Contacts of the helix formed by residues 399 - 420 (chain A) in PDB entry 3BI6
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 LYS 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A SER* 3.8 18.0 + - - +
397A TYR 3.4 22.2 + - - +
398A PHE* 1.3 73.8 - - - +
400A GLU* 1.3 67.9 + - - +
401A ALA* 3.3 4.9 - - + +
402A GLU* 2.8 38.1 + - + +
403A LEU* 2.9 10.2 + - - +
536A GLN* 3.8 9.6 + - - +
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Residues in contact with GLU 400 (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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399A LYS* 1.3 73.6 - - - +
401A ALA* 1.3 56.2 + - - +
403A LEU* 3.2 12.7 + - - +
404A LYS* 2.9 55.3 + - + +
536A GLN* 4.2 4.6 + - - +
537A VAL 4.6 2.3 - - - +
538A LEU* 3.3 16.4 - - + -
539A SER* 2.7 50.6 + - - -
542A PHE* 3.3 16.3 - - + +
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LYS* 3.3 3.4 - - + +
400A GLU* 1.3 76.7 - - - +
402A GLU* 1.3 60.7 + - + +
404A LYS* 3.7 10.2 - - - +
405A ASP* 3.1 27.5 + - - +
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR 4.0 2.3 - - - +
398A PHE* 3.4 25.5 - - + -
399A LYS* 2.8 49.9 + - + +
401A ALA* 1.3 76.8 - - + +
403A LEU* 1.3 61.2 + - - +
405A ASP* 3.5 8.9 + - - +
406A LEU* 2.9 27.5 + - - +
459A PHE* 4.8 1.9 - - - -
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE* 3.4 37.9 - - + +
399A LYS 2.9 13.3 + - - +
400A GLU* 3.4 6.7 - - - +
402A GLU* 1.3 75.3 - - - +
404A LYS* 1.3 61.2 + - - +
406A LEU* 3.5 5.7 + - + +
407A LEU* 2.9 28.9 + - - +
507A VAL* 3.5 19.4 - - + +
510A ALA* 3.6 9.4 - - + -
511A ALA* 3.4 41.1 - - + +
536A GLN* 4.0 0.2 - - - +
538A LEU* 3.8 24.7 - - + -
542A PHE* 3.7 20.2 - - + -
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Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU* 2.9 48.1 + - + +
401A ALA* 3.7 10.5 - - - +
403A LEU* 1.3 73.3 - - - +
405A ASP* 1.3 56.8 + - - +
407A LEU* 3.3 3.4 + - - +
408A LEU* 2.8 37.2 + - - +
539A SER* 4.6 3.4 + - - -
541A GLU* 4.9 5.5 + - - -
542A PHE* 3.7 17.5 - - + -
568A VAL* 3.4 41.0 + - - +
569A LEU* 4.0 16.7 - - + +
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Residues in contact with ASP 405 (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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401A ALA 3.1 16.1 + - - +
402A GLU* 3.6 8.4 - - - +
404A LYS* 1.3 76.3 - - - +
406A LEU* 1.3 58.7 + - - +
408A LEU* 3.3 7.6 + - - +
409A GLN* 2.8 66.6 + - - +
456A LYS* 3.7 12.7 + - - +
457A VAL* 4.1 10.4 - - - +
459A PHE* 4.1 9.7 - - - -
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Residues in contact with LEU 406 (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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384A LEU* 3.9 24.0 - - + -
398A PHE* 4.4 7.2 - - + -
402A GLU 2.9 17.8 + - - +
403A LEU* 3.6 6.7 - - + +
405A ASP* 1.3 73.6 - - - +
407A LEU* 1.3 64.5 + - - +
409A GLN* 4.0 0.3 - - - +
410A VAL* 3.1 39.0 + - + +
432A ILE* 4.5 0.9 - - + -
459A PHE* 3.7 45.0 - - + -
503A LEU* 5.5 0.9 - - + -
506A THR* 4.8 2.9 - - + -
507A VAL* 4.1 21.5 - - + -
510A ALA* 3.5 31.9 - - + -
