Contacts of the helix formed by residues 80 - 88 (chain A) in PDB entry 2DME
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 ILE 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 4.5 0.4 - - - +
79A ASN* 1.3 98.6 - - - +
81A LEU* 1.3 55.4 + - - +
82A PHE 3.3 2.0 - - - -
83A LYS* 2.7 19.2 + - + +
84A LYS* 2.6 72.9 + - + +
106A LYS* 4.5 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 4.7 1.8 - - - +
72A ASN* 3.6 43.1 - - + +
73A LEU* 4.0 15.9 - - + -
78A ASN* 4.1 13.6 - - + +
79A ASN 4.7 0.2 - - - +
80A ILE* 1.3 76.2 - - - +
82A PHE* 1.3 56.1 + - - +
84A LYS* 2.7 45.6 + - + +
85A VAL* 3.1 15.8 + - + +
90A VAL* 5.2 2.5 - - + -
95A LEU* 4.5 15.7 - - + -
98A MET* 5.1 8.1 - - + -
103A LEU* 3.7 37.0 - - + +
106A LYS* 6.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 14.8 - - + -
27A ARG* 4.0 48.2 - - + +
28A LEU 4.5 2.0 - - - -
31A SER* 3.1 32.1 - - - -
33A LEU* 4.1 9.6 - - + -
73A LEU* 3.4 25.1 - - + +
78A ASN 4.6 1.3 - - - -
79A ASN* 3.0 40.6 - - + -
81A LEU* 1.3 78.5 - - - +
83A LYS* 1.3 85.6 + - + +
85A VAL* 5.4 1.1 - - - -
86A LEU* 2.6 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.8 32.0 + - - -
33A LEU* 4.2 18.6 - - + -
79A ASN 4.6 4.7 + - - +
80A ILE* 2.7 26.8 + - + +
82A PHE* 1.3 102.1 - - + +
84A LYS* 1.3 56.6 + - - -
86A LEU* 4.3 4.0 - - - -
87A LYS* 2.8 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 2.6 47.0 + - + +
81A LEU* 2.7 40.6 + - + +
83A LYS* 1.3 70.8 - - - +
85A VAL* 1.3 57.5 + - + +
88A GLY 2.8 9.2 + - - -
89A GLU* 2.7 51.3 + - + -
90A VAL* 3.6 13.7 - - + -
106A LYS* 4.0 27.3 - - - +
107A GLU 4.3 6.5 + - - +
108A LEU* 6.0 1.2 - - - +
111A TRP* 3.4 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.8 2.2 - - + -
39A LYS* 4.8 1.6 + - - -
43A VAL* 3.1 40.2 - - + +
73A LEU* 5.5 3.4 - - + -
81A LEU* 3.1 14.7 + - + +
82A PHE* 4.7 1.8 - - - +
84A LYS* 1.3 75.0 - - + +
86A LEU* 1.3 69.7 + - + +
88A GLY* 3.4 8.7 + - - -
90A VAL* 3.3 29.8 - - + +
91A THR 4.6 0.2 - - - -
92A PRO* 4.4 15.2 - - + +
95A LEU* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.4 42.0 - - + +
28A LEU* 3.8 22.9 - - + -
33A LEU* 3.6 28.0 - - + -
35A VAL* 4.5 10.3 - - + +
39A LYS* 3.2 42.7 + - + +
40A ALA* 4.9 4.0 - - + -
43A VAL* 4.9 2.2 - - + -
82A PHE* 2.6 29.3 + - + +
83A LYS* 4.0 3.6 - - - +
84A LYS 3.3 0.4 - - - -
85A VAL* 1.3 87.0 - - + +
87A LYS* 1.3 64.9 + - + +
88A GLY* 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.5 30.9 - - + +
34A LYS 5.6 1.8 - - - +
35A VAL* 4.8 9.3 - - + +
83A LYS* 2.8 41.0 + - + +
84A LYS* 4.0 2.5 - - - +
86A LEU* 1.3 74.9 - - + +
88A GLY* 1.3 57.3 + - - +
89A GLU* 3.7 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS 2.8 4.2 + - - -
85A VAL 3.8 7.9 - - - -
86A LEU 3.2 2.9 - - - -
87A LYS* 1.3 80.1 - - - +
89A GLU* 1.3 69.4 + - - +
90A VAL 3.0 11.1 + - - +
91A THR* 5.1 4.9 - - - +
----------------------------------------------------------
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