Contacts of the helix formed by residues 338 - 355 (chain B) in PDB entry 1B3U
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 GLN 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ALA 3.9 2.0 + - - -
337B ASN* 1.3 72.3 + - - +
339B HIS* 1.3 70.3 + - + +
340B VAL 3.1 2.2 - - - -
341B LYS* 3.5 10.8 + - + +
342B SER* 2.9 31.4 + - - +
375B GLU 3.9 6.5 + - - -
376B CYS* 3.0 48.1 - - + +
378B GLU* 5.1 3.4 - - - +
379B VAL* 4.9 2.5 - - + -
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Residues in contact with HIS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA* 4.3 12.8 - - + +
337B ASN* 2.9 27.4 + - - +
338B GLN* 1.3 84.4 + - + +
340B VAL* 1.3 55.9 + - - +
342B SER* 3.6 6.0 + - - -
343B ALA* 3.1 28.8 + - - +
378B GLU* 5.2 4.5 - - - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 3.8 14.6 - - - +
298B ARG* 3.1 31.4 - - - +
299B ALA* 4.0 8.3 - - + +
302B SER* 3.5 21.0 + - - +
332B LEU* 3.7 23.8 - - + -
335B ASP* 3.6 19.5 - - + +
337B ASN* 3.7 17.0 - - + +
338B GLN 3.1 0.2 - - - -
339B HIS* 1.3 74.0 - - - +
341B LYS* 1.3 66.6 + - - +
342B SER 3.1 1.5 + - - -
343B ALA* 3.1 3.5 + - - +
344B LEU* 3.0 23.0 + - + +
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU 4.1 10.1 - - - +
333B VAL 4.0 21.4 + - - +
334B SER* 4.7 2.7 - - - +
335B ASP* 3.2 23.8 - - + +
336B ALA 4.9 1.6 - - - +
337B ASN 3.1 24.4 + - - +
338B GLN* 3.5 12.7 + - + +
340B VAL* 1.3 76.3 - - - +
342B SER* 1.3 62.2 + - - +
344B LEU* 3.4 2.8 + - - -
345B ALA* 3.1 21.0 + - - +
371B GLN* 3.1 20.4 + - - +
374B ASP* 2.7 36.9 + - - +
379B VAL* 3.9 11.8 - - + +
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 2.9 22.5 + - - +
339B HIS* 3.7 6.1 - - - -
341B LYS* 1.3 73.7 - - - +
343B ALA* 1.3 65.9 + - - +
344B LEU 3.1 0.7 + - - -
345B ALA* 3.2 12.3 + - - +
346B SER* 3.2 17.3 + - - -
378B GLU* 2.8 42.1 + - - +
379B VAL* 3.3 19.8 - - - +
382B ASN* 3.7 6.4 + - - +
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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
----------------------------------------------------------
299B ALA* 3.6 26.5 - - + +
302B SER* 4.1 4.9 - - - -
303B HIS* 4.3 18.0 - - + +
339B HIS 3.1 14.9 + - - +
340B VAL 3.1 5.4 + - - +
342B SER* 1.3 79.6 - - - +
344B LEU* 1.3 63.6 + - - +
346B SER* 3.6 13.6 + - - -
347B VAL* 3.7 11.8 - - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 4.1 9.8 - - - +
305B VAL* 4.4 22.7 - - + -
329B ILE* 4.1 28.3 - - + -
332B LEU* 3.8 18.6 - - + +
333B VAL* 3.7 29.2 - - - +
340B VAL 3.0 12.7 + - - +
341B LYS* 3.6 8.1 - - - +
342B SER 3.1 0.2 - - - -
343B ALA* 1.3 74.1 - - - +
345B ALA* 1.3 54.1 + - - +
347B VAL* 2.8 14.6 + - + +
348B ILE* 2.7 48.0 + - + +
371B GLN* 3.8 17.3 - - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LYS 3.1 13.3 + - - +
342B SER 3.2 4.7 + - - +
344B LEU* 1.3 79.3 - - - +
346B SER* 1.3 61.2 + - - +
347B VAL 3.1 1.4 + - - -
348B ILE* 3.5 7.1 + - - +
349B MET* 4.7 1.4 + - - +
371B GLN* 3.1 25.0 + - - +
379B VAL* 3.8 17.9 - - + +
382B ASN* 4.0 10.8 - - + +
383B ILE* 3.3 32.4 - - + +
386B ASN* 4.2 3.8 + - - +
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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
----------------------------------------------------------
303B HIS* 5.8 2.9 - - - -
306B LYS* 4.3 4.9 + - - -
342B SER 3.2 6.7 + - - -
343B ALA* 3.8 12.4 - - - -
344B LEU 2.9 1.4 + - - -
345B ALA* 1.3 78.0 - - - +
347B VAL* 1.3 65.1 - - - +
382B ASN* 3.1 28.8 + - - -
386B ASN* 3.4 30.7 + - - +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER 3.6 23.8 - - - +
303B HIS* 4.2 27.1 - - + +
305B VAL* 4.5 13.0 - - + -
306B LYS* 3.1 38.0 - - + +
343B ALA 3.7 6.5 - - - +
