Contacts of the helix formed by residues 383 - 400 (chain A) in PDB entry 3FO5
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 ASN 383 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP* 2.8 38.2 + - + +
382A SER* 1.3 85.2 + - - +
384A GLN* 1.3 65.9 + - - +
385A VAL 3.0 3.8 + - - -
386A TYR* 3.0 22.3 + - + -
387A LEU* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TRP* 3.7 32.9 - - + -
380A ASP 3.3 2.5 + - - -
381A PRO* 2.9 31.8 + - - +
382A SER 3.4 1.7 - - - +
383A ASN* 1.3 76.2 - - - +
385A VAL* 1.3 76.4 + - + +
387A LEU* 3.9 1.8 - - - +
388A SER* 3.2 26.3 + - - -
465A VAL* 3.6 28.5 - - + +
466A ASP* 4.9 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASN 3.0 1.4 + - - -
384A GLN* 1.3 89.2 - - + +
386A TYR* 1.3 78.1 + - + +
388A SER* 3.5 3.8 + - - -
389A TYR* 2.9 28.6 + - + +
495A ARG* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER 5.4 2.5 - - - -
383A ASN* 3.0 28.5 + - + +
385A VAL* 1.3 91.3 - - + +
387A LEU* 1.3 60.7 + - - +
389A TYR* 4.0 12.8 - + + -
390A ASN* 2.8 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 3.9 30.3 - - + -
378A PRO 3.9 8.7 - - - +
379A TRP* 3.7 27.1 - - + -
380A ASP* 3.6 38.8 - - + +
383A ASN* 2.9 23.1 + - + +
384A GLN 3.9 3.4 - - - +
386A TYR* 1.3 77.1 - - - +
388A SER* 1.3 56.4 + - - +
390A ASN* 3.5 9.5 + - + +
391A ASN* 3.1 27.5 + - - +
491A LEU* 3.9 8.0 - - + +
509A ARG* 5.4 3.0 - - - +
511A VAL* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TRP* 5.0 2.4 - - - -
384A GLN 3.2 16.5 + - - -
385A VAL* 3.8 4.3 - - - -
387A LEU* 1.3 74.5 - - - +
389A TYR* 1.3 65.9 + - - +
391A ASN* 3.2 4.8 + - - +
392A VAL* 3.0 27.4 + - - +
465A VAL* 5.5 0.9 - - - +
466A ASP* 5.2 1.0 + - - -
469A ASP* 2.8 41.0 + - - +
491A LEU* 4.1 8.9 - - - +
493A SER* 3.3 10.4 + - - -
495A ARG* 3.6 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 2.9 21.4 + - + +
386A TYR* 3.6 16.2 - + + +
388A SER* 1.3 76.6 - - - +
390A ASN* 1.3 73.5 + - - +
392A VAL* 3.3 5.8 + - + +
393A SER* 2.9 47.9 + - - -
396A LYS* 6.2 2.5 - - - -
495A ARG* 4.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A TYR* 2.8 34.4 + - - +
387A LEU* 3.8 10.1 - - + +
389A TYR* 1.3 90.2 - - - +
391A ASN* 1.3 53.1 + - - +
393A SER* 4.0 4.3 - - - -
394A SER* 2.7 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU 3.1 15.3 + - - +
388A SER 3.2 9.6 + - - +
390A ASN* 1.3 75.8 - - - +
392A VAL* 1.3 61.8 + - - +
394A SER* 3.5 5.6 + - - -
395A LEU* 3.3 16.3 + - - +
491A LEU* 3.1 30.6 + - + +
493A SER* 2.9 21.5 + - - +
507A ALA* 3.1 24.7 + - - +
508A LEU 3.4 15.1 - - - +
509A ARG* 3.3 30.4 - - + +
529A CYS* 5.0 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER 3.0 14.0 + - - +
389A TYR* 3.7 8.3 - - + +
391A ASN* 1.3 72.7 - - - +
393A SER* 1.3 59.6 + - - +
395A LEU* 3.1 4.5 + - - +
396A LYS* 2.9 55.0 + - - +
493A SER* 3.7 25.6 - - - +
495A ARG* 3.7 38.8 - - + +
505A VAL* 4.2 13.8 - - + +
507A ALA* 3.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 2.9 45.6 + - - -
390A ASN* 4.0 5.2 - - - -
392A VAL* 1.3 74.8 - - - +
394A SER* 1.3 58.1 + - - +
396A LYS* 3.2 13.4 + - - +
397A MET* 2.9 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASN* 2.7 26.6 + - - +
391A ASN* 3.7 6.1 - - - -
393A SER* 1.3 76.9 - - - +
395A LEU* 1.3 61.4 + - - +
397A MET* 3.3 22.2 + - - +
398A LEU* 3.0 22.3 + - - +
528A LEU 5.8 1.1 - - - -
529A CYS* 3.7 17.1 - - - -
549A GLN* 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN 3.3 10.0 + - - +
392A VAL 3.1 8.2 + - - +
394A SER* 1.3 77.3 - - - +
396A LYS* 1.3 64.5 + - - +
398A LEU* 3.1 11.8 + - + +
399A VAL* 3.0 28.1 + - + +
505A VAL* 3.8 14.4 - - + -
506A ILE 3.4 25.1 - - - +
507A ALA* 3.7 14.1 - - + -
529A CYS* 3.6 11.6 - - - -
530A SER 3.8 10.8 - - - +
531A GLY 4.0 4.5 - - - -
532A PHE 3.8 10.1 - - - +
533A CYS* 4.1 8.5 - - - -
547A TYR* 3.8 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 6.2 2.2 - - - -
392A VAL* 2.9 37.8 + - + +
393A SER* 3.2 12.7 + - - +
395A LEU* 1.3 77.4 - - - +
397A MET* 1.3 60.8 + - + +
399A VAL* 3.5 10.3 + - - +
400A ALA* 3.2 21.8 + - - +
495A ARG* 5.9 1.7 - - - +
498A CYS* 4.6 18.7 - - - -
503A PRO* 5.8 3.8 - - + -
505A VAL* 4.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A SER* 2.9 25.5 + - - +
394A SER* 3.6 29.6 - - - +
395A LEU 3.2 0.4 - - - -
396A LYS* 1.3 74.5 - - + +
398A LEU* 1.3 66.5 + - - +
400A ALA* 3.1 16.6 + - - +
401A LYS* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER 3.0 12.9 + - - +
395A LEU* 3.4 10.3 - - + +
397A MET* 1.3 75.8 - - - +
399A VAL* 1.3 63.0 + - - +
401A LYS* 3.2 25.5 + - + +
404A TRP* 3.0 44.5 + - + -
418A LEU* 5.2 1.1 - - + -
425A SER* 4.7 3.6 - - - +
529A CYS* 4.0 18.2 - - - +
547A TYR* 3.9 27.8 - - + -
548A ASN 4.8 0.7 - - - +
549A GLN* 3.8 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.0 20.0 + - + +
396A LYS* 3.5 9.6 - - - +
397A MET 3.3 0.2 - - - -
398A LEU* 1.3 77.8 - - - +
400A ALA* 1.3 58.8 + - + +
401A LYS 3.2 9.9 + - - +
404A TRP* 3.8 7.3 + - - -
533A CYS* 3.5 26.7 - - - -
535A TRP* 3.9 22.4 - - + -
547A TYR* 3.5 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LYS 3.2 12.0 + - - +
397A MET* 3.1 10.0 + - - +
399A VAL* 1.3 76.4 - - + +
401A LYS* 1.3 66.3 + - - +
402A ASP* 3.5 4.3 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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