Contacts of the helix formed by residues 491 - 512 (chain F) in PDB entry 5I4V
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 491 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E ILE* 4.8 2.7 - - + -
396E GLN* 3.7 31.9 - - - +
400E VAL* 3.9 22.0 - - + -
422E LEU* 4.4 19.1 - - + -
425E LEU* 4.1 26.5 - - + -
487F ALA* 2.9 26.4 + - + +
488F LYS* 4.0 10.8 - - + +
489F LEU 3.2 0.6 - - - -
490F LEU* 1.3 72.2 - - - +
492F ARG* 1.3 80.6 + - - +
493F LEU 3.3 0.4 - - - -
494F PRO* 3.5 15.3 - - + +
495F ALA* 4.5 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 492 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E ALA* 6.3 1.0 - - - +
382E ASP* 6.2 0.4 - - - +
393E GLU* 4.7 10.3 + - - +
396E GLN* 6.2 0.2 - - - +
423F GLU* 2.7 61.4 + - - +
424F LEU* 4.6 10.6 - - + +
427F LYS* 3.6 32.7 - - - +
428F MET* 6.0 1.3 - - + -
431F MET* 5.2 4.5 - - - -
433F MET* 4.8 15.7 - - + -
441F LEU* 5.1 6.5 - - + -
488F LYS 3.8 11.8 + - - +
489F LEU* 3.1 16.9 + - - +
491F LEU* 1.3 93.8 + - - +
493F LEU* 1.3 60.6 + - + +
494F PRO 3.5 0.4 - - - -
495F ALA* 3.2 15.6 + - - +
496F LEU* 2.8 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E MET* 3.6 31.6 - - + -
426E VAL* 3.8 15.4 - - + +
378F GLU* 5.5 0.3 - - - +
441F LEU* 4.3 30.7 - - + +
444F ILE* 3.8 19.5 - - + -
445F ILE* 3.9 31.9 - - + -
490F LEU* 3.0 17.8 + - + +
492F ARG* 1.3 74.9 - - + +
494F PRO* 1.3 64.4 - - + +
496F LEU* 3.1 11.6 + - + +
497F ARG* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 494 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422E LEU 5.0 1.6 - - - +
423E MET* 5.3 0.2 - - + -
425E LEU* 4.0 37.5 - - + +
426E VAL* 3.7 13.4 - - + -
429E ARG* 3.3 37.9 + - + +
490F LEU 3.4 11.7 - - - +
491F LEU* 3.5 20.6 - - + +
493F LEU* 1.3 91.2 - - + +
495F ALA* 1.3 61.1 + - - +
497F ARG* 3.2 3.6 + - + +
498F SER 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 495 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E ASP* 3.5 27.2 + - + +
429E ARG* 4.1 1.0 - - - +
419F ARG* 4.9 0.2 + - - -
423F GLU* 4.3 14.6 - - + +
424F LEU* 5.1 1.3 - - + -
491F LEU 4.5 2.2 + - - +
492F ARG* 3.2 35.5 + - - +
494F PRO* 1.3 79.7 - - - +
496F LEU* 1.3 63.0 + - - +
498F SER* 3.4 2.3 + - - -
499F ILE* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F GLU* 4.0 23.5 - - + +
381F ILE* 3.7 35.7 - - + -
382F ALA* 4.3 11.0 - - + +
424F LEU* 4.0 20.8 - - + +
445F ILE* 3.4 33.4 - - + -
492F ARG 2.8 15.7 + - - +
493F LEU* 3.1 14.6 + - + +
495F ALA* 1.3 74.9 - - - +
497F ARG* 1.3 59.6 + - - +
499F ILE* 3.7 4.2 - - + -
500F GLY* 2.8 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E VAL* 3.5 36.8 + - + +
427E SER* 4.8 2.8 - - - +
429E ARG* 3.7 21.1 - - + -
430E THR* 2.8 37.1 + - - +
378F GLU* 2.7 39.0 + - - +
445F ILE* 5.9 3.2 + - - +
448F ASN* 4.1 22.1 - - - +
464F ARG* 5.3 6.1 - - - +
493F LEU 2.8 19.4 + - - +
494F PRO 3.2 5.4 + - - +
496F LEU* 1.3 73.0 - - - +
498F SER* 1.3 58.2 + - - +
500F GLY* 3.2 2.4 + - - -
501F LEU* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E ARG* 2.7 48.0 + - - +
419F ARG* 3.7 19.8 + - - -
494F PRO 3.1 3.3 + - - -
495F ALA 3.9 2.2 - - - -
497F ARG* 1.3 74.9 - - - +
499F ILE* 1.3 66.7 + - - +
501F LEU* 3.3 13.1 + - - +
502F LYS* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 499 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F ILE* 4.4 14.6 - - + -
416F ILE* 4.1 9.2 - - + -
419F ARG* 3.7 54.7 - - + +
420F VAL* 3.9 21.3 - - + +
423F GLU* 4.1 15.9 - - + -
424F LEU* 4.1 16.2 - - + -
495F ALA 3.1 22.4 + - - +
496F LEU* 3.7 5.2 - - - +
498F SER* 1.3 77.9 - - - +
500F GLY* 1.3 61.6 + - - +
502F LYS* 3.3 2.8 + - - +
503F CYS* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 500 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ASN* 2.7 34.0 + - - -
378F GLU* 4.6 7.4 - - - -
381F ILE* 4.0 11.4 - - - -
496F LEU 2.8 16.8 + - - -
497F ARG 3.2 4.9 + - - -
499F ILE* 1.3 77.2 - - - +
501F LEU* 1.3 60.0 + - - +
