Contacts of the helix formed by residues 501 - 510 (chain E) in PDB entry 6NYY
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 GLU 501 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E LEU* 5.3 0.4 - - - -
499E THR 3.7 3.6 + - - +
500E LEU* 1.3 73.0 - - - +
502E LYS* 1.3 57.8 + - - +
503E ASP* 3.6 27.8 - - - +
504E LYS* 2.4 56.2 + - + +
505E LEU* 2.6 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 502 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488E LYS* 4.2 10.7 - - + +
491E LEU* 3.7 25.1 + - + +
492E ARG* 3.4 37.9 + - + +
494E LEU 4.0 9.0 + - - -
496E LEU* 3.7 26.0 - - + -
500E LEU 4.0 1.1 + - - +
501E GLU* 1.3 74.8 - - - +
503E ASP* 1.3 61.7 + - - +
505E LEU* 4.4 5.6 - - - +
506E ALA* 3.4 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 503 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488E LYS* 5.0 16.1 + - - +
501E GLU* 3.2 22.8 - - - +
502E LYS* 1.3 80.1 - - - +
504E LYS* 1.3 59.6 + - - +
506E ALA* 4.6 1.0 - - - +
507E ARG* 3.3 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 504 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499E THR 5.9 1.8 - - - +
501E GLU* 2.4 51.9 + - + +
503E ASP* 1.3 83.0 + - - +
505E LEU* 1.3 64.5 + - - +
507E ARG* 3.3 11.7 + - - +
508E LYS* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491E LEU* 4.4 5.4 - - + -
496E LEU* 3.7 26.2 - - + -
500E LEU* 4.0 33.9 - - + -
501E GLU 2.6 21.7 + - - +
502E LYS* 4.6 2.2 - - - -
504E LYS* 1.3 71.5 - - - +
506E ALA* 1.3 60.7 + - - +
508E LYS* 3.0 8.6 + - + +
509E LEU* 2.8 52.7 + - + +
542E GLN* 4.8 13.5 - - + +
545E PHE* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484E ALA* 3.4 29.5 - - + +
487E PHE* 3.7 16.2 - - + -
488E LYS* 3.7 14.1 - - + -
491E LEU* 3.8 12.7 - - + +
502E LYS 3.4 18.9 + - - +
503E ASP 5.0 0.9 - - - +
505E LEU* 1.3 77.8 - - - +
507E ARG* 1.3 61.1 + - + +
509E LEU* 4.2 0.9 - - - +
510E ALA* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484E ALA* 4.5 7.0 - - + -
503E ASP* 3.3 44.8 + - - +
504E LYS* 3.3 14.2 + - - +
505E LEU 3.2 0.6 - - - -
506E ALA* 1.3 80.0 - - + +
508E LYS* 1.3 59.0 + - - +
510E ALA* 3.9 1.3 + - - +
511E SER* 3.3 21.3 + - - -
756E TYR* 3.4 57.4 + - + +
757E GLU* 4.5 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E LYS 3.2 12.2 + - - +
505E LEU* 3.0 14.1 + - + +
507E ARG* 1.3 75.7 - - - +
509E LEU* 1.3 61.7 + - + +
510E ALA 3.2 1.3 - - - -
511E SER* 3.0 22.1 + - - -
512E LEU* 3.0 37.5 + - + +
542E GLN* 3.1 32.2 - - - +
756E TYR* 5.2 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
487E PHE* 3.7 35.9 - - + -
491E LEU* 4.5 6.7 - - + -
505E LEU* 2.8 40.2 + - + +
508E LYS* 1.3 73.1 - - + +
510E ALA* 1.3 51.9 + - - +
512E LEU* 3.2 21.0 + - + +
513E THR* 2.6 41.8 + - + +
524E VAL* 5.4 3.4 - - + -
542E GLN* 5.5 3.8 - - + +
545E PHE* 3.7 56.1 - - + +
549E ILE* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480E ILE* 3.4 21.5 - - + +
483E ARG* 2.6 39.3 + - + +
484E ALA* 3.8 23.8 - - + +
487E PHE* 3.7 5.3 - - + -
506E ALA 3.3 19.9 + - - +
507E ARG 4.0 4.3 - - - +
508E LYS 3.2 0.8 - - - -
509E LEU* 1.3 78.8 - - - +
511E SER* 1.3 56.6 + - - +
513E THR* 3.7 7.2 - - - +
----------------------------------------------------------
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