344B LEU* 2.8 14.0 + - + +
346B SER* 1.3 88.8 - - - +
348B ILE* 1.3 58.5 + - - +
349B MET 3.2 2.7 - - - -
350B GLY* 2.6 28.6 + - - -
351B LEU* 4.0 1.4 + - - +
386B ASN* 6.1 0.4 - - - -
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Residues in contact with ILE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 5.8 1.3 - - - -
329B ILE* 3.9 27.8 - - + -
333B VAL* 5.1 1.3 - - + -
344B LEU* 2.7 29.0 + - + +
345B ALA* 3.5 16.2 - - - +
347B VAL* 1.3 73.9 - - - +
349B MET* 1.3 89.4 + - + +
350B GLY 3.1 1.0 + - - -
351B LEU* 3.3 28.4 + - + +
364B LEU* 4.3 8.9 - - + +
367B LEU* 4.0 23.8 - - + -
371B GLN* 3.4 28.5 - - - +
383B ILE* 3.6 10.8 - - + -
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Residues in contact with MET 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 4.7 1.2 + - - +
347B VAL 3.0 2.2 + - - -
348B ILE* 1.3 120.6 - - + +
350B GLY* 1.3 56.4 + - - +
351B LEU 3.0 10.2 + - - -
352B SER* 3.1 22.3 + - - -
360B THR* 5.8 0.2 - - - -
364B LEU* 3.9 27.6 - - + +
365B LEU* 5.9 0.9 - - - -
368B PHE* 3.6 50.3 - - + -
383B ILE* 4.6 4.9 - - + -
386B ASN* 3.8 24.2 - - + +
389B CYS* 3.8 6.3 - - + +
390B VAL* 3.6 30.4 - - + +
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 3.2 40.9 - - - +
310B GLU* 4.6 2.9 - - - +
347B VAL 2.6 15.4 + - - -
349B MET* 1.3 72.0 - - - +
351B LEU* 1.3 56.0 + - - -
352B SER 3.2 2.8 + - - -
353B PRO* 3.6 16.4 - - - +
354B ILE* 4.5 4.2 - - - +
386B ASN* 6.2 0.6 - - - +
389B CYS* 3.9 16.5 - - - -
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Residues in contact with LEU 351 (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* 3.7 21.8 - - + +
306B LYS* 3.7 28.5 - - - -
309B CYS* 3.7 29.2 - - + -
321B ILE* 4.7 8.3 - - + -
325B ILE* 5.3 2.7 - - + -
329B ILE* 5.0 10.5 - - + -
347B VAL 4.7 1.8 - - - +
348B ILE* 3.6 21.8 - - + +
349B MET 3.0 1.4 - - - -
350B GLY* 1.3 76.6 - - - +
352B SER* 1.3 64.4 + - - +
353B PRO 3.6 0.9 - - - -
354B ILE* 3.5 15.5 + - + +
355B LEU* 3.3 31.1 + - + +
364B LEU* 3.9 16.8 - - + -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B MET 3.1 14.2 + - - -
351B LEU* 1.3 74.1 - - - +
353B PRO* 1.3 74.6 - - - +
355B LEU 3.0 2.4 + - - -
356B GLY* 2.9 20.4 + - - -
360B THR* 2.9 37.0 + - - +
364B LEU* 3.7 9.0 - - - +
390B VAL* 3.6 19.5 - - - -
393B VAL* 3.4 19.0 - - - +
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Residues in contact with PRO 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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350B GLY 3.6 16.2 - - - +
352B SER* 1.3 95.2 - - - +
354B ILE* 1.3 71.8 + - + +
355B LEU 3.0 1.2 + - - -
356B GLY* 3.2 11.7 + - - +
389B CYS* 4.2 15.5 - - + -
393B VAL* 3.5 20.2 - - + -
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Residues in contact with ILE 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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309B CYS* 4.2 8.7 - - + +
310B GLU* 3.3 48.2 - - + +
317B ARG* 4.1 34.7 + - + +
318B GLU* 3.4 26.5 - - + +
321B ILE* 3.8 22.9 - - + -
350B GLY 4.5 1.6 - - - +
351B LEU* 3.7 21.3 - - + +
352B SER 3.3 0.4 - - - -
353B PRO* 1.3 84.8 - - + +
355B LEU* 1.3 56.6 + - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 4.9 0.3 + - - -
318B GLU* 4.1 9.5 - - + +
321B ILE* 3.7 36.1 - - + -
322B MET* 3.8 29.2 - - + -
326B LEU* 6.2 3.4 - - + -
351B LEU* 3.3 23.1 + - + +
352B SER 3.0 5.3 + - - +
353B PRO 3.9 0.2 - - - -
354B ILE* 1.3 81.4 - - - +
356B GLY* 1.3 61.2 + - - +
359B ASN* 2.7 43.6 + - + +
360B THR* 4.3 3.1 - - - +
363B HIS* 5.7 3.4 - - + -
364B LEU* 4.0 29.4 - - + -
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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