Contacts of the strand formed by residues 70 - 75 (chain E) in PDB entry 2A3W
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 GLU 70 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LYS* 3.5 12.2 - - - +
66E GLU* 3.7 16.8 + - + +
67E ARG* 3.2 63.0 + - + +
68E VAL 4.3 2.5 - - - +
69E GLY* 1.3 84.0 - - - +
71E TYR* 1.3 64.7 + - - +
81E THR* 4.0 18.6 - - + +
82E SER 3.5 3.4 - - - -
83E LYS* 3.6 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 4.7 8.1 - - + -
63E VAL* 5.4 2.2 - - + -
64E TYR 4.0 2.9 - - - -
65E LYS* 3.5 33.2 + - + -
70E GLU* 1.3 77.1 - - - +
72E SER* 1.3 62.3 + - - +
81E THR* 3.2 2.7 - - - -
82E SER 2.9 37.7 + - - +
84E VAL* 3.6 22.7 - - + -
86E GLU* 2.5 32.6 + - - -
92E VAL* 3.7 18.9 - - + +
94E ILE* 3.6 26.7 - - + -
107E PHE* 3.7 32.7 - + + -
109E ILE* 3.7 23.6 - - + -
114E LEU* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LEU 3.6 0.5 - - - +
63E VAL* 3.5 4.9 - - - -
64E TYR 2.9 38.1 + - - -
66E GLU* 2.8 33.3 + - - +
71E TYR* 1.3 74.7 - - - +
73E LEU* 1.3 58.1 + - - +
74E TYR* 4.2 15.7 - - - -
79E LYS* 4.3 2.2 - - - -
80E VAL 3.1 9.0 - - - -
81E THR* 2.6 21.6 + - - +
107E PHE* 3.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 4.2 6.5 - - + -
61E LEU* 3.9 24.7 - - + -
62E LEU 3.3 12.3 - - - +
63E VAL* 4.0 12.3 - - + -
72E SER* 1.3 73.7 - - - +
74E TYR* 1.3 68.2 + - - +
75E ILE* 3.9 19.1 - - + -
78E HIS 3.8 0.3 - - - +
79E LYS* 3.4 2.8 - - - -
80E VAL* 2.9 40.1 + - + +
96E VAL* 4.0 15.3 - - + -
98E TRP* 4.1 12.6 - - + -
105E ALA* 3.8 25.8 - - + -
107E PHE* 3.7 16.4 - - + -
119E LEU* 4.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ASN* 3.9 22.0 - - + +
61E LEU* 3.2 6.2 - - - -
62E LEU* 2.7 65.0 + - + +
64E TYR* 3.9 23.6 - + + -
66E GLU* 3.7 5.4 + - - -
72E SER* 4.2 6.3 - - - -
73E LEU* 1.3 78.2 - - - +
75E ILE* 1.3 66.8 + - - +
76E GLY 4.2 0.4 - - - -
77E ARG 4.1 14.1 - - - +
78E HIS 3.0 12.8 - - - +
79E LYS* 3.3 40.8 - - + -
345E CPJ 3.3 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.6 35.7 - - + -
60E GLU 3.4 2.9 - - - +
61E LEU* 4.3 9.9 - - + -
73E LEU* 3.9 18.8 - - + -
74E TYR* 1.3 80.7 - - - +
76E GLY* 1.3 68.1 + - - +
77E ARG 3.2 0.9 - - - -
78E HIS* 2.9 19.9 + - - +
98E TRP* 3.9 33.0 - - + -
119E LEU* 3.7 16.2 - - + +
120E ARG* 3.1 16.5 - - + +
123E TYR* 3.7 26.2 - - + -
125E VAL* 4.4 4.5 - - + -
----------------------------------------------------------
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