Contacts of the helix formed by residues 327 - 342 (chain B) in PDB entry 2DB3
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 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B SER* 2.8 20.7 + - - -
326B PRO* 1.3 89.1 + - - +
328B ARG* 1.3 66.1 + - - +
329B GLU* 3.5 14.4 - - + +
330B LEU* 3.3 27.1 - - + +
331B ALA 3.1 7.6 + - - -
375B THR* 3.5 9.1 - - - +
548B VAL* 3.2 30.7 + - + +
551B ARG* 5.5 3.4 - - - +
553B LEU* 4.9 4.0 - - + -
4F U 3.6 13.7 + - - -
5F U 3.5 3.1 - - - -
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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
----------------------------------------------------------
327B THR* 1.3 70.9 - - - +
329B GLU* 1.3 72.8 + - - +
331B ALA* 3.1 6.1 + - - +
332B ILE* 3.0 25.5 + - - +
353B TYR* 3.7 20.2 - - + -
354B GLY* 3.4 31.2 + - - -
355B GLY* 3.6 11.1 - - - +
375B THR* 3.6 14.1 - - + +
525B GLN* 3.0 31.8 + - - +
528B ARG* 3.9 14.1 - - - +
5F U 2.9 31.2 + - - +
6F U 2.8 32.6 + - - +
7F U 4.1 10.3 + - - -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR* 3.5 8.8 - - + +
328B ARG* 1.3 75.0 - - - +
330B LEU* 1.3 57.9 + - - +
332B ILE* 3.4 11.1 + - + +
333B GLN* 3.0 27.4 + - - +
519B ILE* 3.8 16.3 - - + +
525B GLN* 3.0 20.8 + - - +
528B ARG* 2.8 50.0 + - - +
529B GLU* 4.9 9.2 - - + -
532B LEU* 3.7 32.1 - - + -
548B VAL* 4.1 2.8 - - - +
553B LEU* 3.9 14.2 - - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 3.3 19.7 - - - +
326B PRO* 4.0 8.1 - - + -
327B THR* 3.3 17.1 + - + +
328B ARG 3.2 0.8 - - - -
329B GLU* 1.3 75.8 - - - +
331B ALA* 1.3 61.2 + - - +
333B GLN* 3.2 14.1 + - - +
334B ILE* 2.9 40.6 + - + +
399B ASP* 4.2 10.1 - - - +
400B GLU* 3.7 32.8 - - + +
551B ARG* 4.1 10.3 - - + +
552B GLY* 3.6 31.0 - - - +
553B LEU* 3.8 8.9 - - + +
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 3.5 13.6 + - - -
327B THR 3.1 12.5 + - - +
328B ARG* 3.1 10.3 + - - +
330B LEU* 1.3 76.3 - - - +
332B ILE* 1.3 57.1 + - - +
334B ILE* 3.2 1.9 + - - +
335B PHE* 2.8 30.5 + - - +
351B ILE* 3.7 12.1 - - + -
353B TYR* 5.0 3.6 - - + -
373B ILE* 3.3 24.9 - - + +
374B ALA* 4.6 6.5 - - - -
375B THR* 4.4 10.3 - - + +
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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
----------------------------------------------------------
328B ARG 3.0 18.1 + - - +
329B GLU* 3.5 15.3 - - + +
331B ALA* 1.3 74.7 - - - +
333B GLN* 1.3 58.3 + - - +
335B PHE* 3.2 6.5 - - + +
336B ASN* 2.9 41.1 + - - +
351B ILE* 3.5 21.3 - - + -
353B TYR* 3.5 30.1 - - + +
525B GLN* 4.6 0.4 - - - +
529B GLU* 3.5 27.8 - - + +
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Residues in contact with GLN 333 (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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296B THR* 5.2 4.4 + - - -
329B GLU 3.0 14.3 + - - +
330B LEU* 3.5 18.3 - - - +
331B ALA 3.2 0.2 - - - -
332B ILE* 1.3 76.6 - - - +
334B ILE* 1.3 66.9 + - - +
336B ASN* 3.2 8.8 + - - +
337B GLU* 3.0 33.0 + - + +
536B LYS* 5.7 4.7 + - - +
552B GLY 2.8 25.6 + - - -
553B LEU* 3.4 9.5 - - + +
554B ASP* 2.6 42.8 + - - +
555B ILE* 5.3 0.9 - - - +
2902B ANP 4.4 5.9 + - - -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 4.6 15.5 - - + +
299B PHE* 4.6 13.7 - - + -
300B LEU* 4.2 4.2 - - + +
323B ILE* 4.4 19.7 - - + -
325B SER* 4.5 11.9 - - - -
330B LEU* 2.9 34.2 + - + +
331B ALA* 3.7 3.8 - - - +
333B GLN* 1.3 79.0 - - + +
335B PHE* 1.3 57.2 + - - +
