Contacts of the helix formed by residues 501 - 520 (chain E) in PDB entry 2IO1
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 GLY 501 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475E ARG* 5.4 0.2 - - - -
493E TYR* 3.4 29.5 - - - -
500E LYS* 1.3 74.9 - - - +
502E HIS* 1.3 64.9 + - - +
503E ARG 3.3 2.9 - - - -
504E ILE* 3.1 27.1 + - - +
505E CYS* 3.2 18.9 + - - -
533E SER* 3.6 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 502 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500E LYS* 3.6 20.1 - - + +
501E GLY* 1.3 78.3 - - - +
503E ARG* 1.3 61.0 + - - +
505E CYS* 3.7 5.9 + - - +
506E GLU* 3.3 41.8 + - + +
531E HIS* 4.7 25.0 - + + +
533E SER* 4.9 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 503 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443E TYR* 4.5 0.7 - - - -
447E LYS* 6.3 0.7 - - - -
501E GLY 3.3 0.4 - - - -
502E HIS* 1.3 77.4 - - - +
504E ILE* 1.3 62.7 + - + +
505E CYS 3.3 0.2 - - - -
506E GLU* 3.6 18.0 + - - +
507E ILE* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 504 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443E TYR* 3.2 37.0 - - + +
447E LYS* 5.7 1.1 - - - +
473E ILE* 3.9 17.0 - - + -
475E ARG* 3.9 22.0 - - - +
482E VAL* 3.7 28.3 - - + -
493E TYR* 3.4 34.5 - - + +
501E GLY* 3.1 13.2 + - - +
503E ARG* 1.3 78.5 - - + +
505E CYS* 1.3 63.0 + - - +
507E ILE* 3.6 2.3 + - - +
508E LEU* 3.2 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 505 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E VAL* 4.4 9.0 - - - -
491E LEU* 3.3 34.2 - - + +
492E LYS* 4.5 0.4 - - - -
493E TYR* 4.0 27.6 - - - -
501E GLY 3.2 14.2 + - - -
502E HIS* 3.9 9.2 - - - +
503E ARG 3.3 0.2 - - - -
504E ILE* 1.3 79.3 - - - +
506E GLU* 1.3 59.0 + - - +
508E LEU* 3.4 2.6 + - - -
509E LEU* 2.9 25.3 + - - +
531E HIS* 3.3 28.0 - - + +
532E HIS 5.6 1.3 - - - -
533E SER* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502E HIS* 3.3 36.2 + - + +
503E ARG* 4.0 19.5 + - + +
504E ILE 3.4 0.4 - - - -
505E CYS* 1.3 74.0 - - - +
507E ILE* 1.3 68.3 + - + +
509E LEU* 3.2 6.2 + - - +
510E GLN* 2.9 25.6 + - - +
531E HIS* 4.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443E TYR* 3.7 22.2 - - + +
446E LEU* 4.2 24.4 - - + +
447E LYS* 4.2 26.9 - - + -
503E ARG* 2.9 40.7 + - + +
504E ILE 3.9 4.5 - - - +
506E GLU* 1.3 76.9 - - + +
508E LEU* 1.3 57.2 + - - +
510E GLN* 3.5 7.5 + - - +
511E TYR* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442E PHE* 4.0 26.7 - - + -
443E TYR* 4.1 15.3 - - + -
446E LEU* 4.1 11.0 - - + -
471E VAL* 4.2 22.4 - - + -
482E VAL* 3.7 40.6 - - + -
484E ILE* 4.6 6.5 - - + -
491E LEU* 4.3 8.7 - - + -
504E ILE* 3.2 23.6 + - + +
505E CYS 3.9 3.6 - - - +
506E GLU 3.2 0.2 - - - -
507E ILE* 1.3 77.2 - - - +
509E LEU* 1.3 59.5 + - - +
511E TYR* 3.0 14.6 - - + +
512E LEU* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491E LEU* 4.0 12.7 - - + +
505E CYS 2.9 19.3 + - - +
506E GLU* 3.2 5.8 + - - +
508E LEU* 1.3 74.3 - - - +
510E GLN* 1.3 64.1 + - - +
512E LEU* 3.4 6.8 + - + +
513E GLN* 3.2 19.4 + - - +
524E LEU* 4.5 6.7 - - + +
526E LEU* 3.6 32.0 - - + +
529E TRP* 3.8 47.6 - - + -
531E HIS* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506E GLU 2.9 16.9 + - - +
507E ILE* 3.6 8.5 - - - +
509E LEU* 1.3 76.6 - - - +
511E TYR* 1.3 59.7 + - - +
513E GLN* 3.1 19.8 + - - +
514E ASP* 2.9 54.9 + - - +
526E LEU* 5.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 511 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E PHE* 3.5 22.0 - + - -
442E PHE* 3.6 31.1 - + - -
446E LEU* 3.9 27.8 - - + -
