Contacts of the helix formed by residues 402 - 420 (chain A) in PDB entry 6BFN
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 ALA 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 3.4 25.3 - - - +
400A ARG 3.9 1.2 + - - +
401A LEU* 1.3 74.1 - - - +
403A VAL* 1.3 66.6 + - + +
404A ASP* 3.1 22.9 - - + +
405A THR* 3.2 18.7 + - - +
406A ASP 4.0 0.2 + - - -
506A LYS* 6.2 2.0 - - - +
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A HIS* 3.4 39.0 - - + +
335A SER* 3.8 31.4 - - - +
337A ILE* 4.1 8.9 - - + +
365A SER* 4.7 2.9 + - - +
402A ALA* 1.3 72.6 - - + +
404A ASP* 1.3 71.5 + - - +
406A ASP* 3.2 4.0 + - - +
407A THR* 3.0 30.4 + - - +
510A PRO* 6.4 1.6 - - + -
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU* 5.2 0.9 - - - +
402A ALA* 3.1 15.9 - - + +
403A VAL* 1.3 85.5 - - - +
405A THR* 1.3 59.7 + - - +
407A THR* 3.3 10.5 + - - -
408A PHE 2.9 24.4 + - - -
505A ALA* 3.2 38.2 - - + +
506A LYS* 4.5 11.7 + - - +
508A ARG* 3.1 34.5 + - - +
509A PRO 5.4 0.9 - - - +
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Residues in contact with THR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 5.0 0.9 - - - -
339A GLY* 5.5 2.0 - - - -
391A LEU* 4.0 17.3 - - + -
392A PRO* 3.9 24.1 - - + +
394A GLU* 4.5 7.6 + - - -
395A TYR* 4.3 14.7 - - + +
400A ARG 4.5 2.4 + - - -
401A LEU* 3.9 17.8 - - + -
402A ALA* 3.3 26.7 + - - +
403A VAL 3.2 0.4 - - - -
404A ASP* 1.3 77.7 - - - +
406A ASP* 1.3 60.1 + - - +
408A PHE* 3.1 5.5 + - - +
409A SER* 2.9 30.7 + - - +
508A ARG* 4.1 6.7 - - - +
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Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ILE* 4.4 3.6 - - + +
330A HIS* 3.0 34.0 + - + +
337A ILE* 3.5 8.6 - - - +
338A HIS* 2.7 27.2 + - - +
339A GLY* 2.8 29.0 + - - -
341A ILE* 3.5 25.0 - - + +
403A VAL 3.2 4.3 + - - +
405A THR* 1.3 79.0 - - - +
407A THR* 1.3 62.3 + - - +
409A SER* 3.2 6.6 + - - -
410A PHE* 2.9 23.0 + - - +
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A HIS* 4.5 0.7 + - - -
403A VAL* 3.0 16.1 + - - +
404A ASP* 3.3 13.0 + - - -
406A ASP* 1.3 75.9 - - - +
408A PHE* 1.3 57.5 + - - +
410A PHE* 3.2 4.7 + - - +
411A GLY 2.9 23.0 + - - -
500A CYS* 3.6 33.4 - - + +
508A ARG* 4.2 9.4 - - + -
509A PRO* 3.6 25.4 + - + +
510A PRO* 5.2 0.2 - - - +
511A MET* 3.5 31.4 + - - +
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR 3.8 5.2 - - - -
391A LEU 3.7 7.6 - - - -
392A PRO* 3.5 40.4 - - + -
393A GLU 5.3 0.2 - - - -
404A ASP 2.9 13.0 + - - +
405A THR 3.1 8.7 + - - +
407A THR* 1.3 73.8 - - - +
409A SER* 1.3 66.3 + - - +
411A GLY 3.0 1.9 + - - -
412A VAL* 3.0 34.8 + - + +
435A LYS* 4.1 21.3 - - + -
500A CYS 3.5 8.4 + - - +
501A LEU* 3.4 45.8 - - + +
503A ARG* 5.8 1.3 - - - -
508A ARG* 3.7 29.2 - - - +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLY* 5.2 2.3 + - - -
341A ILE* 3.7 35.4 + - - +
390A TYR* 2.9 26.8 + - - +
391A LEU* 4.2 9.9 - - - +
405A THR* 2.9 16.5 + - - +
406A ASP* 3.5 10.3 + - - -
408A PHE* 1.3 75.5 - - - +
410A PHE* 1.3 63.1 + - - +
412A VAL* 3.1 7.0 + - - +
413A VAL* 2.9 24.3 + - - +
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.5 34.5 - - + -
322A THR* 3.9 13.7 - - + -
323A ALA* 3.7 19.1 - - + -
326A ILE* 3.6 24.7 - - + -
341A ILE* 4.4 4.4 - - + +
406A ASP 2.9 13.7 + - - +
407A THR 3.4 8.5 - - - +
409A SER* 1.3 75.4 - - - +
411A GLY* 1.3 58.4 + - - +
413A VAL* 3.1 11.1 + - + +
414A VAL* 2.9 50.4 + - + +
496A LEU* 4.6 1.8 - - + -
500A CYS* 4.6 6.3 - - - -
511A MET* 4.0 11.0 - - + -
514A VAL* 3.6 30.5 - - + -
518A LEU* 3.8 9.6 - - + -
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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
----------------------------------------------------------
407A THR 2.9 11.1 + - - -
408A PHE 3.0 5.5 + - - -
410A PHE* 1.3 76.9 - - - +
412A VAL* 1.3 56.1 + - - +
414A VAL* 3.2 9.6 + - - +
415A LEU* 2.9 31.0 + - - +
497A ALA* 4.2 5.7 - - - +
500A CYS* 3.7 22.8 - - - +
501A LEU* 3.9 11.7 - - - -
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 3.9 13.7 - - - +
390A TYR* 3.5 31.4 - - + -
408A PHE* 3.0 27.9 + - + +