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Residues in contact with LEU 407 (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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403A LEU 2.9 18.6 + - - +
404A LYS* 3.5 5.6 - - - +
406A LEU* 1.3 76.2 - - - +
408A LEU* 1.3 53.6 + - - +
411A GLY* 2.8 33.3 + - - -
503A LEU* 3.6 31.9 - - + +
507A VAL* 3.9 15.7 - - + +
542A PHE* 3.8 24.5 - - + -
545A LEU* 4.0 22.0 - - + -
546A LEU* 4.1 13.7 - - + -
549A MET* 3.8 18.4 - - + -
563A LEU* 4.2 5.3 - - + +
569A LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 408 (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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404A LYS 2.8 21.0 + - - +
405A ASP* 3.8 7.0 - - - +
407A LEU* 1.3 74.4 - - - +
409A GLN* 1.3 60.3 + - + +
411A GLY* 3.4 2.0 + - - -
412A ARG* 2.8 62.2 + - - +
563A LEU* 6.0 0.2 - - - -
564A VAL* 3.7 42.0 - - + +
569A LEU* 4.1 35.6 - - + +
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Residues in contact with GLN 409 (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 HIS* 3.1 45.5 - - + +
405A ASP* 2.8 51.9 + - - +
406A LEU 4.0 2.5 - - - +
408A LEU* 1.3 72.8 - - + +
410A VAL* 1.3 62.3 + - - +
412A ARG* 3.2 8.2 + - - +
413A GLY 3.1 16.8 + - - -
456A LYS* 3.5 15.4 - - - +
457A VAL 3.2 19.1 + - - -
458A MET* 3.4 2.8 - - - -
459A PHE* 2.8 40.9 + - + -
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A HIS* 5.2 1.1 - - - -
406A LEU* 3.1 28.1 + - + +
409A GLN* 1.3 71.7 - - - +
411A GLY* 1.3 56.4 + - - +
413A GLY* 3.2 3.3 + - - +
414A LEU* 2.8 38.2 + - + +
427A ILE* 4.9 6.7 - - + -
432A ILE* 4.1 24.9 - - + -
459A PHE* 4.0 23.6 - - + -
461A ILE* 3.8 25.4 - - + -
503A LEU* 3.6 28.0 - - + -
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Residues in contact with GLY 411 (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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407A LEU 2.8 23.3 + - - -
408A LEU* 3.5 2.2 - - - -
410A VAL* 1.3 70.8 - - - +
412A ARG* 1.3 61.1 + - - +
414A LEU* 3.3 5.7 + - - +
415A ARG* 3.0 23.4 + - - +
503A LEU* 3.9 4.8 - - - +
560A ALA* 4.1 2.9 - - - +
563A LEU* 4.1 22.0 - - - -
564A VAL* 3.6 11.1 - - - +
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Residues in contact with ARG 412 (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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356A HIS* 3.5 22.4 + - + -
358A HIS* 4.2 15.9 - - + -
408A LEU* 2.8 52.0 + - + +
409A GLN* 3.2 9.7 + - - +
411A GLY* 1.3 73.3 - - - +
413A GLY* 1.3 62.4 + - - +
415A ARG* 3.3 34.4 + - - +
416A TYR* 3.2 18.5 + - - +
564A VAL* 3.8 22.0 + - + +
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Residues in contact with GLY 413 (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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356A HIS* 3.7 14.6 - - - -
358A HIS* 3.9 12.3 - - - -
359A VAL* 4.1 3.4 - - - +
409A GLN 3.1 11.7 + - - -
410A VAL 3.2 3.8 + - - -
412A ARG* 1.3 74.6 - - - +
414A LEU* 1.3 57.3 + - - +
416A TYR* 3.5 3.0 - - - +
417A ILE* 3.0 32.4 + - - +
461A ILE* 3.7 15.3 - - - -
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Residues in contact with LEU 414 (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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410A VAL* 2.8 21.5 + - + +
