Contacts of the helix formed by residues 478 - 492 (chain J) in PDB entry 5A31
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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 3.7 17.2 - - - +
472J LEU* 4.9 1.2 - - - +
475J ILE* 3.3 40.3 + - + +
476J PRO 3.5 3.6 + - - -
477J GLN* 1.3 75.6 - - - +
479J ALA* 1.3 85.4 + - - +
480J SER* 3.0 20.2 + - - -
481J THR* 3.6 11.9 + - - +
482J TYR* 3.2 25.0 + - - -
509J ARG* 5.0 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477J GLN 3.3 3.4 + - - -
478J ASN* 1.3 80.6 + - - +
480J SER* 1.3 62.5 + - - +
482J TYR* 3.1 8.7 + - - +
483J SER* 3.1 18.6 + - - -
505J ALA* 3.8 11.8 - - + +
508J LEU* 4.1 20.8 - - + +
509J ARG* 3.8 41.7 - - + +
512J ASP* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 480 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 2.7 37.2 + - - -
10G GLU* 3.5 24.7 + - - -
11G LEU* 4.3 4.4 - - - +
478J ASN* 3.0 9.6 + - - -
479J ALA* 1.3 80.0 - - - +
481J THR* 1.3 55.7 + - - +
483J SER* 3.2 11.1 + - - -
484J ALA* 2.8 29.7 + - - +
509J ARG* 4.3 15.4 - - - +
512J ASP* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 481 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 3.1 21.5 + - - +
449J ASN* 5.4 1.0 - - - +
468J HIS* 3.5 40.2 - - + +
471J ALA* 4.6 8.0 - - + +
472J LEU* 3.9 25.1 + - + +
475J ILE* 4.7 3.8 - - - +
478J ASN* 3.6 17.3 + - - +
479J ALA 3.2 0.8 - - - -
480J SER* 1.3 75.5 + - - +
482J TYR* 1.3 61.7 + - - +
484J ALA* 3.2 5.6 + - - +
485J ILE* 2.8 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 482 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472J LEU* 3.6 28.1 - - + +
476J PRO 3.5 20.1 + - - -
477J GLN* 4.3 4.0 - - - -
478J ASN 3.2 19.0 + - - -
479J ALA* 3.1 8.8 + - - +
481J THR* 1.3 80.6 - - - +
483J SER* 1.3 56.1 + - - +
485J ILE* 3.1 9.1 - - + +
486J GLY* 2.8 27.4 + - - -
501J TYR* 3.7 32.3 - + - +
504J THR* 3.2 30.3 - - + +
505J ALA* 3.9 9.4 - - + -
508J LEU* 3.8 25.1 - - + -
183P ASP* 3.6 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 483 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 3.5 14.6 - - - +
479J ALA 3.1 8.3 + - - -
480J SER* 3.2 17.0 + - - -
482J TYR* 1.3 75.8 - - - +
484J ALA* 1.3 58.0 + - - +
486J GLY* 3.2 1.4 + - - -
487J TYR* 2.9 30.7 + - - +
501J TYR 5.1 0.2 - - - -
502J PHE* 3.8 12.1 - - - -
505J ALA* 3.9 9.4 - - - +
512J ASP* 4.1 7.8 + - - -
514J PHE* 4.0 7.5 - - - -
515J SER* 3.8 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 3.7 20.4 - - + +
449J ASN* 5.1 0.7 - - - +
453J HIS* 4.4 8.3 - - + -
456J ARG* 4.8 2.0 - - - +
468J HIS* 3.2 35.2 - - + +
480J SER 2.8 16.9 + - - +
481J THR* 3.7 1.8 - - - +
483J SER* 1.3 78.7 + - - +
485J ILE* 1.3 62.5 + - - +
487J TYR* 3.3 5.0 + - - +
488J ILE* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465J LEU* 4.2 15.9 - - + +
468J HIS* 3.3 35.0 - - + -
469J ARG* 4.6 5.6 - - + +
472J LEU* 4.0 16.6 - - + -
481J THR 2.8 23.8 + - - +