409A SER 3.4 6.5 - - - +
411A GLY* 1.3 75.9 - - - +
413A VAL* 1.3 57.1 + - - +
415A LEU* 3.2 8.2 + - - +
416A GLU* 2.9 27.3 + - - +
423A ALA* 4.3 11.4 - - + -
434A LEU* 5.0 5.2 - - + -
435A LYS* 3.8 26.9 - - + +
501A LEU* 3.7 15.5 - - + -
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 4.0 24.9 - - + -
319A LEU* 4.1 13.0 - - + -
322A THR* 5.5 3.4 - - + +
341A ILE* 4.1 15.7 - - + -
342A LYS 4.0 18.4 - - - -
343A SER* 4.0 3.4 - - - +
346A VAL* 5.1 7.9 - - + -
390A TYR* 3.9 18.2 - - + -
409A SER 2.9 16.6 + - - +
410A PHE* 3.1 17.0 + - + +
412A VAL* 1.3 75.4 - - - +
414A VAL* 1.3 57.7 + - - +
416A GLU* 3.3 8.5 + - - +
417A THR* 2.8 33.4 + - - -
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Residues in contact with VAL 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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319A LEU* 4.1 25.9 - - + +
410A PHE* 2.9 48.3 + - + +
411A GLY* 3.2 10.3 + - - +
413A VAL* 1.3 76.1 - - - +
415A LEU* 1.3 57.9 + - - +
417A THR* 3.1 3.8 + - - -
418A LEU* 2.9 34.1 + - + +
493A LEU* 3.7 29.8 - - + +
496A LEU* 4.6 9.9 - - + -
497A ALA* 3.8 11.0 - - + +
500A CYS* 5.9 0.2 - - - -
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Residues in contact with LEU 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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411A GLY 2.9 10.3 + - - +
412A VAL* 3.5 8.7 - - - +
414A VAL* 1.3 74.8 - - - +
416A GLU* 1.3 59.0 + - - +
418A LEU* 3.1 14.0 + - + +
419A ALA* 2.9 34.7 + - + +
434A LEU* 3.6 39.7 - - + +
435A LYS* 4.7 0.7 - - - -
437A LEU* 4.3 18.6 - - + -
438A VAL* 4.4 5.6 - - + -
473A ILE* 4.2 27.1 - - + -
497A ALA* 4.1 13.0 - - + -
501A LEU* 3.6 29.2 - - + -
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 4.6 0.7 - - - +
300A LEU* 3.9 8.0 - - + +
301A HIS* 2.5 28.3 + - + +
343A SER* 2.7 31.5 + - - -
390A TYR* 2.5 33.3 + - - -
412A VAL* 2.9 15.4 + - + +
413A VAL* 3.5 6.1 - - - +
414A VAL 3.3 0.2 - - - -
415A LEU* 1.3 75.2 - - - +
417A THR* 1.3 57.9 + - - +
420A GLY* 3.0 27.9 + - - -
421A GLN 3.3 18.8 + - - +
422A ARG* 4.6 0.3 - - - -
423A ALA* 4.4 8.0 + - - +
434A LEU* 3.5 13.8 - - + +
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Residues in contact with THR 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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296A LEU* 4.0 20.8 - - + +
300A LEU* 3.9 14.6 - - + +
312A TRP* 4.3 1.0 - - + -
315A ARG* 2.8 68.4 + - + +
318A ILE* 6.1 0.9 - - + -
319A LEU* 3.6 27.5 - - + +
413A VAL 2.8 21.5 + - - -
414A VAL 3.6 4.3 - - - -
416A GLU* 1.3 76.9 - - - +
418A LEU* 1.3 59.0 + - - +
493A LEU* 6.3 0.7 - - + -
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Residues in contact with LEU 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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312A TRP* 3.6 27.0 - - + -
414A VAL* 2.9 18.2 + - + +
415A LEU* 3.5 19.7 - - + +
417A THR* 1.3 77.7 - - - +
419A ALA* 1.3 59.5 + - + +
473A ILE* 4.7 8.5 - - + -
478A LEU* 3.6 27.9 - - + -
479A ASP* 2.9 23.7 + - - +
490A GLY* 4.4 12.8 - - - +
493A LEU* 3.8 30.7 - - + +
494A GLY* 3.7 31.9 - - - +
497A ALA* 5.0 0.2 - - + -
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Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 2.9 20.4 + - + +
418A LEU* 1.3 74.7 - - + +
420A GLY* 1.3 64.1 + - - +
421A GLN* 3.2 26.6 + - + +
434A LEU* 4.7 11.0 - - + -
437A LEU* 5.8 1.6 - - + -
473A ILE* 6.3 0.9 - - + -
477A HIS* 3.2 30.6 - - + +
478A LEU 4.2 0.9 - - - +
479A ASP* 3.7 14.3 + - - -
480A PRO* 5.1 1.4 - - - +
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Residues in contact with GLY 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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300A LEU* 5.0 4.5 - - - -
301A HIS* 3.9 13.0 + - - -
315A ARG* 4.7 3.1 - - - -
416A GLU 3.0 13.6 + - - -
417A THR 4.1 0.8 + - - -
418A LEU 3.4 3.0 - - - -
419A ALA* 1.3 77.2 - - - +
421A GLN* 1.3 64.8 + - - +
479A ASP* 3.4 23.2 - - - +
481A ARG* 3.0 22.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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