Contacts of the helix formed by residues 324 - 342 (chain B) in PDB entry 3RU0
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 ASN 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP 4.4 0.7 - - - -
275B MET 3.4 16.1 + - - -
276B LEU* 3.8 3.4 - - - +
277B THR 3.0 27.9 + - - +
283B TRP* 3.2 35.2 - - - +
320B LEU* 4.0 6.6 - - + +
321B PRO 3.3 15.1 + - - +
322B ASP 3.6 0.9 - - - +
323B ILE* 1.3 81.2 - - - +
325B ILE* 1.3 58.9 - - - +
326B TYR* 3.0 24.7 + - - +
327B GLN* 3.2 12.0 + - + +
328B LEU* 2.8 25.1 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.8 42.3 - - + +
244B MET 4.3 0.7 - - - +
245B THR* 4.2 13.5 - - + -
248B GLU* 3.9 9.2 - - - +
275B MET* 2.9 45.1 + - + +
323B ILE 4.0 0.7 - - - -
324B ASN* 1.3 72.7 - - - +
326B TYR* 1.3 94.4 + - + +
328B LEU* 3.7 6.5 - - + +
329B LYS* 3.0 36.2 + - - +
361B PHE* 3.8 16.4 - - + -
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Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 4.4 1.4 - - - +
248B GLU* 2.6 34.2 + - - -
276B LEU* 3.7 20.6 - - + +
283B TRP* 3.5 37.4 - + - +
286B VAL* 3.7 19.5 - - + -
287B GLN* 3.6 38.0 + - + +
290B LEU* 3.6 18.3 - - + +
324B ASN* 3.0 14.7 + - - +
325B ILE* 1.3 91.6 - - + +
327B GLN* 1.3 66.5 + - - +
329B LYS* 3.3 8.7 + - + -
330B VAL* 3.1 26.5 + - - +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 3.8 6.1 - - - +
312B ILE* 4.1 23.6 - - - +
313B ILE* 4.6 16.0 + - - +
316B ASN* 4.1 15.1 + - - +
317B SER* 5.3 1.0 - - - +
320B LEU* 3.2 46.4 + - + +
321B PRO 3.7 18.2 - - - +
322B ASP* 3.9 20.1 + - - +
324B ASN* 3.2 10.6 + - - +
326B TYR* 1.3 78.1 - - - +
328B LEU* 1.3 55.6 + - - +
330B VAL* 3.2 5.2 + - - +
331B LEU* 2.9 30.6 + - + +
353B ARG* 4.7 5.5 - - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.9 20.0 - - + -
322B ASP 3.4 16.8 + - - +
323B ILE 4.7 0.2 - - - +
324B ASN 2.8 13.6 + - - +
325B ILE* 3.7 5.6 - - - +
327B GLN* 1.3 76.4 - - - +
329B LYS* 1.3 56.9 + - - +
331B LEU* 3.2 9.1 + - + +
332B ASP* 2.9 29.0 + - - +
354B THR* 3.7 38.1 - - + -
357B PRO* 3.6 29.6 - - + -
358B TYR* 4.0 15.5 - - + -
361B PHE* 3.8 23.6 - - + -
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ASP* 2.6 30.7 + - - -
243B LEU* 2.9 43.9 + - + +
244B MET* 4.8 2.2 - - - +
290B LEU* 3.9 26.9 - - + -
294B GLU* 4.3 16.3 + - - +
325B ILE* 3.0 30.9 + - - +
326B TYR* 3.3 11.2 + - + +
328B LEU* 1.3 75.0 - - - +
330B VAL* 1.3 56.6 + - - +
332B ASP* 3.4 7.5 + - - +
333B CYS* 2.9 35.0 + - - -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 3.6 19.5 - - + -
290B LEU* 3.7 20.9 - - + -
293B ILE* 4.1 11.0 - - + -
309B CYS* 3.5 27.9 - - + +
312B ILE* 4.0 12.8 - - + -
313B ILE* 3.7 24.5 - - + -
326B TYR 3.1 15.4 + - - +
327B GLN* 3.2 10.7 + - - +
329B LYS* 1.3 74.3 - - - +
331B LEU* 1.3 59.1 + - - +
333B CYS* 3.4 0.7 + - - -
334B ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 3.9 14.4 - - + -
322B ASP* 3.5 39.3 - - + +
327B GLN* 2.9 22.5 + - + +
328B LEU* 3.2 12.5 + - + +
330B VAL* 1.3 72.4 - - - +
332B ASP* 1.3 61.6 + - - +
334B ALA* 3.4 2.6 + - - +
335B MET* 2.9 29.3 + - - +
350B TYR* 3.7 30.2 - - + +
353B ARG* 3.7 41.3 - - + +
354B THR* 3.9 13.2 - - + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 6.1 0.4 - - + -
297B LYS* 5.2 5.2 + - - -
328B LEU 2.9 16.1 + - - +
329B LYS* 3.7 8.3 - - - +
330B VAL 3.3 0.2 - - - -
331B LEU* 1.3 78.4 - - - +
333B CYS* 1.3 60.2 + - - +
335B MET* 3.4 10.3 + - - +
336B ASP* 3.0 36.6 + - - +
354B THR* 4.2 6.2 - - + +
358B TYR* 3.3 19.6 + - + +
372B GLN* 2.9 35.1 + - - +
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Residues in contact with CYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.7 5.4 - - - -
293B ILE* 3.8 20.2 - - + -
294B GLU* 5.0 7.2 - - - -
297B LYS* 3.9 28.0 - - + +
302B TRP* 4.9 1.4 - - - -
305B VAL* 3.7 10.1 - - + +
309B CYS* 3.8 18.6 - - - -
329B LYS* 2.9 26.7 + - - +
330B VAL* 4.6 0.2 - - - -
331B LEU 3.3 0.2 - - - -
332B ASP* 1.3 79.2 - - - +
334B ALA* 1.3 57.5 + - - +
336B ASP* 3.5 5.3 + - - +
