Contacts of the helix formed by residues 383 - 398 (chain A) in PDB entry 4BBZ
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 GLU 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ILE* 3.9 10.7 - - + +
381A ARG* 3.3 56.1 + - - +
382A PRO* 1.3 89.3 - - - +
384A ASN* 1.3 56.6 + - - +
385A TYR 3.3 1.8 - - - -
386A ARG* 3.1 38.5 + - - +
387A GLU* 2.8 43.3 + - + +
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TRP* 3.4 57.5 - - + +
377A VAL 5.4 0.9 + - - +
378A ASP 4.7 1.1 + - - +
379A ASP 4.1 2.6 - - - +
380A GLN 4.0 5.7 - - - +
381A ARG* 3.1 57.6 + - - +
382A PRO 3.3 0.6 - - - -
383A GLU* 1.3 77.4 - - - +
385A TYR* 1.3 61.7 + - + +
387A GLU* 3.4 5.2 + - - +
388A ALA* 2.9 30.5 + - - +
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 3.7 29.9 - - + +
346A THR* 3.9 6.5 - - - +
347A ARG* 3.2 60.9 + - + +
350A PHE* 3.3 33.9 - + + -
374A THR* 4.0 11.9 - - + -
376A TRP* 3.4 34.7 + + - -
381A ARG 5.8 0.4 - - - -
382A PRO 4.7 2.8 + - - -
383A GLU 3.3 0.4 - - - -
384A ASN* 1.3 79.9 - - + +
386A ARG* 1.3 65.4 + - - +
388A ALA* 4.3 0.2 - - - -
389A LEU* 3.1 21.5 + - - +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU* 4.3 1.9 - - - +
337A PHE* 3.8 22.2 - - + -
342A ASN* 2.7 44.1 + - - +
343A SER* 3.4 24.9 - - - +
344A ILE* 3.6 16.5 - - - +
345A ILE* 3.7 13.2 + - + +
383A GLU* 3.1 31.4 + - - +
385A TYR* 1.3 81.1 - - - +
387A GLU* 1.3 84.9 + - - +
390A GLY* 3.5 15.1 + - - -
433A TRP* 3.4 40.3 - - + +
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG* 3.8 17.1 + - - +
383A GLU* 2.8 41.1 + - + +
384A ASN* 3.9 5.2 - - - +
386A ARG* 1.3 95.0 + - - +
388A ALA* 1.3 58.1 + - - +
390A GLY* 3.5 2.0 + - - -
391A ASP* 3.0 38.2 + - - +
433A TRP 4.7 7.1 - - - +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 3.7 19.1 - - + -
373A TYR* 3.7 28.7 - - + +
376A TRP* 3.8 7.6 - - + -
384A ASN 2.9 18.0 + - - +
385A TYR* 3.9 0.7 - - - +
386A ARG 3.3 0.2 - - - -
387A GLU* 1.3 78.8 - - - +
389A LEU* 1.3 57.6 + - - +
391A ASP* 3.2 9.3 + - - +
392A VAL* 2.9 31.7 + - - +
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.9 15.9 - - + -
334A ALA* 4.2 7.0 - - + -
337A PHE* 3.5 31.0 - - + -
345A ILE* 4.5 5.4 - - + -
349A GLU 5.1 0.4 - - - +
350A PHE* 3.4 17.4 - - + +
353A GLY* 4.2 28.3 - - - +
354A LEU* 3.8 28.5 - - + -
357A PHE* 4.6 9.2 - - + -
385A TYR 3.1 17.9 + - - +
386A ARG 4.2 3.1 - - - +
387A GLU 3.3 0.2 - - - -
388A ALA* 1.3 74.6 - - - +
390A GLY* 1.3 64.0 + - - +
392A VAL* 3.1 8.8 + - + +
393A VAL* 3.1 24.2 + - + +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLY* 3.6 17.0 + - - -
327A THR* 4.7 8.7 - - - -
330A LEU* 3.5 23.9 - - - +
386A ARG 3.5 7.1 + - - -
387A GLU* 3.5 6.4 + - - -
388A ALA 3.4 0.6 - - - -
389A LEU* 1.3 77.7 - - - +
391A ASP* 1.3 56.3 + - - +
393A VAL 3.4 0.5 + - - -
394A GLY* 2.9 24.8 + - - -
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Residues in contact with ASP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS 4.8 4.0 - - - +
324A ASP* 4.8 6.9 - - - +
373A TYR* 4.1 10.8 - - + -
387A GLU* 3.0 28.2 + - - +
388A ALA* 3.2 7.0 + - - +