337B GLU* 3.0 9.6 + - - +
338B ALA* 2.8 28.2 + - - +
373B ILE* 3.9 19.7 - - + -
399B ASP* 3.2 37.0 - - + +
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 4.1 22.7 - - + -
331B ALA 2.8 17.1 + - - +
332B ILE* 3.2 10.3 - - + +
334B ILE* 1.3 77.4 - - - +
336B ASN* 1.3 74.7 + - - +
338B ALA* 3.2 6.4 + - - +
339B ARG* 3.0 46.7 + - - +
349B ILE* 3.5 42.6 - - + -
350B GLY* 3.7 13.7 - - - -
351B ILE* 3.6 39.5 - - + -
373B ILE* 4.0 11.2 - - + +
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Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 4.2 15.6 - - - +
214B ILE* 4.9 4.6 - - - +
217B SER* 5.3 8.2 + - - +
332B ILE* 2.9 32.3 + - - +
333B GLN* 3.2 9.1 + - - +
335B PHE* 1.3 93.5 - - - +
337B GLU* 1.3 68.1 + - - +
339B ARG* 3.3 10.9 + - - +
340B LYS* 3.0 22.0 + - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER* 2.6 33.3 + - - -
218B GLY* 5.5 1.6 - - - -
265B TYR* 3.9 8.0 + - - -
296B THR* 4.2 15.9 - - + -
300B LEU* 3.8 16.2 - - + -
333B GLN* 3.0 28.4 + - + +
334B ILE* 3.0 7.4 + - - +
336B ASN* 1.3 78.0 - - - +
338B ALA* 1.3 64.1 + - - +
340B LYS* 2.8 39.8 + - - +
341B PHE* 3.1 23.6 + - + -
554B ASP* 6.0 1.1 - - - -
2902B ANP 4.2 8.5 + - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.6 26.6 - - + +
304B LEU* 4.1 7.4 - - + +
334B ILE 2.8 12.3 + - - +
335B PHE* 3.5 9.4 - - - +
337B GLU* 1.3 78.2 - - - +
339B ARG* 1.3 61.4 + - - +
341B PHE* 3.5 0.9 + - - +
342B ALA* 3.1 27.5 + - - +
349B ILE* 3.8 26.4 - - + +
371B VAL* 5.1 2.0 - - + -
373B ILE* 4.6 6.1 - - + -
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Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 3.6 29.9 + - - +
208B SER 2.9 22.4 + - - -
209B ASN* 2.6 33.5 + - - +
214B ILE* 3.7 26.0 - - + +
335B PHE* 3.0 42.6 + - + +
336B ASN* 3.6 15.0 - - - +
337B GLU 3.2 0.2 - - - -
338B ALA* 1.3 76.8 - - - +
340B LYS* 1.3 61.4 + - - +
342B ALA* 3.7 2.2 - - - -
343B PHE* 3.1 23.4 + - - +
349B ILE* 4.2 23.3 + - + -
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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
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214B ILE* 3.6 28.0 - - - +
215B PHE* 3.4 42.4 - - + -
217B SER* 4.0 20.6 + - - +
218B GLY* 5.0 0.2 - - - -
259B ASN* 3.6 1.9 - - - +
263B SER* 3.5 23.9 + - - +
265B TYR* 3.6 13.9 + - - -
336B ASN 3.0 12.4 + - - +
337B GLU* 2.8 38.8 + - - +
339B ARG* 1.3 76.9 - - - +
341B PHE* 1.3 73.5 + - - +
343B PHE* 3.2 19.8 + - - +
2902B ANP 4.2 5.1 + - - -
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.2 18.5 - - + +
259B ASN* 2.7 34.3 + - + +
260B VAL* 4.7 3.1 - - + -
263B SER* 3.4 25.6 - - - -
265B TYR* 3.5 39.7 - + - -
296B THR* 5.5 0.7 - - + -
297B ALA* 4.0 18.4 - - + -
300B LEU* 4.0 24.2 - - + -
301B LEU* 3.6 27.1 - - + -
304B LEU* 3.8 17.5 - - + -
337B GLU* 3.1 28.8 + - + +
340B LYS* 1.3 84.0 - - - +
342B ALA* 1.3 53.8 + - - +
343B PHE 3.3 1.1 - - - -
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 4.7 3.6 - - - -
259B ASN* 3.7 0.9 - - - +
304B LEU* 4.4 5.4 - - + -
338B ALA 3.1 18.9 + - - +
339B ARG* 3.7 3.4 - - - +
341B PHE* 1.3 75.6 - - - +
343B PHE* 1.3 68.2 + - - +
344B GLU 3.2 0.5 + - - -
345B SER* 2.8 38.5 + - - +
347B LEU* 4.2 23.4 - - + +
349B ILE* 4.3 13.7 - - + -
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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
------------------------------------------------------------
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