337B ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 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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305B VAL* 5.1 0.2 - - - -
306B LEU* 4.3 5.2 - - + -
309B CYS* 3.8 20.1 - - + -
313B ILE* 3.8 9.0 - - + -
330B VAL 2.9 17.1 + - - +
331B LEU 3.6 4.7 - - - +
332B ASP 3.3 0.2 - - - -
333B CYS* 1.3 74.5 - - - +
335B MET* 1.3 59.6 + - - +
337B ALA* 3.4 6.3 + - - +
338B CYS* 3.0 34.7 + - - -
350B TYR* 3.7 27.8 - - + -
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Residues in contact with MET 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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331B LEU 2.9 18.2 + - - +
332B ASP* 3.6 13.5 - - - +
334B ALA* 1.3 74.6 - - - +
336B ASP* 1.3 81.4 + - - +
338B CYS* 3.2 4.2 + - - +
339B ILE* 3.0 43.3 + - + +
347B ALA* 3.6 22.7 - - - +
350B TYR* 3.9 6.3 - - + +
351B GLY* 3.7 27.4 - - - +
354B THR* 5.7 0.2 - - + -
372B GLN* 3.3 35.2 - - - +
375B LYS* 3.7 17.7 - - + -
376B VAL* 4.7 8.5 - - - -
379B LEU* 4.7 2.7 - - + -
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Residues in contact with ASP 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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189B GLU* 4.7 4.6 - - - +
297B LYS* 4.3 15.7 + - - -
302B TRP* 4.3 14.4 - - + -
332B ASP* 3.0 27.3 + - - +
333B CYS 4.1 3.1 - - - +
335B MET* 1.3 88.9 - - - +
337B ALA* 1.3 62.8 + - - +
339B ILE* 3.4 6.8 + - - +
340B ASN* 2.8 37.5 + - - +
375B LYS* 2.8 36.0 + - - +
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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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302B TRP* 3.6 37.5 - - + +
305B VAL* 3.9 13.2 - - + -
306B LEU* 3.9 12.1 - - + -
333B CYS 2.9 19.3 + - - +
334B ALA 3.6 5.2 - - - +
335B MET 3.3 0.2 - - - -
336B ASP* 1.3 76.3 - - - +
338B CYS* 1.3 57.2 + - - +
340B ASN* 3.3 3.3 + - - +
341B LEU* 2.9 36.4 + - - +
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Residues in contact with CYS 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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66A ARG* 6.0 0.2 - - - -
306B LEU* 3.8 27.4 - - - -
334B ALA 3.0 24.2 + - - +
337B ALA* 1.3 73.4 - - - +
339B ILE* 1.3 63.4 + - - +
341B LEU* 3.2 4.5 + - - -
342B GLY 3.0 5.2 + - - -
343B LEU* 2.8 49.2 + - - +
346B GLU* 3.6 25.4 - - - -
347B ALA* 3.5 15.9 - - + +
350B TYR* 3.9 7.4 - - - -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 6.3 2.9 - - + -
335B MET* 3.0 33.2 + - + +
336B ASP* 3.8 11.4 - - - +
337B ALA 3.4 0.2 - - - -
338B CYS* 1.3 73.1 - - - +
340B ASN* 1.3 66.8 + - - +
342B GLY* 3.3 12.3 + - - -
344B LEU* 4.3 14.1 - - + +
347B ALA* 3.8 13.5 - - + -
375B LYS* 4.0 37.2 - - + -
379B LEU* 4.3 14.6 - - + -
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 6.4 0.6 - - - +
300B TRP* 4.1 13.0 - - - -
302B TRP* 3.4 53.7 + - + +
336B ASP* 2.8 34.1 + - - +
337B ALA 3.8 0.2 - - - +
339B ILE* 1.3 80.9 - - - +
341B LEU* 1.3 62.7 + - - +
342B GLY 3.3 0.2 - - - -
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 4.8 4.0 - - - +
91A LYS* 2.8 33.2 + - - +
302B TRP* 3.9 32.5 - - + +
303B GLU* 3.7 31.0 - - + +
306B LEU* 3.9 26.5 - - + -
337B ALA 2.9 21.2 + - - +
338B CYS 3.2 4.0 + - - +
340B ASN* 1.3 78.1 - - - +
342B GLY* 1.3 54.5 + - - +
343B LEU* 3.6 16.4 + - + +
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Residues in contact with GLY 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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91A LYS* 3.2 30.4 - - - +
92A SER* 5.2 2.4 - - - -
338B CYS 3.0 4.5 + - - -
339B ILE 3.3 10.9 + - - -
340B ASN 3.3 1.0 - - - -
341B LEU* 1.3 76.7 - - - +
343B LEU* 1.3 58.5 + - - +
344B LEU* 3.2 21.3 + - - +
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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
------------------------------------------------------------
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