LYS* 3.8 25.1 - - - +
301B GLN* 2.7 34.9 + - - +
323B LEU* 5.4 1.2 - - - +
327B ASP* 2.8 35.0 + - - +
328B PRO* 1.3 80.8 - - - +
330B PRO* 1.3 66.0 - - + +
331B VAL* 4.4 4.9 - - + +
332B ILE* 3.0 42.5 + - + +
333B ARG* 3.1 14.9 + - - +
31X A 3.5 31.1 + - - +
32X C 3.5 34.5 + - - +
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Residues in contact with PRO 330 (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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224B PHE* 3.2 14.5 - - + -
328B PRO 3.6 7.6 - - - +
329B ARG* 1.3 85.9 - - + +
331B VAL* 1.3 66.0 + - + +
332B ILE 3.3 0.2 - - - -
333B ARG* 3.4 26.2 - - - +
334B GLY 3.2 17.8 + - - -
361B ASP* 3.6 35.9 - - + +
364B ALA* 3.4 4.9 - - + +
32X C 5.7 1.3 - - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS 3.6 26.9 - - - +
223B GLY* 3.8 20.0 - - - +
224B PHE* 3.7 21.6 - - + +
298B LYS* 3.7 24.7 - - + +
302B ARG* 4.1 22.2 - - + -
329B ARG* 3.1 1.5 - - + -
330B PRO* 1.3 81.6 - - + +
332B ILE* 1.3 60.6 + - + +
335B THR* 2.4 39.4 + - - +
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Residues in contact with ILE 332 (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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298B LYS* 4.3 13.2 - - + +
301B GLN* 4.3 7.0 - - + -
302B ARG* 4.2 28.9 - - + +
305B ILE* 3.9 15.0 - - + -
323B LEU* 4.1 17.7 - - + -
327B ASP* 3.3 28.7 - - + +
329B ARG* 3.0 42.5 + - + +
331B VAL* 1.3 79.5 - - + +
333B ARG* 1.3 59.3 + - - +
335B THR* 4.0 2.3 - - - -
336B ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU 3.4 18.2 - - - +
324B MET* 3.5 26.5 - - + +
325B HIS 4.9 4.9 - - - -
327B ASP 2.8 45.2 + - - +
328B PRO* 3.2 23.6 + - - +
329B ARG 3.1 6.9 + - - +
330B PRO* 3.4 32.9 - - - +
332B ILE* 1.3 76.5 - - - +
334B GLY* 1.3 58.1 + - - +
336B ALA* 4.0 0.9 - - - +
337B ALA* 3.0 28.6 + - - +
359B GLU* 2.7 43.9 + - - +
361B ASP* 4.2 3.0 - - - +
364B ALA* 4.8 1.3 - - + -
368B ILE* 5.6 3.1 - - + -
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Residues in contact with GLY 334 (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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224B PHE* 4.1 3.8 - - - -
330B PRO 3.2 14.0 + - - -
333B ARG* 1.3 77.0 - - - +
335B THR* 1.3 59.9 + - - +
337B ALA* 3.4 4.1 + - - +
338B TRP* 2.9 24.4 + - - +
364B ALA* 4.1 11.8 - - - +
367B GLU* 3.3 33.8 - - - +
368B ILE* 5.1 0.7 - - - -
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Residues in contact with THR 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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224B PHE* 4.1 10.2 - - - -
230B ARG* 5.8 5.3 + - - +
302B ARG* 3.9 25.6 - - + +
305B ILE* 3.8 16.2 - - + -
306B LEU* 3.7 30.3 - - + -
331B VAL* 2.4 30.7 + - - +
332B ILE* 4.0 3.6 - - - -
334B GLY* 1.3 73.4 - - - +
336B ALA* 1.3 60.7 + - - +
338B TRP* 3.2 9.4 + - + +
339B ALA* 2.8 27.2 + - - +
367B GLU* 5.4 1.3 - - - -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 3.8 21.9 - - + +
320B LEU* 3.4 30.5 - - + +
323B LEU* 4.3 8.7 - - + -
324B MET 4.5 1.8 - - - +
332B ILE 2.9 19.1 + - - +
333B ARG 4.0 2.5 - - - +
335B THR* 1.3 77.6 - - - +
337B ALA* 1.3 58.5 - - - +
339B ALA* 3.1 3.4 + - - +
340B ILE* 3.0 34.9 + - - +
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Residues in contact with ALA 337 (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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324B MET* 3.7 29.1 - - - +
333B ARG 3.0 19.7 + - - +
334B GLY 3.5 5.4 - - - +
336B ALA* 1.3 75.6 - - - +
338B TRP* 1.3 61.9 + - - +
339B ALA 3.5 0.2 + - - -
340B ILE* 3.5 7.0 + - - -
