Contacts of the helix formed by residues 341 - 355 (chain B) in PDB entry 4RPP
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 THR 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA* 4.8 7.3 - - - +
329A GLN* 5.2 4.0 - - - -
333B SER* 3.6 24.0 - - - +
337B LYS* 6.0 2.5 - - + -
340B PRO* 1.3 85.3 - - - +
342B ARG* 1.3 67.6 + - - +
343B ALA* 3.3 7.1 + - - +
344B GLU* 3.0 34.5 + - - +
345B GLY* 3.8 13.0 + - - -
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 2.7 40.4 + - - +
295A GLY* 3.8 15.1 + - - +
298A GLY* 2.8 40.8 - - - +
303A ALA* 5.5 9.1 - - + +
306A VAL* 3.0 33.1 - - - +
329A GLN* 3.2 37.7 + - + +
347A ASP* 5.1 0.3 - - - +
340B PRO 5.5 0.4 - - - +
341B THR* 1.3 82.9 - - - +
343B ALA* 1.3 60.3 + - - +
344B GLU 3.4 0.7 - - - -
345B GLY* 3.9 1.5 + - - -
346B SER* 3.7 20.1 + - - -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN* 4.5 16.9 + - + +
330A MET 5.6 0.2 - - - +
343A ALA* 4.1 14.6 - - + +
344A GLU* 4.4 25.4 - - + +
347A ASP* 4.4 10.7 - - - +
341B THR* 4.0 5.8 - - - +
342B ARG* 1.3 79.9 - - - +
344B GLU* 1.3 57.8 - - + +
346B SER* 3.4 7.6 + - - -
347B ASP* 3.2 26.7 + - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA* 5.2 11.4 - - + -
329B GLN 5.2 1.6 - - - +
330B MET 3.5 15.1 - - - +
331B LEU* 3.5 18.0 - - + -
332B GLU* 3.2 20.5 + - - +
333B SER* 3.1 38.9 + - - -
340B PRO* 4.0 4.2 - - - +
341B THR* 3.0 29.0 + - - +
343B ALA* 1.3 76.9 - - + +
345B GLY* 1.3 64.3 + - - +
347B ASP* 3.3 5.8 + - - +
348B VAL* 3.1 28.6 + - - +
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 5.1 14.4 - - - -
304A GLU* 5.9 0.6 - - - -
307A PHE* 5.2 2.0 - - - -
331B LEU* 4.6 1.7 - - - +
340B PRO* 5.2 2.2 - - - +
341B THR 3.8 12.9 + - - -
342B ARG* 3.9 2.8 + - - -
343B ALA 3.5 0.4 - - - -
344B GLU* 1.3 79.2 - - - +
346B SER* 1.3 60.9 + - - +
348B VAL* 3.8 0.3 + - - +
349B ALA* 3.3 6.9 + - - +
381B ILE* 3.3 46.0 - - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 5.9 1.1 - - - -
307A PHE* 4.0 20.8 - - - +
310A GLN* 5.8 4.0 - - - -
347A ASP* 2.7 27.8 + - - +
342B ARG 3.7 13.1 + - - -
343B ALA 3.4 6.2 + - - -
344B GLU 3.3 0.4 - - - -
345B GLY* 1.3 75.3 - - - +
347B ASP* 1.3 63.5 + - - +
349B ALA* 3.6 7.5 - - - +
350B ASN* 2.8 41.4 + - - -
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA* 4.1 18.2 - - + +
346A SER* 2.8 26.6 + - - +
347A ASP* 6.0 1.8 - - + +
350A ASN* 5.6 1.3 + - - +
294B ARG* 3.2 37.3 + - - -
310B GLN* 5.2 3.7 + - - +
329B GLN 4.6 4.7 - - - +
330B MET* 4.6 6.4 - - - +
343B ALA 3.2 16.6 + - - +
344B GLU* 3.3 8.7 + - - +
346B SER* 1.3 79.5 + - - +
348B VAL* 1.3 65.2 + - - +
350B ASN* 3.9 6.1 - - - +
351B ALA* 3.1 22.3 + - - +
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Residues in contact with VAL 348 (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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330B MET* 3.7 33.9 - - + +
331B LEU* 4.0 13.5 - - + -
344B GLU 3.1 15.1 + - - +
345B GLY 3.9 4.7 - - - +
347B ASP* 1.3 79.7 - - - +
349B ALA* 1.3 62.9 + - - +
351B ALA* 3.2 4.9 + - - +
352B VAL* 3.1 24.7 + - + +