482J TYR* 3.1 24.5 - - + +
484J ALA* 1.3 70.5 - - - +
486J GLY* 1.3 65.8 + - - +
488J ILE* 3.2 32.5 - - + +
489J HIS* 3.3 15.5 + - + -
501J TYR* 3.2 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482J TYR 2.8 11.6 + - - -
483J SER 3.6 3.1 - - - -
485J ILE* 1.3 77.9 - - - +
487J TYR* 1.3 57.6 + - - +
489J HIS* 3.0 20.4 + - - +
490J SER 3.0 10.2 + - - -
498J ALA* 3.5 9.8 - - - +
501J TYR* 3.6 24.5 - - - -
502J PHE* 3.4 16.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 487 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 3.9 12.1 - - + -
15G ASP* 2.4 33.1 + - + -
16G ILE* 3.8 1.7 - - - -
18G GLU* 3.6 10.6 - - - +
19G PHE* 3.6 9.3 + - + -
456J ARG* 3.5 39.5 - - - -
483J SER 2.9 16.1 + - - +
484J ALA* 3.6 5.4 - - - +
485J ILE 3.2 0.2 - - - -
486J GLY* 1.3 74.2 - - - +
488J ILE* 1.3 66.1 + - - +
490J SER* 3.0 21.6 + - - -
491J LEU* 3.1 30.6 + - + +
502J PHE* 3.3 8.1 - - + -
514J PHE* 3.4 27.4 - + + -
518J MET* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456J ARG* 3.3 38.1 - - + +
461J TYR* 4.7 12.6 - - + +
464J ALA* 4.1 12.8 - - + +
465J LEU* 3.1 52.0 - - + +
468J HIS* 4.3 5.8 - - + +
484J ALA 3.1 10.4 + - - +
485J ILE* 3.2 25.8 - - + +
487J TYR* 1.3 76.2 - - - +
489J HIS* 1.3 65.8 + - + +
491J LEU* 3.4 6.7 + - - +
492J MET* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 489 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465J LEU* 3.7 35.6 - - + +
485J ILE* 3.4 16.5 + - - +
486J GLY* 3.0 8.1 + - - +
488J ILE* 1.3 82.9 - - - +
490J SER* 1.3 63.2 + - - +
492J MET* 3.0 22.5 + - + +
493J GLY 3.0 5.7 + - - -
494J ASN* 3.0 30.9 + - + +
497J ASN* 4.1 26.1 + - + +
498J ALA* 3.8 12.6 - - + -
501J TYR* 3.6 35.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 490 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 3.8 7.2 - - - -
22G ILE* 5.4 1.0 - - - +
486J GLY 3.0 10.6 + - - -
487J TYR* 3.0 15.4 + - - -
489J HIS* 1.3 78.4 - - - +
491J LEU* 1.3 75.7 + - - +
493J GLY 3.1 9.0 + - - -
494J ASN 4.8 0.9 - - - +
495J PHE* 3.4 21.7 - - - -
498J ALA* 3.8 5.8 - - - +
502J PHE* 4.6 0.7 - - - -
518J MET* 3.6 21.3 - - - +
522J CYS* 3.6 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU* 4.3 18.2 - - + +
19G PHE* 3.8 19.1 - - + +
22G ILE* 3.8 34.8 - - + +
456J ARG* 4.7 8.3 - - + +
459J LYS* 5.0 2.0 - - - +
461J TYR* 3.8 36.4 - - + +
487J TYR* 3.1 50.2 + - + +
488J ILE* 3.9 3.8 - - - +
490J SER* 1.3 96.8 + - - +
492J MET* 1.3 59.4 + - - +
493J GLY* 3.1 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 492 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461J TYR* 4.2 37.2 - - + +
462J ALA* 5.5 1.6 - - - -
465J LEU* 3.9 27.6 - - + -
488J ILE* 3.1 17.1 + - - +
489J HIS* 3.0 28.5 + - + +
491J LEU* 1.3 74.7 - - - +
493J GLY* 1.3 59.6 + - - +
494J ASN* 3.8 22.8 - - - +
----------------------------------------------------------
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