341B GLY 3.5 9.0 + - - -
352B LEU* 3.6 14.4 - - + +
367B GLU 4.7 1.6 - - - -
368B ILE* 3.8 28.9 - - + -
371B GLY* 3.9 4.9 - - - -
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Residues in contact with TRP 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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227B ASP* 4.2 10.9 + - + +
230B ARG* 3.2 56.0 - - + +
231B THR* 5.2 4.7 - - + -
306B LEU* 3.8 28.9 - - + -
309B ALA* 3.9 19.1 - - + -
334B GLY 2.9 16.8 + - - +
335B THR* 3.5 7.4 - - + +
337B ALA* 1.3 74.3 - - - +
339B ALA* 1.3 65.5 + - + +
341B GLY* 3.5 1.4 + - - -
342B LYS* 3.0 52.3 + - + +
367B GLU* 3.8 15.6 + - - +
370B LYS* 3.9 25.7 - - + +
371B GLY* 4.4 2.7 - - - -
374B LEU* 3.9 17.4 - - + +
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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
----------------------------------------------------------
305B ILE* 3.6 22.2 - - + +
309B ALA* 3.9 24.9 - - + -
320B LEU* 4.0 13.5 - - + -
335B THR 2.8 12.7 + - - +
336B ALA 3.1 8.7 + - - +
338B TRP* 1.3 79.5 - - + +
340B ILE* 1.3 55.5 + - - +
342B LYS* 3.0 1.2 + - - +
343B ILE* 2.7 41.0 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.8 22.9 - - + +
320B LEU* 4.0 16.2 - - + +
321B THR* 3.6 36.6 - - - +
324B MET* 4.2 22.7 - - + -
336B ALA 3.0 19.5 + - - +
337B ALA* 3.8 5.8 - - - +
338B TRP 3.4 0.2 - - - -
339B ALA* 1.3 77.0 - - - +
341B GLY* 1.3 61.3 + - - +
343B ILE* 3.4 4.0 + - - +
344B GLY 3.3 15.1 + - - -
345B ASP 4.1 7.8 + - - +
348B TYR* 3.7 28.5 - - + -
351B GLU* 6.3 0.2 - - + -
352B LEU* 4.5 12.1 - - + -
375B LEU* 4.5 1.4 - - + +
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Residues in contact with GLY 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 ALA 3.5 7.5 + - - -
338B TRP 4.0 2.0 - - - -
339B ALA 3.2 0.2 - - - -
340B ILE* 1.3 77.5 - - - +
342B LYS* 1.3 65.9 + - - +
344B GLY* 3.2 11.8 + - - -
352B LEU* 4.8 0.6 - - - +
371B GLY* 3.5 27.1 - - - -
374B LEU* 3.4 26.3 - - - +
375B LEU* 3.9 10.9 - - - +
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Residues in contact with LYS 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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231B THR* 4.2 25.7 - - - +
309B ALA* 3.8 31.2 - - + +
310B HIS* 6.0 1.6 - - - +
312B LYS* 3.1 38.9 + - - +
338B TRP* 3.0 39.8 + - + +
339B ALA* 3.4 5.6 - - - +
341B GLY* 1.3 74.7 - - - +
343B ILE* 1.3 64.2 + - - +
344B GLY* 3.5 0.7 + - - -
374B LEU* 3.6 17.9 - - + +
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Residues in contact with ILE 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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308B LEU 4.4 4.0 - - - +
309B ALA* 4.2 9.4 - - - -
312B LYS* 3.9 48.4 + - - +
313B ASP 3.4 24.5 - - - +
314B ALA* 4.1 15.0 - - + -
316B ALA* 5.2 0.2 - - + -
317B LEU* 3.7 28.3 - - + -
320B LEU* 3.8 21.3 - - + -
339B ALA 2.7 19.7 + - - +
340B ILE 3.6 5.2 - - - +
341B GLY 3.2 0.2 - - - -
342B LYS* 1.3 74.2 - - - +
344B GLY* 1.3 59.5 + - - +
345B ASP* 4.8 3.4 - - + +
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Residues in contact with GLY 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 ILE 3.3 2.2 + - - -
341B GLY 3.2 17.3 + - - -
342B LYS 4.3 1.1 - - - -
343B ILE* 1.3 81.3 - - - +
345B ASP* 1.3 61.2 + - - +
346B PRO* 3.7 8.2 - - - +
374B LEU 5.0 2.9 - - - -
375B LEU* 3.9 8.3 - - - -
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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
------------------------------------------------------------
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