Contacts of the helix formed by residues 52 - 58 (chain B) in PDB entry 3NYN
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 ASP 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 3.2 34.3 + - + +
51B ARG* 1.3 72.4 - - - +
53B TYR* 1.3 69.8 + - - +
54B HIS* 2.7 16.3 + - - +
55B SER* 2.7 48.4 + - - -
56B LEU* 2.9 15.1 + - - +
158B PHE* 3.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 1.3 70.7 + - - +
54B HIS* 1.3 60.6 + - + +
57B CYS* 2.8 51.1 + - + +
58B GLU* 3.8 24.3 + - + -
67B PHE* 4.1 12.8 - + - -
150B HIS* 3.4 21.9 + + + -
153B LEU* 3.8 12.9 - - - +
154B SER* 3.6 46.4 - - - +
158B PHE* 3.3 32.5 - + + -
583B BU3 3.3 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TRP* 3.5 42.4 - + - -
52B ASP* 2.7 16.8 + - - +
53B TYR* 1.3 81.4 - - + +
55B SER* 1.3 61.5 + - - +
58B GLU* 3.0 34.9 + - + +
59B ARG* 3.0 52.4 + - + +
582B SO4 4.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 5.7 2.2 - - - -
52B ASP* 2.7 30.7 + - - -
54B HIS* 1.3 72.9 - - - +
56B LEU* 1.3 59.2 + - - -
59B ARG* 4.3 13.0 + - - +
60B GLN* 2.9 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.6 11.2 - - + -
50B GLU 3.5 18.2 - - - +
51B ARG* 3.7 7.9 - - + -
52B ASP 2.9 31.1 + - - +
55B SER* 1.3 80.3 - - - +
57B CYS* 1.3 69.4 + - - +
60B GLN* 4.0 13.2 - - - +
63B GLY* 3.2 29.1 - - - +
64B ARG 4.8 0.2 - - - -
158B PHE* 4.0 11.2 - - + -
161B TYR* 4.4 8.0 + - + -
162B LEU* 4.2 13.9 - - + -
167B PHE* 4.4 9.0 - - + -
170B PHE* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 2.8 27.1 + - + +
56B LEU* 1.3 80.3 - - - +
58B GLU* 1.3 68.5 + - - +
63B GLY 4.5 0.7 - - - -
64B ARG* 3.6 28.1 - - - +
67B PHE* 3.6 34.4 - - + -
158B PHE* 3.5 37.7 - - - -
161B TYR* 4.3 5.2 - - - -
583B BU3 3.6 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TRP* 3.2 52.5 + - + +
53B TYR* 3.8 30.6 - - + +
54B HIS* 3.0 37.3 + - - +
56B LEU 3.8 0.6 - - - -
57B CYS* 1.3 86.1 - - - +
59B ARG* 1.3 68.4 + - - +
60B GLN 3.5 1.5 - - - +
61B PRO* 5.0 0.9 - - - +
64B ARG* 3.7 16.1 + - - +
150B HIS* 3.5 23.0 + - - -
583B BU3 3.7 9.8 + - + +
----------------------------------------------------------
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