Contacts of the helix formed by residues 500 - 512 (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 LEU 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A LYS* 6.0 5.4 - - - +
348A GLN* 4.8 15.9 - - + +
349A ASP 5.6 3.0 + - - +
350A ALA* 5.8 0.8 - - - +
351A GLY 4.8 1.0 + - - -
353A LEU* 3.6 15.8 - - + +
357A THR* 3.8 19.7 - - + -
361A THR* 3.7 20.4 - - - +
499A ASN* 1.3 75.6 - - - +
501A GLU* 1.3 64.1 + - - +
503A LEU* 3.1 6.9 + - + +
504A LYS* 3.0 54.8 + - + +
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Residues in contact with GLU 501 (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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499A ASN* 3.2 11.3 + - - +
500A LEU* 1.3 79.2 - - - +
502A GLN* 1.3 66.5 + - + +
504A LYS* 3.5 9.0 + - - +
505A GLY* 3.1 18.4 + - - -
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Residues in contact with GLN 502 (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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496A LYS* 3.9 9.2 - - - +
497A ALA* 3.7 11.4 - - - -
498A ASP* 2.8 35.3 + - - +
499A ASN* 2.9 35.0 + - - +
501A GLU* 1.3 77.0 - - + +
503A LEU* 1.3 57.0 + - - +
505A GLY* 3.3 2.0 + - - -
506A SER* 2.8 39.9 + - - -
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Residues in contact with LEU 503 (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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353A LEU* 4.1 20.6 - - + -
358A VAL* 4.0 35.0 - - + +
361A THR* 4.1 19.7 - - + +
362A LEU* 6.3 0.2 - - + -
451A VAL* 5.7 2.2 - - + -
497A ALA* 3.7 12.5 - - + +
499A ASN 2.9 13.2 + - - +
500A LEU* 3.1 12.1 + - + +
502A GLN* 1.3 76.6 - - - +
504A LYS* 1.3 57.6 - - - +
506A SER* 3.8 1.0 - - - -
507A LEU* 3.0 48.3 + - + +
519A ILE* 5.2 4.5 - - + -
521A VAL* 4.2 26.0 - - + -
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Residues in contact with LYS 504 (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* 4.1 20.4 + - + +
364A ASP* 5.2 6.3 + - - +
365A MET* 3.5 19.3 - - - +
500A LEU* 3.0 56.0 + - + +
501A GLU* 3.8 7.0 - - - +
503A LEU* 1.3 75.0 - - - +
505A GLY* 1.3 63.0 + - - +
507A LEU 3.4 0.5 + - - -
508A GLN* 3.0 37.0 + - - +
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Residues in contact with GLY 505 (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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501A GLU 3.1 12.7 + - - -
502A GLN* 3.3 2.9 + - - -
504A LYS* 1.3 78.2 - - - +
506A SER* 1.3 62.9 + - - +
508A GLN* 3.2 16.9 + - - +
509A GLU* 3.0 22.7 + - - +
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Residues in contact with SER 506 (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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495A LEU* 3.4 27.7 - - - +
496A LYS 3.3 19.8 + - - -
497A ALA* 4.8 0.2 - - - -
502A GLN* 2.8 24.1 + - - +
503A LEU* 3.8 4.0 - - - -
505A GLY* 1.3 73.5 - - - +
507A LEU* 1.3 56.8 + - - +
509A GLU* 3.3 2.3 + - - -
510A ALA* 2.8 30.3 + - - +
519A ILE* 4.0 23.6 - - - -
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Residues in contact with LEU 507 (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* 3.9 26.7 - - + -
362A LEU* 3.8 37.2 - - + +
365A MET* 4.0 15.0 - - + -
423A ILE* 5.8 2.7 - - + -
449A ILE* 5.2 5.2 - - + -
451A VAL* 4.9 5.6 - - + -
503A LEU* 3.0 36.2 + - + +
504A LYS 3.8 4.3 - - - +
505A GLY 3.3 0.2 - - - -
506A SER* 1.3 73.3 - - - +
508A GLN* 1.3 66.9 + - - +
510A ALA* 3.7 4.7 - - + +
511A LEU* 2.8 42.9 + - + +
519A ILE* 4.0 17.5 - - + -
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Residues in contact with GLN 508 (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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365A MET* 3.5 18.5 - - + +
504A LYS* 3.0 29.5 + - - +
505A GLY* 3.2 12.7 + - - +
507A LEU* 1.3 77.9 - - - +
509A GLU* 1.3 64.4 + - - +
511A LEU* 3.4 5.4 + - - +
512A SER* 3.2 25.2 + - - -
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Residues in contact with GLU 509 (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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493A GLN* 3.2 27.6 + - - +
495A LEU* 3.9 21.0 - - + +
505A GLY 3.0 10.0 + - - +
506A SER* 3.6 7.8 - - - +
508A GLN* 1.3 80.1 - - - +
510A ALA* 1.3 64.0 + - - +
512A SER* 3.0 16.8 + - - -
513A ALA* 3.0 12.9 + - + +
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Residues in contact with ALA 510 (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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421A GLN* 5.5 0.7 - - - +
449A ILE* 3.8 25.7 - - + +
495A LEU* 4.3 1.0 - - - +
506A SER 2.8 21.0 + - - +
507A LEU* 3.7 4.9 - - + +
509A GLU* 1.3 72.0 - - - +
511A LEU* 1.3 62.7 + - - +
513A ALA* 3.1 18.7 + - - +
515A GLY 5.3 0.3 - - - +
517A VAL* 4.0 26.6 - - + +
519A ILE* 3.8 21.8 - - + -
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Residues in contact with LEU 511 (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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365A MET* 3.5 39.5 - - + +
366A ALA* 4.6 0.7 - - - -
367A PRO* 4.2 15.7 - - + -
421A GLN* 4.2 22.0 - - + +
423A ILE* 4.8 8.3 - - + -
449A ILE* 3.8 20.4 - - + -
507A LEU* 2.8 31.8 + - + +
508A GLN* 3.9 4.9 - - - +
510A ALA* 1.3 75.7 - - - +
512A SER* 1.3 60.3 + - - +
513A ALA 4.5 2.6 - - - +
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Residues in contact with SER 512 (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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508A GLN 3.2 16.1 + - - -
509A GLU* 3.0 7.6 + - - -
511A LEU* 1.3 76.4 - - - +
513A ALA* 1.3 66.9 + - - +
514A LYS* 3.8 19.2 + - - +
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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