503F CYS 3.4 0.5 + - - -
504F LEU* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E ARG 4.1 12.6 - - - +
430E THR* 4.5 7.2 - - + +
433E SER* 3.9 34.3 - - - +
497F ARG* 3.0 37.1 + - + +
498F SER* 3.3 12.1 + - - +
500F GLY* 1.3 77.5 - - - +
502F LYS* 1.3 61.7 + - - +
504F LEU* 3.5 15.2 + - + +
505F GLU* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 502 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416F ILE* 3.8 34.1 - - + -
419F ARG* 4.0 15.0 - - - +
498F SER 3.2 11.9 + - - +
499F ILE 3.8 1.6 - - - +
501F LEU* 1.3 77.9 - - - +
503F CYS* 1.3 57.6 + - - +
505F GLU* 2.8 55.3 + - - +
506F HIS* 3.3 25.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 503 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ASN* 4.3 4.5 - - - +
381F ILE* 4.0 25.1 - - + -
384F PHE* 6.0 3.1 - - - -
416F ILE* 3.7 21.8 - - - -
420F VAL* 5.0 5.4 - - - -
499F ILE* 3.0 27.6 + - - +
500F GLY 3.9 4.3 - - - +
502F LYS* 1.3 72.5 - - - +
504F LEU* 1.3 66.8 + - - +
506F HIS* 3.1 11.8 + - - +
507F LEU* 3.0 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F TRP* 4.3 26.9 - - + +
377F ASN* 4.1 13.6 - - + +
500F GLY 3.0 17.5 + - - +
501F LEU* 3.7 16.4 - - + +
503F CYS* 1.3 76.2 - - - +
505F GLU* 1.3 63.9 + - - +
507F LEU* 3.0 10.4 + - + +
508F PHE* 2.9 51.7 + - + -
526F LEU* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 505 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F LEU 3.1 11.1 + - - +
502F LYS* 2.8 55.6 + - - +
504F LEU* 1.3 77.1 - - - +
506F HIS* 1.3 63.4 + - + +
508F PHE* 3.1 19.8 + - - +
509F PHE* 3.1 42.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 506 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F GLY 3.9 11.0 - - - -
413F VAL* 3.4 29.7 - - + +
416F ILE* 3.9 27.9 - - + +
502F LYS* 3.3 40.2 + - + -
503F CYS* 3.1 10.6 + - - +
505F GLU* 1.3 80.2 - - + +
507F LEU* 1.3 63.6 + - + +
509F PHE* 3.0 35.3 + + - +
510F PHE* 3.0 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F ILE* 5.6 7.6 - - + -
340F CYS* 4.0 27.6 - - - -
343F ALA* 5.6 3.6 - - + -
376F TRP* 3.9 28.9 - - + -
377F ASN* 4.1 14.6 - - - +
503F CYS* 3.0 21.6 + - + +
504F LEU* 3.0 11.9 + - + +
506F HIS* 1.3 75.7 - - + +
508F PHE* 1.3 57.6 + - - +
510F PHE* 3.4 6.8 + - - +
511F LYS* 3.1 24.3 + - - +
522F LEU* 4.7 13.5 - - + -
526F LEU* 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 508 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504F LEU* 2.9 51.3 + - + -
505F GLU* 3.1 10.5 + - - +
507F LEU* 1.3 73.7 - - - +
509F PHE* 1.3 70.0 + - + +
511F LYS* 3.4 17.1 + - + +
512F LEU* 3.2 27.0 + - + +
526F LEU* 3.7 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 509 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502F LYS* 6.3 0.2 - - - -
505F GLU* 3.1 42.3 + - + -
506F HIS* 3.0 29.7 + + - +
508F PHE* 1.3 80.0 - - + +
510F PHE* 1.3 65.2 + - - +
512F LEU* 3.1 21.7 + - + +
513F ILE* 3.2 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 510 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F VAL* 3.9 21.5 - - + -
337F THR* 3.5 34.1 - - + -
340F CYS* 3.5 37.2 - - + -
506F HIS 3.0 11.1 + - - +
507F LEU* 3.8 9.2 - - - +
508F PHE 3.3 0.2 - - - -
509F PHE* 1.3 77.2 - - - +
511F LYS* 1.3 62.6 + - - +
513F ILE* 2.7 37.4 + - + +
514F GLY* 4.0 23.1 - - - +
519F ASP 6.1 2.9 - - - -
522F LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 511 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507F LEU 3.1 14.2 + - - +
508F PHE* 3.4 20.8 - - + +
509F PHE 3.2 0.2 - - - -
510F PHE* 1.3 78.3 - - - +
512F LEU* 1.3 63.9 + - + +
513F ILE 3.3 1.2 + - - -
523F MET* 4.0 30.1 - - + +
526F LEU* 3.7 34.9 + - + -
527F GLU* 2.8 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F PHE* 3.2 15.0 + - + +
509F PHE* 3.1 19.1 + - + +
511F LYS* 1.3 83.1 - - + +
513F ILE* 1.3 68.6 + - + +
----------------------------------------------------------
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