Contacts of the helix formed by residues 478 - 492 (chain K) in PDB entry 5G04
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 478 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K GLU* 3.8 3.2 + - - -
472K LEU* 4.4 1.8 - - + +
475K ILE* 3.4 33.9 - - + +
476K PRO 3.9 2.4 + - - -
477K GLN* 1.3 75.1 - - - +
479K ALA* 1.3 74.9 + - - +
480K SER* 3.1 19.0 + - - -
481K THR* 3.2 17.0 + - - +
482K TYR* 3.2 28.9 + - - -
508K LEU* 3.5 4.7 - - - +
8W ARG* 3.6 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K ASN* 1.3 75.6 + - - +
480K SER* 1.3 62.7 + - - +
482K TYR 3.4 1.0 + - - -
483K SER* 3.1 19.9 + - - -
505K ALA* 3.5 22.5 - - - +
508K LEU* 3.9 14.0 - - + +
509K ARG* 3.6 41.1 - - + -
512K ASP* 5.1 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 480 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449K ASN* 5.9 2.2 - - - -
478K ASN* 3.1 7.5 + - - -
479K ALA* 1.3 79.6 - - - +
481K THR* 1.3 52.8 + - - -
483K SER* 3.0 10.5 + - - -
484K ALA* 2.7 36.0 + - - +
512K ASP* 5.3 3.6 + - - -
8W ARG* 2.5 32.9 + - - -
10W GLU* 3.4 25.1 - - - -
11W LEU* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 481 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K GLU* 5.0 1.9 + - - -
449K ASN* 5.8 2.3 - - + +
468K HIS* 3.3 31.2 - - + +
471K ALA* 4.7 5.6 - - + +
472K LEU* 3.2 39.8 + - + +
475K ILE* 5.1 1.4 - - - +
478K ASN* 3.2 29.4 + - - +
479K ALA 3.4 0.6 - - - -
480K SER* 1.3 76.0 + - - +
482K TYR* 1.3 57.4 + - - +
484K ALA* 3.3 5.7 + - - +
485K ILE* 2.7 40.3 + - + +
8W ARG* 4.6 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 482 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H LYS 4.3 12.1 + - - -
128H THR 4.7 0.7 + - - -
129H ASP* 4.4 17.6 - - + +
629H ARG* 5.0 8.4 - - + +
472K LEU* 3.8 35.1 - - + +
476K PRO 4.0 10.2 + - - -
477K GLN* 4.2 10.8 + - - -
478K ASN 3.2 21.0 + - - +
481K THR* 1.3 80.6 - - - +
483K SER* 1.3 51.8 + - - +
485K ILE* 3.3 4.2 + - + +
486K GLY* 2.7 32.6 + - - -
501K TYR* 3.9 23.8 - + - +
504K THR* 3.3 31.6 - - + +
505K ALA* 3.7 15.5 - - + -
508K LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 483 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479K ALA 3.1 15.3 + - - -
480K SER* 3.0 21.0 + - - -
482K TYR* 1.3 76.8 - - - +
484K ALA* 1.3 56.0 + - - +
486K GLY* 3.2 1.0 + - - -
487K TYR* 2.8 31.6 + - - +
502K PHE* 3.6 10.6 - - - -
505K ALA* 3.6 6.4 - - - +
512K ASP* 4.1 4.9 + - - -
514K PHE* 3.9 17.8 - - - -
515K SER* 3.7 30.7 - - - -
11W LEU* 4.2 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449K ASN* 5.2 0.9 - - - +
453K HIS* 4.5 6.1 - - + -
456K ARG* 4.9 3.1 + - - +
468K HIS* 3.4 33.9 - - + +
480K SER 2.7 21.4 + - - +
481K THR* 3.6 1.1 - - - +
483K SER* 1.3 74.6 + - - +
485K ILE* 1.3 60.9 + - - +
487K TYR* 3.2 5.3 + - - +
488K ILE* 3.1 29.3 + - - +
11W LEU* 3.8 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ASP* 4.0 10.8 - - - +
465K LEU* 3.9 18.7 - - + +
468K HIS* 3.5 30.7 - - + -
469K ARG* 4.3 8.7 - - + +
