Contacts of the strand formed by residues 65 - 70 (chain B) in PDB entry 3T0E
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 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 4.7 1.6 + - + +
58B ARG* 3.2 45.5 + - + +
59B TYR 3.5 10.3 - - - +
60B PHE* 3.5 17.7 - - + -
63B GLN 3.4 2.0 + - - -
64B GLU* 1.3 74.8 - - - +
66B TYR* 1.3 60.4 + - - +
67B VAL 4.4 4.0 - - - +
68B ARG* 2.9 41.8 + - - +
79B VAL* 3.4 26.5 - - + +
80B THR* 3.3 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 4.8 5.2 - - - +
73A MET* 3.3 52.5 - - + +
38B GLU* 3.3 13.0 + - - -
59B TYR* 3.3 21.2 + - + +
60B PHE* 3.1 42.6 - - - -
61B TYR* 4.0 4.0 - - + -
64B GLU* 4.3 5.6 - - + +
65B GLU* 1.3 74.4 - - - +
67B VAL* 1.3 77.0 + - + +
78B ALA* 3.9 1.2 - - - -
79B VAL* 2.5 35.0 + - - -
80B THR* 3.4 8.8 + - - +
82B LEU* 4.4 7.2 - - + -
83B GLY* 3.7 29.6 - - - +
86B ASP* 3.6 14.5 + - - -
90B TRP* 5.2 1.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.3 41.3 + - + +
65B GLU* 4.4 1.7 - - - +
66B TYR* 1.3 92.6 - - + +
68B ARG* 1.3 66.4 + - - +
76B TYR* 4.5 2.0 - - + -
77B ARG 3.1 24.5 - - - +
79B VAL* 4.3 0.4 - - - +
83B GLY 4.2 7.6 - - - +
86B ASP* 4.7 1.1 - - + -
87B ALA* 4.0 22.2 - - + +
90B TRP* 3.3 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 5.0 6.5 - - - +
56B LEU* 4.2 19.1 - - + +
57B ASP 3.4 9.2 - - - +
58B ARG* 4.3 11.0 - - + +
65B GLU* 2.9 38.2 + - - +
67B VAL* 1.3 79.0 - - - +
69B PHE* 1.3 73.6 + - - +
70B ASP* 4.2 18.0 + - - +
76B TYR* 3.0 17.4 - - - -
77B ARG* 3.1 32.9 + - + +
79B VAL* 3.7 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 4.4 8.1 - + - -
56B LEU* 3.4 8.5 - - - +
57B ASP* 2.8 39.1 + - + -
68B ARG* 1.3 75.7 - - - +
70B ASP* 1.3 80.4 + - - +
71B SER* 3.7 10.8 - - - -
74B GLY* 4.0 15.5 - - - -
75B GLU* 4.1 10.5 - - - -
76B TYR* 3.1 42.4 - + + -
97B LEU* 4.2 18.4 - - + -
100B LYS* 3.2 48.5 - - + -
101B ARG* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 3.5 34.4 + - - +
55B PHE 4.0 1.1 - - - -
56B LEU* 3.9 13.3 - - + +
68B ARG* 4.2 18.2 + - - +
69B PHE* 1.3 78.4 - - - +
71B SER* 1.3 59.8 + - - +
72B ASP* 2.9 18.5 + - - +
73B VAL* 2.7 49.4 + - + +
74B GLY 3.1 9.5 + - - -
75B GLU 4.2 5.1 + - - -
77B ARG* 5.7 1.5 - - + +
----------------------------------------------------------
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