Contacts of the helix formed by residues 479 - 496 (chain J) in PDB entry 6GYS
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 SER 479 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428J LEU* 5.6 2.8 - - - +
473J TYR* 4.5 6.7 - - - -
474J GLN* 2.4 38.4 + - - +
477J VAL* 3.2 10.1 + - - -
478J GLU* 1.3 73.7 - - - +
480J ALA* 1.3 68.3 + - - +
481J ALA* 3.6 10.0 + - - +
482J VAL* 4.3 17.6 + - - +
483J LYS* 3.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 480 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479J SER* 1.3 75.8 + - - +
481J ALA* 1.3 60.2 + - - +
482J VAL 3.3 0.9 - - - -
483J LYS* 3.3 7.1 + - - +
484J GLN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 481 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432J ILE* 4.3 21.5 - - + +
436J LYS* 6.0 0.2 - - - -
479J SER* 3.6 6.9 + - - +
480J ALA* 1.3 75.4 - - - +
482J VAL* 1.3 61.1 + - + +
484J GLN* 3.2 8.9 + - - +
485J LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 482 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428J LEU* 3.8 23.6 - - + -
432J ILE* 3.9 7.6 - - + -
470J ILE* 3.2 54.5 - - + +
473J TYR* 3.6 39.3 - - + -
474J GLN* 3.7 13.0 - - - +
479J SER* 4.0 8.5 + - - +
480J ALA 3.3 0.4 - - - -
481J ALA* 1.3 76.6 - - + +
483J LYS* 1.3 57.7 + - - +
485J LEU* 3.3 6.4 + - - +
486J LEU 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 483 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474J GLN* 3.1 35.5 - - + +
479J SER 3.9 2.2 - - - +
480J ALA* 3.3 11.5 + - - +
482J VAL* 1.3 75.1 - - - +
484J GLN* 1.3 57.9 + - - +
486J LEU* 3.2 20.6 + - + +
487J VAL* 2.9 35.8 + - + +
518J LYS* 5.3 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436J LYS* 5.4 1.6 - - - +
480J ALA 2.9 17.0 + - - +
481J ALA* 3.5 10.1 - - - +
482J VAL 3.2 0.4 - - - -
483J LYS* 1.3 74.9 - - - +
485J LEU* 1.3 59.5 + - - +
487J VAL* 3.2 21.1 + - - +
488J ASP* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 485 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432J ILE* 3.7 24.2 - - + +
435J SER* 3.7 24.7 - - - +
436J LYS* 3.6 40.1 - - + +
439J ILE* 4.2 0.7 - - + -
470J ILE* 3.7 31.9 - - + -
481J ALA 2.9 13.7 + - - +
482J VAL* 3.5 9.6 - - - +
484J GLN* 1.3 75.4 - - - +
486J LEU* 1.3 58.3 + - - +
488J ASP* 3.3 5.8 + - - +
489J LEU* 2.9 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 486 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467J VAL* 4.2 17.4 - - + +
470J ILE* 3.9 13.8 - - + +
471J SER* 3.4 29.4 - - - +
474J GLN* 5.0 10.1 - - + -
482J VAL 2.9 14.0 + - - +
483J LYS* 3.2 27.5 + - + +
485J LEU* 1.3 76.3 - - - +
487J VAL* 1.3 54.2 + - + +
489J LEU* 3.5 3.3 + - - +
490J THR* 2.5 45.8 + - - +
511J THR* 4.5 7.9 - - + +
515J SER* 5.0 14.8 - - - -
518J LYS* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483J LYS* 2.9 29.2 + - + +
484J GLN* 3.2 25.3 + - - +
486J LEU* 1.3 76.2 - - + +
488J ASP* 1.3 60.0 + - - +
490J THR* 3.5 7.5 - - - -
