Contacts of the helix formed by residues 66 - 73 (chain A) in PDB entry 2WMH
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 THR 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 3.9 - - - +
59A ASN* 3.7 13.7 - - - +
61A LEU* 3.7 9.2 - - - -
64A GLY 4.9 3.1 - - - +
65A ASN* 1.3 81.2 - - - +
67A LEU* 1.3 60.4 + - - +
68A LYS* 3.8 7.0 + - - +
69A GLY 3.0 13.2 + - - -
70A ALA* 2.9 29.6 + - - +
115A GLU* 5.9 0.7 - - - -
311A ASP* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 21.3 - - + -
61A LEU* 3.8 7.8 - - + +
66A THR* 1.3 72.5 - - - +
68A LYS* 1.3 64.3 + - - +
70A ALA* 3.2 3.5 + - - +
71A TRP* 3.1 18.5 + - - +
84A ILE* 4.0 16.4 - - + -
86A LEU* 4.4 9.2 - - + -
112A MET* 3.6 41.5 - - + +
115A GLU* 3.6 36.1 + - + +
116A ALA* 3.9 7.2 - - + +
119A LEU* 5.1 0.7 - - + -
121A ILE* 3.7 34.1 - - + +
123A VAL* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.3 6.5 + - - +
67A LEU* 1.3 78.3 - - - +
69A GLY* 1.3 57.9 + - - +
71A TRP* 3.4 2.3 + - - +
72A GLU* 2.9 56.7 + - + +
115A GLU* 5.0 3.0 + - - +
119A LEU* 3.8 40.5 - - + +
121A ILE* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.0 12.7 + - - -
68A LYS* 1.3 73.3 - - - +
70A ALA* 1.3 64.5 + - - +
72A GLU* 3.3 14.5 + - - +
73A ALA* 3.0 23.2 + - - +
308A MET* 3.7 9.8 - - - +
311A ASP* 3.6 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 21.3 - - + -
66A THR 2.9 19.4 + - - +
67A LEU 3.2 5.4 + - - +
69A GLY* 1.3 76.8 - - - +
71A TRP* 1.3 62.4 + - - +
73A ALA* 3.1 16.8 + - - +
74A ILE* 3.5 11.3 - - - +
84A ILE* 4.0 13.5 - - + -
307A PHE* 3.8 16.1 - - + -
308A MET* 3.5 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU 3.1 6.9 + - - +
68A LYS* 4.1 2.5 - - - +
70A ALA* 1.3 74.7 - - - +
72A GLU* 1.3 66.1 + - - +
74A ILE* 3.2 22.7 + - + +
79A LYS* 3.0 83.9 + - + +
82A ALA* 3.6 25.1 - - + -
83A ALA* 4.2 5.2 - - - -
84A ILE* 4.0 15.2 - - + +
119A LEU* 4.9 4.7 + - + -
120A ASN 4.4 8.2 + - - -
121A ILE* 3.8 37.9 - - + -
122A PRO* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 2.9 50.3 + - + +
69A GLY* 3.5 13.3 - - - +
70A ALA 3.3 0.2 - - - -
71A TRP* 1.3 77.6 - - - +
73A ALA* 1.3 59.4 + - - +
74A ILE 3.3 5.7 + - - +
79A LYS* 4.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.0 12.6 + - - +
70A ALA 3.4 11.7 - - - +
71A TRP 3.1 0.8 - - - -
72A GLU* 1.3 76.0 - - - +
74A ILE* 1.3 62.2 + - - +
75A PRO* 3.3 10.7 - - - +
307A PHE* 4.0 12.1 - - + -
308A MET* 3.8 10.8 - - - -
311A ASP 5.7 0.2 - - - +
313A PRO* 3.4 33.2 - - + +
317A PHE* 3.6 10.7 - - + -
318A THR* 6.0 0.7 - - - +
----------------------------------------------------------
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