Contacts of the helix formed by residues 355 - 365 (chain A) in PDB entry 1BFD
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 PRO 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A LEU 4.0 2.7 - - - +
354A HIS* 1.3 83.7 - - + +
356A GLU* 1.3 73.3 + - - +
358A VAL* 3.0 6.5 + - + +
359A PHE* 3.0 33.8 + - + -
379A THR* 3.6 37.7 - - + -
382A GLN* 4.5 9.0 - - - +
453A MET* 4.2 15.7 - - + -
523A THR* 5.1 7.2 - - - -
524A VAL* 4.0 17.9 - - + +
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Residues in contact with GLU 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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346A VAL* 3.7 34.4 - - + +
354A HIS* 3.6 10.0 + - + +
355A PRO* 1.3 87.3 - - - +
357A THR* 1.3 56.0 - - - +
359A PHE* 3.4 2.3 + - - -
360A ASP* 2.9 37.5 + - - +
382A GLN* 3.4 33.6 + - + +
386A ARG* 3.4 37.8 - - - +
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Residues in contact with THR 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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346A VAL* 4.9 6.3 + - - +
348A GLN* 2.7 40.7 + - + +
353A LEU* 3.7 19.1 - - + -
354A HIS* 3.0 16.9 + - - +
356A GLU* 1.3 77.2 - - - +
358A VAL* 1.3 64.6 + - - +
360A ASP* 3.3 6.5 + - - +
361A THR* 2.9 31.7 + - - +
500A LEU* 3.8 21.8 - - + -
503A LEU* 5.0 0.2 - - + -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 4.1 19.1 - - + -
354A HIS 3.7 11.7 - - - +
355A PRO* 3.0 7.7 + - + +
357A THR* 1.3 77.3 - - - +
359A PHE* 1.3 60.5 + - + +
361A THR* 3.2 2.3 + - - -
362A LEU* 2.9 45.2 + - + +
425A VAL* 5.7 0.4 - - + -
451A VAL* 4.6 12.1 - - + -
453A MET* 4.1 31.0 - - + -
503A LEU* 4.0 20.6 - - + +
521A VAL* 4.1 16.4 - - + -
523A THR* 4.5 1.8 - - + -
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Residues in contact with PHE 359 (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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355A PRO* 3.0 31.8 + - + +
356A GLU* 3.9 2.5 - - - +
358A VAL* 1.3 76.2 - - + +
360A ASP* 1.3 63.1 + - - +
362A LEU* 3.3 14.9 + - + -
363A ASN* 2.9 25.1 + - - +
379A THR* 3.6 42.4 - - - -
382A GLN* 4.1 7.4 - - + -
383A MET* 3.8 45.8 - - + -
386A ARG* 3.8 19.7 - - + -
387A LEU* 3.6 13.0 - - + +
425A VAL* 3.9 26.0 - - + -
453A MET* 4.0 12.1 - - + -
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Residues in contact with ASP 360 (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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343A PRO* 4.9 2.4 - - - +
345A LYS* 4.5 17.3 - - - +
346A VAL 5.1 1.2 + - - -
356A GLU 2.9 19.9 + - - +
357A THR* 3.3 7.7 + - - +
359A PHE* 1.3 75.5 - - - +
361A THR* 1.3 57.9 + - - +
363A ASN* 3.4 7.6 + - - +
364A ASP* 2.9 38.1 + - - +
386A ARG* 3.0 44.4 + - - +
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Residues in contact with THR 361 (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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357A THR* 2.9 18.7 + - - +
358A VAL 3.6 4.0 - - - -
360A ASP* 1.3 75.0 - - - +
362A LEU* 1.3 58.8 + - - +
364A ASP* 3.1 9.4 + - + +
365A MET* 2.9 51.5 + - + +
500A LEU* 3.7 17.7 - - - +
503A LEU* 4.1 11.7 - - + -
504A LYS* 4.1 24.6 + - + +
507A LEU* 3.9 12.6 - - + -
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Residues in contact with LEU 362 (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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358A VAL* 2.9 31.7 + - + +
359A PHE* 3.6 18.8 - - + +
361A THR* 1.3 74.1 - - - +
363A ASN* 1.3 59.6 - - - +
364A ASP 3.3 0.2 + - - -
365A MET* 4.6 0.7 - - - +
366A ALA* 2.8 37.7 + - + +
372A TYR* 4.2 16.4 - - + -
387A LEU* 4.2 6.7 - - + -
423A ILE* 4.2 24.2 - - + -
425A VAL* 3.9 27.8 - - + -
451A VAL* 4.7 6.5 - - + -
507A LEU* 3.8 33.0 - - + -
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Residues in contact with ASN 363 (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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245A ARG* 5.6 3.0 - - - +
359A PHE 2.9 12.9 + - - +
360A ASP* 3.5 6.2 + - - +
362A LEU* 1.3 77.5 - - - +
364A ASP* 1.3 68.9 + - - +
366A ALA* 4.3 8.3 + - - +
372A TYR* 4.5 4.3 + - - -
386A ARG 3.3 24.9 + - - +
387A LEU* 3.8 6.8 - - + +
388A ASN* 2.9 37.8 + - - +
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Residues in contact with ASP 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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360A ASP* 2.9 24.9 + - - +
361A THR* 3.1 12.3 + - + +
363A ASN* 1.3 83.0 + - - +
365A MET* 1.3 64.9 + - + +
366A ALA 4.6 2.1 - - - +
504A LYS* 5.2 6.5 + - - +
532A CA 2.5 28.9 - - - -
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Residues in contact with MET 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 THR* 2.9 37.6 + - + +
362A LEU* 5.1 0.4 - - - -
364A ASP* 1.3 83.7 - - + +
366A ALA* 1.3 64.3 + - - +
367A PRO* 3.8 1.6 - - - +
504A LYS* 3.5 33.2 - - - +
507A LEU* 4.0 16.2 - - + -
508A GLN* 3.5 33.4 - - + +
511A LEU* 3.5 22.6 - - + +
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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