491J GLU* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 488 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436J LYS* 2.0 39.0 + - - +
439J ILE* 3.9 16.8 - - + +
484J GLN* 2.9 37.3 + - - +
485J LEU* 3.3 10.3 - - - +
487J VAL* 1.3 77.6 - - - +
489J LEU* 1.3 58.1 + - - +
491J GLU* 3.3 11.6 + - - +
492J LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435J SER* 4.6 3.4 - - - +
439J ILE* 3.7 31.6 - - + -
463J ILE* 3.7 25.1 - - + -
466J VAL* 3.8 28.7 - - + -
467J VAL* 5.3 13.9 - - + +
470J ILE* 6.5 0.2 - - + -
485J LEU* 2.9 38.2 + - + +
486J LEU* 4.2 3.6 - - + +
488J ASP* 1.3 74.2 - - - +
490J THR* 1.3 58.0 + - - +
492J LEU* 3.7 28.2 - - + +
493J THR* 2.6 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 490 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467J VAL* 5.6 0.6 - - - +
486J LEU* 2.5 28.9 + - - +
487J VAL* 3.5 9.7 - - - -
489J LEU* 1.3 76.0 - - - +
491J GLU* 1.3 57.3 + - - +
493J THR* 3.4 4.8 + - - -
494J ALA* 2.9 29.7 + - + +
511J THR* 4.1 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 491 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487J VAL* 2.9 22.3 + - + +
488J ASP* 3.6 11.3 - - - +
490J THR* 1.3 76.5 - - - +
492J LEU* 1.3 57.2 + - - +
494J ALA* 3.5 7.8 + - + +
495J ASN* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439J ILE* 3.7 37.0 - - + -
442J ILE* 3.7 35.9 - - + -
443J VAL* 3.7 25.6 - - + -
446J PHE* 3.9 1.1 - - + -
463J ILE* 4.4 4.0 - - + -
488J ASP 2.9 16.1 + - - +
489J LEU* 3.7 20.4 - - + +
490J THR 3.3 0.4 - - - -
491J GLU* 1.3 77.1 - - - +
493J THR* 1.3 50.9 + - - +
495J ASN* 3.0 13.2 + - - +
496J LEU* 2.7 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 493 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463J ILE* 3.9 18.9 - - + +
467J VAL* 5.8 3.6 - - - +
489J LEU* 2.6 26.8 + - - +
490J THR* 3.4 5.1 + - - -
492J LEU* 1.3 69.5 - - - +
494J ALA* 1.3 61.3 + - - +
496J LEU* 3.0 40.6 + - + +
504J LEU* 4.8 11.6 - - + +
507J LEU* 4.8 20.2 - - + -
508J VAL* 5.2 11.7 - - + -
511J THR* 5.4 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490J THR* 2.9 18.5 + - + +
491J GLU* 3.7 7.4 - - - +
493J THR* 1.3 77.7 - - - +
495J ASN* 1.3 61.0 + - - +
496J LEU 3.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 495 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443J VAL* 5.0 8.9 - - - +
446J PHE* 3.2 36.7 - - + -
491J GLU* 2.9 38.4 + - - +
492J LEU* 3.0 12.5 + - - +
494J ALA* 1.3 74.8 - - - +
496J LEU* 1.3 63.5 + - - +
497J PRO* 3.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442J ILE* 3.9 9.9 - - + -
446J PHE* 3.6 20.4 - - + -
454J ASN* 3.9 24.9 - - + +
459J VAL* 5.5 6.7 - - + -
460J MET* 6.1 2.7 - - - -
463J ILE* 4.5 14.8 - - + -
492J LEU* 2.7 35.9 + - + +
493J THR* 3.0 39.9 + - + +
494J ALA 3.9 4.2 - - - +
495J ASN* 1.3 72.0 - - - +
497J PRO* 1.3 73.6 - - + +
498J THR* 5.2 1.0 - - - +
500J PHE* 4.9 8.3 - - + -
504J LEU* 4.2 14.3 - - + +
507J LEU* 5.9 2.9 - - + -
----------------------------------------------------------
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