359B ILE* 4.1 18.8 - - + +
378B GLN* 3.2 29.2 - - - +
381B ILE* 3.7 18.2 - - + -
382B ALA 4.9 1.6 - - - +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.7 43.7 - - + -
345B GLY 3.3 15.6 + - - +
346B SER 3.6 5.4 - - - +
347B ASP 3.3 0.2 - - - -
348B VAL* 1.3 79.8 - - - +
350B ASN* 1.3 58.8 + - - +
352B VAL* 3.3 5.1 + - - +
353B LEU* 3.0 31.9 + - - +
381B ILE* 4.0 7.9 - - + -
385B ALA* 3.9 10.1 - - + +
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 5.8 0.8 - - - +
311A LYS* 3.2 32.1 + - - +
347A ASP* 5.2 3.0 + - - +
350A ASN* 3.1 47.8 - - - +
354A ASP* 5.3 0.8 + - - -
310B GLN* 6.0 0.4 - - - +
346B SER* 2.8 32.0 + - - +
347B ASP* 3.9 5.8 - - - +
349B ALA* 1.3 74.5 - - - +
351B ALA* 1.3 55.5 + - - +
353B LEU* 3.5 7.3 - - - +
354B ASP* 2.6 44.2 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLN* 4.0 5.1 - - - +
314B ILE* 5.1 0.4 - - + -
326B CYS* 3.7 35.2 - - + -
330B MET* 4.3 7.6 - - + -
347B ASP 3.1 14.5 + - - +
348B VAL 3.2 9.8 + - - +
350B ASN* 1.3 76.8 - - - +
352B VAL* 1.3 63.9 + - - +
354B ASP* 3.3 13.0 + - - +
355B GLY 3.3 5.0 + - - -
356B ALA* 3.1 26.5 + - + +
359B ILE* 4.7 2.7 - - + -
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.7 28.9 - - + +
348B VAL* 3.1 16.2 + - + +
349B ALA 3.4 7.9 - - - +
351B ALA* 1.3 76.3 - - - +
353B LEU* 1.3 61.3 + - - +
355B GLY* 3.1 15.2 + - - -
356B ALA* 3.9 9.8 + - - +
359B ILE* 4.4 11.9 - - + -
382B ALA* 4.5 10.8 - - - +
385B ALA* 3.9 20.9 - - + -
386B GLU* 3.4 25.4 - - - +
389B ILE* 4.3 12.6 - - + +
467B ARG* 5.3 5.3 + - - +
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Residues in contact with LEU 353 (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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307A PHE* 3.8 14.6 - - + -
311A LYS* 3.5 34.3 - - + +
30B MET* 5.3 4.0 - - + -
349B ALA 3.0 20.5 + - - +
350B ASN* 3.6 11.9 - - - +
352B VAL* 1.3 73.7 - - - +
354B ASP* 1.3 66.4 + - - +
355B GLY* 3.3 1.2 + - - -
385B ALA* 3.4 26.2 - - + +
388B ALA* 3.7 19.7 - - + +
389B ILE* 3.6 18.6 - - + -
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Residues in contact with ASP 354 (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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350A ASN* 5.2 0.7 + - - -
310B GLN* 3.3 23.4 + - - -
311B LYS* 2.5 45.3 + - + +
314B ILE* 3.3 28.6 - - + +
315B GLY* 5.2 1.9 + - - -
318B ASN* 4.3 3.6 + - - -
350B ASN* 2.6 30.6 + - - +
351B ALA 3.4 7.4 - - - +
353B LEU* 1.3 74.2 - - - +
355B GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 355 (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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314B ILE* 3.5 7.1 - - - +
318B ASN* 3.1 32.7 + - - +
324B VAL* 4.1 0.2 - - - +
352B VAL 3.1 12.1 + - - -
353B LEU 3.1 1.7 - - - -
354B ASP* 1.3 79.4 - - - +
356B ALA* 1.3 69.0 + - - +
357B ASP* 3.5 4.5 + - - +
394B LEU* 5.7 3.6 - - - -
445B ARG* 4.4 6.5 + - - -
467B ARG* 5.2 6.1 - - - -
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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