451E TYR* 3.8 19.7 - + - -
454E VAL* 4.0 11.6 + - + -
458E THR* 3.7 6.6 + - - +
463E LEU* 3.6 16.2 - - + +
484E ILE* 6.2 1.6 - - + -
507E ILE 3.1 14.2 + - - +
508E LEU* 3.0 17.7 - - + +
510E GLN* 1.3 75.5 - - - +
512E LEU* 1.3 69.2 + - + +
514E ASP* 3.4 6.9 + - - +
515E GLU* 2.9 65.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E PHE* 6.0 0.4 - - + -
463E LEU* 4.0 16.4 - - + -
464E PHE* 3.6 14.2 - - + -
469E ILE* 4.6 10.1 - - + -
484E ILE* 3.8 35.9 - - + -
486E LEU* 4.3 5.4 - - + -
491E LEU* 5.7 0.4 - - + -
508E LEU 2.9 14.9 + - - +
509E LEU* 3.7 14.6 - - + +
510E GLN 3.3 0.4 - - - -
511E TYR* 1.3 96.0 - - + +
513E GLN* 1.3 53.9 + - - +
515E GLU* 3.2 2.9 + - - +
516E SER* 2.8 36.7 + - - -
524E LEU* 3.9 11.0 - - + -
529E TRP* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 513 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E LEU 3.2 10.5 + - - +
510E GLN* 3.1 27.5 + - - +
512E LEU* 1.3 79.5 - - - +
514E ASP* 1.3 65.1 + - - +
515E GLU 3.2 0.2 + - - -
516E SER* 3.3 1.1 + - - -
517E LYS* 3.0 27.5 + - - +
523E ASP* 2.7 35.6 + - - +
524E LEU* 2.8 47.0 + - + +
526E LEU* 5.1 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 514 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E TYR* 3.4 38.8 - - + +
510E GLN* 2.9 41.9 + - - +
511E TYR* 3.9 2.1 - - - +
513E GLN* 1.3 76.5 - - - +
515E GLU* 1.3 55.9 + - - +
517E LYS* 4.0 23.3 + - - +
518E THR* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 515 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E TYR* 3.0 14.7 + - + -
455E LYS* 3.9 1.9 - - - +
458E THR* 3.1 16.5 + - - -
461E VAL 5.2 1.7 - - - +
463E LEU* 3.8 21.0 + - + +
464E PHE* 4.5 8.5 - - + -
511E TYR* 2.9 46.9 + - + +
512E LEU* 3.4 8.3 - - - +
513E GLN 3.1 0.2 - - - -
514E ASP* 1.3 75.4 - - - +
516E SER* 1.3 57.0 + - - +
518E THR 3.3 0.2 + - - -
519E LYS* 2.4 86.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 516 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464E PHE* 3.5 24.0 - - - -
512E LEU 2.8 20.6 + - - -
513E GLN 3.8 2.0 - - - -
515E GLU* 1.3 73.8 - - - +
517E LYS* 1.3 58.3 + - - +
520E ARG* 2.8 57.4 + - - +
521E ASN 3.0 5.4 + - - -
522E SER* 2.8 20.3 + - - +
524E LEU* 3.4 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 517 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513E GLN* 3.0 19.8 + - - +
514E ASP* 4.0 23.6 + - - +
516E SER* 1.3 77.8 - - - +
518E THR* 1.3 61.0 + - - +
521E ASN* 2.9 35.2 + - - +
522E SER 3.2 11.8 + - - +
523E ASP* 3.2 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 518 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E TYR* 3.2 30.2 - - + +
455E LYS* 4.2 20.6 - - - +
514E ASP* 2.7 23.8 + - - +
517E LYS* 1.3 82.6 - - - +
519E LYS* 1.3 66.3 + - + +
521E ASN* 4.4 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 519 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E TYR* 3.4 9.4 + - - +
455E LYS* 2.7 39.5 + - - +
458E THR* 3.5 13.6 + - - -
459E LYS* 5.5 3.6 - - - +
461E VAL 5.8 2.0 - - - -
462E ASN* 5.9 2.0 - - - +
464E PHE* 5.9 1.3 - - + -
515E GLU* 2.4 65.0 + - - +
518E THR* 1.3 82.3 - - + +
520E ARG* 1.3 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 520 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E ASN* 4.4 12.8 - - - +
464E PHE* 3.4 51.5 - - + +
516E SER* 2.8 40.1 + - - +
519E LYS* 1.3 80.4 - - + +
521E ASN* 1.3 72.5 + - - +
522E SER* 3.7 19.7 + - - +
523E ASP 5.3 0.8 + - - -
524E LEU* 3.4 19.6 - - - +
----------------------------------------------------------
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