Contacts of the helix formed by residues 38 - 43 (chain B) in PDB entry 2NYM
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 GLN 38 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN 2.8 23.3 + - - +
35B LYS* 2.7 9.7 + - - +
37B ARG* 1.3 77.3 - - - +
39B CYS* 1.3 59.3 + - - +
41B VAL* 3.1 22.0 - - - +
42B LEU* 3.3 9.2 + - - +
62B ALA* 4.6 9.6 - - + +
65B GLU* 5.1 10.3 - - - +
66B MSE 4.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS 2.5 19.7 + - - +
36B LEU* 4.9 0.4 - - - -
38B GLN* 1.3 69.8 - - - +
40B CYS* 1.3 50.6 + - - +
41B VAL 2.9 4.3 - - - -
42B LEU* 2.8 7.6 + - - +
43B PHE* 2.6 36.7 + - - +
66B MSE 3.6 30.4 - - + -
82B TYR* 5.9 1.6 - - + -
84B GLU* 4.4 27.4 - - + +
85B VAL* 5.4 2.0 - - + +
88B MSE 4.2 7.1 - - + +
130B PHE* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS 4.2 0.6 + - - -
36B LEU 4.1 7.6 - - - +
37B ARG* 3.8 11.5 + - - +
39B CYS* 1.3 77.6 - - - +
41B VAL* 1.3 61.6 + - - +
43B PHE* 3.5 19.9 - - - +
44B ASP* 3.9 9.4 + - - +
84B GLU* 3.7 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG 3.4 12.2 + - - +
38B GLN* 3.1 15.2 + - - +
39B CYS 2.9 0.2 - - - -
40B CYS* 1.3 81.7 - - - +
42B LEU* 1.3 59.6 + - - +
43B PHE 3.1 1.2 + - - -
45B PHE* 3.8 16.8 + - - +
59B LYS* 4.9 1.7 - - - +
62B ALA* 5.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN 3.3 7.5 + - - +
39B CYS* 2.8 9.9 + - - +
41B VAL* 1.3 76.2 - - - +
43B PHE* 1.3 65.9 + - - +
45B PHE* 4.0 0.2 - - - -
59B LYS* 2.9 44.2 + - + -
62B ALA* 4.1 10.5 - - + +
63B LEU* 3.3 32.5 - - + -
66B MSE 5.3 0.4 - - - -
88B MSE 3.7 9.1 - - + +
92B ASN* 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS 2.6 20.7 + - - +
40B CYS* 3.5 16.6 - - - +
41B VAL 3.1 1.6 - - - -
42B LEU* 1.3 79.2 - - - +
44B ASP* 1.3 55.1 - - + +
45B PHE* 2.1 25.2 + - - +
46B VAL 4.0 1.7 + - - -
59B LYS* 4.2 2.3 + - - -
84B GLU 5.5 0.4 - - - +
87B HIS* 5.1 10.8 - - + +
88B MSE 3.9 28.3 - - + +
91B VAL* 5.0 5.3 - - + +
92B ASN* 4.2 10.2 + - - +
----------------------------------------------------------
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