472K LEU* 3.3 34.5 - - + -
481K THR* 2.7 23.0 + - + +
482K TYR* 3.6 6.5 - - + +
484K ALA* 1.3 70.3 - - - +
486K GLY* 1.3 64.1 + - - +
488K ILE* 3.4 10.1 + - - +
489K HIS* 3.3 23.0 + - + +
501K TYR* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482K TYR 2.7 18.5 + - - -
483K SER 3.5 3.6 - - - -
485K ILE* 1.3 74.1 - - - +
487K TYR* 1.3 58.3 + - - +
489K HIS* 2.9 23.3 + - - +
490K SER 3.0 10.6 + - - -
498K ALA* 3.4 7.6 - - - +
501K TYR* 3.6 20.6 - - - +
502K PHE* 3.4 16.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 487 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456K ARG* 3.4 41.3 - - - -
483K SER 2.8 16.0 + - - +
484K ALA* 3.2 6.9 + - - +
486K GLY* 1.3 73.6 - - - +
488K ILE* 1.3 64.4 + - - +
490K SER* 2.9 21.0 + - - -
491K LEU* 3.1 24.8 + - + +
502K PHE* 3.3 7.5 - - + -
514K PHE* 3.6 20.4 - + + -
518K MET* 3.3 38.8 - - + -
11W LEU* 3.7 13.9 - - + -
15W ASP* 2.4 32.1 + - + -
18W GLU* 3.6 13.4 + - - +
19W PHE* 3.8 10.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456K ARG* 3.7 28.9 - - + +
461K TYR* 3.7 42.6 - - + +
464K ALA* 3.4 24.7 - - + -
465K LEU* 3.9 18.2 - - + -
468K HIS* 3.8 18.4 - - + +
484K ALA 3.1 18.9 + - - +
485K ILE* 3.9 8.5 - - - +
486K GLY 3.3 0.4 - - - -
487K TYR* 1.3 77.8 - - - +
489K HIS* 1.3 57.0 + - - +
491K LEU* 3.4 6.2 + - - +
492K MET* 2.9 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 489 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465K LEU* 3.9 29.6 - - + +
469K ARG* 5.5 3.9 + - - -
485K ILE* 3.3 18.8 + - + +
486K GLY 2.9 10.1 + - - +
488K ILE* 1.3 76.5 - - - +
490K SER* 1.3 58.2 + - - +
492K MET* 3.1 24.8 + - + +
493K GLY 2.9 22.7 + - - -
494K ASN* 3.0 15.5 + - - +
497K ASN* 4.3 22.7 + - + +
498K ALA* 3.7 15.3 - - + +
501K TYR* 3.6 38.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 490 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486K GLY 3.0 10.7 + - - -
487K TYR* 2.9 26.7 + - - -
489K HIS* 1.3 77.4 - - - +
491K LEU* 1.3 57.1 + - - +
493K GLY* 2.9 19.1 + - - +
494K ASN 4.6 0.9 - - - +
495K PHE* 3.7 17.4 - - - -
498K ALA* 3.7 8.2 - - - +
502K PHE* 4.7 0.8 - - - -
518K MET* 4.6 0.9 - - - -
522K CYS* 3.3 33.2 - - - -
19W PHE* 3.8 21.0 - - - -
22W ILE* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456K ARG* 4.0 17.7 - - + -
459K LYS* 3.9 12.8 - - - +
461K TYR* 3.7 31.5 + - + +
487K TYR* 3.1 50.9 + - + +
488K ILE 3.8 4.3 - - - +
490K SER* 1.3 82.7 + - - +
492K MET* 1.3 56.8 + - - +
493K GLY* 3.1 4.7 + - - -
18W GLU* 4.3 23.6 - - + +
19W PHE* 4.7 6.3 - - + -
22W ILE* 3.7 45.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 492 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461K TYR* 4.2 30.9 - - + -
462K ALA* 6.0 0.4 - - - -
465K LEU* 3.8 28.0 - - + -
488K ILE 2.9 20.7 + - - +
489K HIS* 3.1 20.4 + - + +
491K LEU* 1.3 74.4 - - - +
493K GLY* 1.3 58.0 + - - +
494K ASN* 3.4 30.4 + - - +
----------------------------------------------------------
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