Contacts of the helix formed by residues 362 - 374 (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 SER 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLY 4.1 0.6 + - - -
361A VAL* 1.3 78.6 - - - +
363A GLU* 1.3 66.4 + - - +
364A PHE* 3.7 11.8 + - - +
365A GLY* 3.0 19.6 + - - -
366A LYS* 3.1 23.9 + - - -
529A VAL* 4.5 16.1 + - - +
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A LYS* 5.5 6.6 - - - -
362A SER* 1.3 74.6 - - - +
364A PHE* 1.3 56.6 + - - +
366A LYS* 3.5 21.3 + - - +
367A GLU* 3.1 38.7 + - - +
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Residues in contact with PHE 364 (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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362A SER* 3.2 9.7 + - - +
363A GLU* 1.3 76.6 - - - +
365A GLY* 1.3 63.1 + - - +
367A GLU* 3.3 8.4 + - + +
368A SER* 2.9 30.5 + - - -
525A PHE* 4.0 29.8 - + - -
529A VAL* 4.4 13.9 - - + -
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Residues in contact with GLY 365 (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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361A VAL* 4.2 10.5 - - - -
362A SER* 3.0 20.0 + - - -
364A PHE* 1.3 75.4 - - - +
366A LYS* 1.3 62.8 + - - +
368A SER* 2.8 24.2 + - - -
369A ILE* 3.2 12.0 + - - +
526A PHE* 4.1 2.4 - - - -
529A VAL* 4.3 21.3 - - - -
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Residues in contact with LYS 366 (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 5.3 0.7 - - - +
354A LEU* 3.4 27.6 - - + +
355A LYS* 4.0 40.6 - - + +
358A PHE* 3.5 21.3 - - + +
359A PRO* 4.4 7.0 + - - -
361A VAL* 2.6 40.6 + - + +
362A SER 3.1 14.2 + - - +
363A GLU* 3.9 19.3 + - - +
365A GLY* 1.3 74.1 - - - +
367A GLU* 1.3 61.1 + - - +
369A ILE* 3.5 9.1 + - - +
370A LEU* 3.2 16.6 + - - +
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Residues in contact with GLU 367 (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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347A ARG* 5.6 0.2 + - - -
351A GLN* 5.3 2.9 + - - -
363A GLU* 3.1 26.9 + - - +
364A PHE* 3.7 10.9 - - + +
365A GLY 3.1 0.8 - - - -
366A LYS* 1.3 77.5 - - - +
368A SER* 1.3 59.5 + - - +
370A LEU* 3.0 20.5 + - + +
371A PHE* 2.8 30.3 + - + +
702A SO4 4.3 13.2 + - - -
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Residues in contact with SER 368 (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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364A PHE* 2.9 21.5 + - - -
365A GLY* 2.8 17.6 + - - -
367A GLU* 1.3 77.6 - - - +
369A ILE* 1.3 60.9 + - - +
371A PHE* 3.4 9.1 + - - +
372A HIS* 3.1 24.3 + - - +
521A PHE* 3.4 18.7 - - - -
525A PHE* 3.8 29.0 - - - -
526A PHE* 4.4 2.8 - - - -
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Residues in contact with ILE 369 (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* 5.3 0.4 - - + -
354A LEU* 4.2 11.4 - - + -
358A PHE* 3.8 28.0 - - + -
365A GLY 3.2 13.6 + - - +
366A LYS* 3.7 13.2 - - - +
367A GLU 3.2 0.4 - - - -
368A SER* 1.3 81.5 + - - +
370A LEU* 1.3 65.5 + - - +
372A HIS 3.2 1.4 + - - -
373A TYR* 3.0 29.5 + - + +
392A VAL* 3.8 34.3 - - + -
521A PHE* 3.8 13.0 - - + -
522A TRP* 3.8 15.9 - - + -
526A PHE* 3.7 27.4 - - + -
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Residues in contact with LEU 370 (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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347A ARG* 3.6 33.0 - - + +
350A PHE* 4.3 24.9 - - + -
351A GLN* 3.4 42.8 - - + +
354A LEU* 4.4 1.8 - - + +
366A LYS 3.2 10.3 + - - +
367A GLU* 3.0 25.2 + - + +
369A ILE* 1.3 78.4 - - - +
371A PHE* 1.3 65.2 + - + +
374A THR* 2.7 45.8 + - + +
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Residues in contact with PHE 371 (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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367A GLU* 2.8 18.0 + - + +
368A SER* 3.7 9.4 - - - +
370A LEU* 1.3 85.2 - - + +
372A HIS* 1.3 65.9 + - + +
374A THR* 4.4 1.5 + - - -
375A ASP* 4.0 30.8 + - + +
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Residues in contact with HIS 372 (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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368A SER 3.1 16.7 + - - +
369A ILE 3.2 3.8 + - - +
371A PHE* 1.3 84.9 - - + +
373A TYR* 1.3 87.2 + + + +
374A THR 3.5 0.4 + - - -
375A ASP* 4.6 5.4 + - - +
517A GLN* 3.6 24.9 - - + +
518A GLN* 3.5 24.2 + - + +
521A PHE* 3.5 37.3 - + + +
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Residues in contact with TYR 373 (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* 4.7 4.3 - - + -
369A ILE* 3.0 21.6 + - + +
370A LEU 4.5 0.7 - - - +
372A HIS* 1.3 95.8 - + + +
374A THR* 1.3 60.0 + - - +
375A ASP 3.6 1.6 - - - -
376A TRP* 3.4 18.0 - - - -
388A ALA* 3.7 20.2 - - + +
391A ASP* 4.1 15.0 - - + -
392A VAL* 3.7 28.0 - - + -
395A ASP* 2.6 31.1 + - - +
518A GLN* 3.5 20.4 - - + +
521A PHE* 4.4 2.9 - + - -
522A TRP* 2.6 44.4 + + - -
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Residues in contact with THR 374 (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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347A ARG* 3.9 13.7 + - - -
350A PHE* 4.2 24.2 - - + -
370A LEU* 2.7 31.1 + - + +
371A PHE* 4.4 2.1 - - - -
372A HIS 3.5 0.2 - - - -
373A TYR* 1.3 82.9 - - - +
375A ASP* 1.3 60.4 + - - +
376A TRP* 3.3 47.0 + - + -
385A TYR* 4.0 13.9 - - + -
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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