Contacts of the helix formed by residues 346 - 358 (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 THR 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ILE 5.5 0.9 - - - +
345A ILE* 1.3 77.1 - - - +
347A ARG* 1.3 57.9 + - - +
348A LYS* 3.5 9.4 + - - +
349A GLU* 2.8 37.3 + - - +
350A PHE* 2.9 28.4 + - - +
385A TYR* 3.9 7.6 - - - +
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Residues in contact with ARG 347 (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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346A THR* 1.3 73.8 - - - +
348A LYS* 1.3 57.3 + - - +
350A PHE* 3.3 2.6 + - - +
351A GLN* 2.9 34.7 + - + +
367A GLU* 5.6 0.2 + - - -
370A LEU* 3.6 37.5 - - + +
374A THR* 3.9 12.5 + - - -
385A TYR* 3.2 50.6 + - + +
702A SO4 2.9 42.0 + - - +
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Residues in contact with LYS 348 (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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346A THR* 3.2 9.4 + - - +
347A ARG* 1.3 76.6 - - - +
349A GLU* 1.3 62.2 + - + +
351A GLN* 3.5 14.3 + - + +
352A GLU* 3.0 37.5 + - + +
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Residues in contact with GLU 349 (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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335A PRO* 4.0 23.4 - - + +
336A GLY* 3.8 8.4 + - - -
337A PHE* 5.7 0.2 - - - -
344A ILE 4.3 2.1 - - - +
345A ILE* 3.2 28.6 - - + +
346A THR* 2.8 46.2 + - - +
348A LYS* 1.3 75.7 - - + +
350A PHE* 1.3 60.6 + - - +
352A GLU* 3.6 7.1 + - - +
353A GLY* 2.9 24.8 + - - -
389A LEU* 5.1 1.0 - - - +
2D NAG 3.0 32.7 - - - +
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Residues in contact with PHE 350 (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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345A ILE* 3.9 6.4 - - + +
346A THR 2.9 12.8 + - - +
347A ARG 3.4 7.6 - - - +
349A GLU* 1.3 76.0 - - - +
351A GLN* 1.3 70.0 + - - +
353A GLY* 3.0 11.2 + - - -
354A LEU* 3.1 36.8 + - + +
369A ILE* 5.3 0.2 - - + -
370A LEU* 4.3 20.0 - - + -
373A TYR* 4.7 4.0 - - + -
374A THR* 4.2 18.6 - - + -
385A TYR* 3.3 39.9 - + + -
388A ALA* 3.7 11.7 - - + -
389A LEU* 3.4 37.4 - - + +
392A VAL* 4.2 18.8 - - + -
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG* 2.9 23.8 + - - +
348A LYS* 3.9 15.7 - - + +
349A GLU 3.4 0.2 - - - -
350A PHE* 1.3 78.6 - - - +
352A GLU* 1.3 64.4 + - - +
354A LEU* 3.0 21.3 + - + +
355A LYS* 3.3 18.0 + - - +
366A LYS* 5.3 1.0 - - - +
367A GLU* 5.3 2.8 + - - -
370A LEU* 3.4 33.1 - - + +
702A SO4 3.0 38.9 + - - -
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Residues in contact with GLU 352 (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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335A PRO* 3.9 16.6 - - + -
348A LYS* 3.0 29.7 + - + +
349A GLU* 3.8 5.6 - - - +
351A GLN* 1.3 75.4 - - - +
353A GLY* 1.3 62.4 + - - +
355A LYS* 2.5 53.2 + - - +
356A ILE* 3.2 16.9 + - - +
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Residues in contact with GLY 353 (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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334A ALA* 5.0 1.3 - - - -
335A PRO* 4.4 7.4 - - - +
349A GLU 2.9 18.0 + - - -
350A PHE 3.0 6.8 + - - -
352A GLU* 1.3 78.1 - - - +
354A LEU* 1.3 59.5 - - - +
356A ILE* 3.4 9.5 + - - +
357A PHE* 3.1 30.8 + - - -
389A LEU* 4.2 19.3 - - - -
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Residues in contact with LEU 354 (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* 3.1 38.0 + - + +
351A GLN* 3.0 12.9 + - + +
353A GLY* 1.3 73.9 - - - +
355A LYS* 1.3 56.5 + - - +
358A PHE* 2.4 66.3 + - + +
366A LYS* 3.4 42.2 - - + +
369A ILE* 4.2 19.7 - - + -
370A LEU* 4.4 4.9 - - + +
389A LEU* 3.8 20.6 - - + -
392A VAL* 4.2 2.9 - - + -
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Residues in contact with LYS 355 (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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351A GLN* 3.3 12.2 + - - +
352A GLU* 2.5 50.3 + - - +
354A LEU* 1.3 78.5 - - - +
356A ILE* 1.3 63.0 + - + +
359A PRO* 3.3 27.3 - - - +
363A GLU* 5.5 6.5 - - - -
366A LYS* 4.0 27.8 - - + +
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Residues in contact with ILE 356 (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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283A GLY 4.3 1.9 - - - +
284A THR* 3.4 21.1 - - - +
285A PRO* 4.0 22.0 - - + -
333A GLY* 4.1 26.2 - - - +
334A ALA* 4.6 0.7 - - - -
335A PRO* 4.0 21.3 - - + -
352A GLU 3.5 13.9 - - - +
353A GLY* 3.4 7.2 - - - +
354A LEU 3.2 0.2 - - - -
355A LYS* 1.3 80.6 - - + +
357A PHE* 1.3 69.3 + - + +
359A PRO* 3.6 3.6 - - - +
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Residues in contact with PHE 357 (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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284A THR* 4.0 10.0 - - - +
285A PRO* 3.9 23.6 - - + -
286A LEU* 3.7 29.4 - - + -
329A PHE* 3.4 28.3 - - + -
330A LEU* 3.6 26.5 - - + -
334A ALA* 4.1 18.2 - - + -
353A GLY 3.1 23.8 + - - +
354A LEU* 4.7 0.9 - - + -
356A ILE* 1.3 86.1 - - + +
358A PHE* 1.3 84.9 + - + +
359A PRO* 3.5 6.2 - - - +
389A LEU* 4.6 5.4 - - + -
393A VAL* 3.6 20.4 - - + -
396A TYR* 5.6 1.6 - - - -
397A ASN* 5.4 1.1 - - - -
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Residues in contact with PHE 358 (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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354A LEU* 2.4 42.0 + - + +
355A LYS 3.7 0.4 - - - -
357A PHE* 1.3 91.6 - - + +
359A PRO* 1.3 66.3 - - - +
360A GLY 3.3 1.8 - - - -
361A VAL* 3.3 32.1 + - + +
366A LYS* 3.5 17.7 - - + -
369A ILE* 3.8 19.3 - - + -
392A VAL* 3.7 22.9 - - + -
393A VAL* 5.4 2.5 - - + -
396A TYR* 3.4 44.6 - + + -
397A ASN* 5.7 0.7 - - - -
522A TRP* 3.8 16.6 - + - -
526A PHE* 4.0 20.0 - + - -
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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