Contacts of the helix formed by residues 526 - 533 (chain A) 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 ASN 526 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ASN* 4.2 20.6 - - - +
525A CYS* 2.4 41.8 - - - +
527A GLU* 1.3 63.4 + - + +
528A ALA 3.1 1.6 - - - -
529A ALA* 2.9 9.4 + - - +
337B GLY 4.8 2.5 - - - -
338B ALA* 1.9 49.1 - - - +
339B LYS* 1.3 99.3 + - + +
340B ILE 4.1 1.8 - - - -
341B PRO* 4.4 1.6 - - - +
470B ASP* 5.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ASN* 4.5 2.4 - - - +
526A ASN* 1.3 80.3 - - + +
528A ALA* 1.3 57.3 + - - +
529A ALA 3.3 0.4 - - - -
530A LEU* 3.8 21.1 - - + +
531A ILE* 3.2 33.3 + - + +
548A ALA* 3.8 15.0 - - + +
551A ARG* 4.3 13.5 - - - +
552A VAL* 3.8 24.2 - - - +
339B LYS 5.2 0.4 - - - +
341B PRO* 4.2 7.5 - - + +
470B ASP* 3.4 32.6 - - - +
471B ARG* 3.8 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN* 3.1 4.0 - - - +
527A GLU* 1.3 77.5 - - - +
529A ALA* 1.3 57.7 + - - +
530A LEU 3.4 0.2 - - - -
531A ILE* 3.9 1.3 - - - +
532A ALA* 3.1 24.9 + - - +
540A ILE* 3.7 6.9 - - + +
544A HIS* 3.3 33.4 - - - +
545A PHE* 3.5 38.4 - - + -
548A ALA* 3.6 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN* 2.9 3.3 + - - +
528A ALA* 1.3 78.4 - - - +
530A LEU* 1.3 58.7 + - - +
531A ILE 3.2 0.4 - - - -
533A ALA* 2.9 28.4 + - - +
540A ILE* 3.7 6.6 - - + +
333B TYR 4.9 0.6 - - - +
336B LEU* 3.1 35.1 - - + +
337B GLY 3.9 0.4 - - - -
338B ALA* 2.5 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN 3.3 4.6 + - - +
527A GLU* 3.6 16.6 + - + +
528A ALA 3.4 0.4 - - - -
529A ALA* 1.3 74.0 - - - +
531A ILE* 1.3 61.2 + - + +
533A ALA 4.0 0.9 - - - -
534A ARG* 3.3 24.1 + - - +
322B GLU* 4.1 10.2 - - - +
326B PHE* 4.2 5.8 - - + -
333B TYR* 2.7 71.6 - - + +
338B ALA* 3.3 9.2 - - + +
339B LYS 3.5 12.1 - - - +
340B ILE* 4.4 4.3 - - + -
341B PRO* 3.1 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 3.2 20.0 + - + +
528A ALA* 3.7 4.9 + - - +
529A ALA 3.2 0.4 - - - -
530A LEU* 1.3 78.6 - - + +
532A ALA* 1.3 63.1 + - - +
533A ALA 3.2 0.4 - - - -
534A ARG* 3.3 39.1 + - - +
535A HIS* 3.0 33.0 + - + +
544A HIS* 4.2 13.0 - - + +
547A GLN* 3.3 61.0 - - + +
548A ALA* 3.9 4.7 - - - +
551A ARG* 5.4 4.3 - - + -
471B ARG* 5.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ALA 3.1 18.6 + - - +
529A ALA 3.3 0.4 + - - -
531A ILE* 1.3 78.5 - - - +
533A ALA* 1.3 56.3 + - - +
535A HIS* 4.0 1.2 + - - +
536A LEU 3.7 2.3 + - - -
537A SER* 2.4 36.9 + - - +
540A ILE* 3.7 10.5 - - + -
544A HIS* 3.3 27.3 + - - +
336B LEU* 2.3 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ALA 2.9 16.4 + - - +
530A LEU 4.8 1.6 - - - +
532A ALA* 1.3 75.9 - - - +
534A ARG* 1.3 64.9 + - - +
535A HIS 3.3 0.7 - - - -
536A LEU* 3.4 14.7 + - + +
537A SER 4.6 1.8 - - - +
332B GLN* 2.3 53.9 - - + +
333B TYR* 4.3 6.3 - - + -
335B ASP* 5.2 2.7 - - + -
336B LEU* 3.8 12.3 - - + -
775B GLY* 5.7 0.3 - - - -
----------------------------------------------------------
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