411A GLY* 3.8 4.9 - - - +
413A GLY* 1.3 69.1 - - - +
415A ARG* 1.3 61.1 + - - +
417A ILE* 4.4 5.4 - - + -
418A HIS* 2.8 40.6 + - + +
424A HIS* 4.3 6.1 - - + -
427A ILE* 3.8 26.5 - - + -
461A ILE* 3.6 8.5 - - + +
499A ASP* 3.8 45.3 - - + +
500A ILE* 4.4 10.8 - - + -
503A LEU* 3.8 30.3 - - + -
560A ALA* 3.9 9.6 - - + -
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Residues in contact with ARG 415 (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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356A HIS* 5.3 4.4 + - - -
411A GLY 3.0 16.5 + - - +
412A ARG* 3.3 44.6 + - - +
414A LEU* 1.3 76.7 - - - +
416A TYR* 1.3 57.7 + - - +
418A HIS* 3.7 3.0 - - - +
419A SER* 2.9 31.8 + - - -
560A ALA* 3.5 17.6 - - + +
561A MET* 4.1 36.6 - - + +
564A VAL* 3.2 23.1 - - + +
565A LYS* 5.3 6.5 - - - +
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Residues in contact with TYR 416 (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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352A VAL 3.5 8.3 + - - -
353A LEU* 3.5 41.6 - - + -
355A GLN* 3.0 40.6 + - + +
356A HIS* 3.3 48.9 - + + +
359A VAL* 4.1 9.4 - - + -
412A ARG 3.2 7.0 + - - +
413A GLY 3.5 7.4 - - - +
415A ARG* 1.3 73.7 - - - +
417A ILE* 1.3 69.2 + - - +
419A SER* 2.8 25.9 + - - -
420A MET* 3.2 22.8 + - + +
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Residues in contact with ILE 417 (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* 3.9 32.8 - - + -
359A VAL* 4.1 12.3 - - + -
413A GLY 3.0 25.4 + - - +
414A LEU* 3.9 6.5 - - + +
416A TYR* 1.3 72.3 - - - +
418A HIS* 1.3 68.7 + - + +
420A MET* 3.1 13.2 + - - +
422A LEU* 3.4 38.4 + - + +
423A VAL* 4.1 6.5 - - - +
424A HIS* 4.3 20.2 - - + +
461A ILE* 4.0 33.7 - - + -
464A LEU* 5.0 3.4 - - + -
467A VAL* 5.6 1.6 - - + -
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Residues in contact with HIS 418 (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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414A LEU* 2.8 38.6 + - + +
415A ARG* 3.8 5.2 - - - +
417A ILE* 1.3 78.4 - - + +
419A SER* 1.3 56.4 + - - +
421A SER* 3.2 13.3 + - - -
422A LEU 3.4 18.6 - - - -
423A VAL* 4.2 3.6 - - + -
470A ILE* 3.7 17.6 - - + +
496A PRO* 3.3 42.3 + - + +
499A ASP* 2.8 33.7 + - + +
500A ILE* 4.9 3.1 - - + -
560A ALA* 3.9 17.2 + - + +
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Residues in contact with SER 419 (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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415A ARG* 2.9 17.8 + - - -
416A TYR* 2.8 26.7 + - - -
418A HIS* 1.3 72.5 - - - +
420A MET* 1.3 65.1 + - - +
421A SER* 3.1 11.6 + - - -
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Residues in contact with MET 420 (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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352A VAL* 3.3 30.5 - - + +
353A LEU* 3.6 23.1 - - + -
416A TYR* 3.7 20.2 - - + +
417A ILE 3.1 9.2 + - - +
419A SER* 1.3 84.7 + - - +
421A SER* 1.3 69.2 + - - -
422A LEU* 3.2 21.8 + - + +
469A ARG* 4.4 4.3 + - - -
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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