390A GLY* 1.3 73.2 - - - +
392A VAL* 1.3 58.9 + - - +
394A GLY* 4.4 1.3 - - - +
395A ASP* 2.8 50.8 + - - +
515A ARG* 4.4 18.4 + - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 4.2 10.3 - - + -
354A LEU* 4.2 4.9 - - + -
358A PHE* 3.7 29.6 - - + -
369A ILE* 3.8 15.3 - - + -
373A TYR* 3.7 35.9 - - + -
388A ALA 2.9 22.9 + - - +
389A LEU* 3.1 10.3 + - + +
391A ASP* 1.3 75.1 - - - +
393A VAL* 1.3 65.6 + - + +
396A TYR* 3.1 25.5 + - - +
522A TRP* 3.6 14.5 - - + -
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.9 14.1 - - + -
326A GLY* 3.8 22.4 - - - +
329A PHE* 4.5 6.3 - - + -
330A LEU* 3.9 9.2 - - + -
357A PHE* 3.6 40.6 - - + -
358A PHE* 5.4 1.8 - - + -
389A LEU* 3.1 17.0 + - + +
390A GLY 4.0 2.9 - - - +
392A VAL* 1.3 81.6 - - + +
394A GLY* 1.3 65.3 + - - +
396A TYR* 4.9 0.4 - - - -
397A ASN* 3.0 49.6 + - + +
398A PHE* 4.3 0.8 - - + -
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLU* 4.1 8.3 - - - -
326A GLY* 3.6 22.0 - - - -
390A GLY 2.9 13.7 + - - -
391A ASP* 3.8 1.1 - - - -
393A VAL* 1.3 77.7 - - - +
395A ASP* 1.3 64.0 + - - +
398A PHE* 3.0 24.6 + - - +
399A ILE* 3.2 15.8 + - - -
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Residues in contact with ASP 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A TYR* 2.6 37.6 + - - +
391A ASP* 2.8 32.6 + - - +
394A GLY* 1.3 71.8 - - - +
396A TYR* 1.3 61.7 + - - +
399A ILE* 3.7 14.1 - - - +
400A CYS* 3.1 37.8 + - - +
515A ARG* 2.9 34.4 + - - +
518A GLN* 3.5 11.0 - - - +
522A TRP* 3.4 9.2 - - + +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO* 3.5 39.0 - - + +
357A PHE 5.6 1.6 - - - -
358A PHE* 3.4 32.4 - + + -
392A VAL 3.1 19.1 + - - +
393A VAL 4.3 0.7 - - - +
395A ASP* 1.3 77.5 - - - +
397A ASN* 1.3 79.0 + - - +
400A CYS* 5.2 0.2 - - - +
401A PRO* 3.4 17.5 - - - +
522A TRP* 3.2 40.3 - + + +
526A PHE* 3.9 24.8 - + - -
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Residues in contact with ASN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA* 3.6 11.1 - - - +
230A PRO* 3.7 14.1 - - - +
231A TRP* 2.9 42.6 + - + +
286A LEU* 3.4 32.3 - - - +
357A PHE* 5.4 1.0 - - - -
358A PHE* 5.7 0.6 - - - -
393A VAL* 3.0 32.4 + - - +
396A TYR* 1.3 95.5 - - - +
398A PHE* 1.3 76.8 + - + +
401A PRO* 4.1 2.7 - - - -
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Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 4.3 0.2 - - - -
224A SER 3.6 21.8 - - - +
225A GLY* 5.0 4.0 + - - +
226A SER* 5.2 0.2 + - - -
229A ALA* 5.6 0.4 - - - -
231A TRP* 3.6 28.5 - + - -
286A LEU* 4.0 4.9 - - + -
321A VAL* 4.3 4.2 - - + +
325A GLU* 4.0 33.4 - - + -
329A PHE* 3.7 26.2 - + - -
393A VAL* 4.3 4.9 - - + -
394A GLY* 3.0 9.4 + - - +
396A TYR 3.5 1.6 - - - -
397A ASN* 1.3 96.8 - - + +
399A ILE* 1.3 67.2 + - - +
401A PRO* 3.2 5.2 - - - +
402A ALA* 3.0 26.1 + - - +
438A HIS* 3.5 26.7 - + - -
1530A 4OJ 3.8 19.7 - - + -
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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
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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