Contacts of the strand formed by residues 70 - 75 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LYS* 3.8 8.5 - - - +
66F GLU* 3.7 19.5 + - + +
67F ARG* 2.8 67.2 + - + +
68F VAL 4.2 2.5 - - - +
69F GLY* 1.3 85.2 - - - +
71F TYR* 1.3 65.2 + - - +
81F THR* 4.2 19.2 - - + +
82F SER 3.6 3.4 - - - -
83F LYS* 3.6 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 4.5 8.1 - - + -
63F VAL* 5.4 1.8 - - + -
64F TYR 4.0 2.5 - - - -
65F LYS* 3.4 32.5 + - + -
70F GLU* 1.3 76.8 - - - +
72F SER* 1.3 61.7 + - - +
81F THR* 3.3 2.0 - - - -
82F SER 3.0 36.0 + - - +
84F VAL* 3.7 21.8 - - + -
86F GLU* 2.5 35.8 + - - -
92F VAL* 3.7 18.9 - - + +
94F ILE* 3.6 27.8 - - + -
107F PHE* 3.5 33.5 - + + -
109F ILE* 3.8 23.8 - - + -
114F LEU* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU 3.6 0.6 - - - +
63F VAL* 3.4 4.7 - - - -
64F TYR* 2.8 41.1 + - - -
66F GLU* 3.1 25.8 + - - +
70F GLU 4.3 0.2 - - - -
71F TYR* 1.3 72.9 - - - +
73F LEU* 1.3 59.9 + - - +
74F TYR* 4.1 15.9 - - - -
79F LYS* 4.3 1.5 - - - +
80F VAL 3.2 7.9 - - - -
81F THR* 2.5 29.0 + - - +
107F PHE* 3.6 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 4.2 6.7 - - + -
61F LEU* 3.7 26.0 - - + -
62F LEU 3.3 13.0 - - - +
63F VAL* 4.1 11.4 - - + -
72F SER* 1.3 73.2 - - - +
74F TYR* 1.3 68.7 + - - +
75F ILE* 3.8 22.1 + - + -
78F HIS 3.8 0.3 - - - +
79F LYS* 3.2 1.6 - - - -
80F VAL* 2.9 38.1 + - + +
96F VAL* 4.2 13.0 - - + -
98F TRP* 4.1 11.7 - - + -
105F ALA* 3.8 26.0 - - + -
107F PHE* 3.7 17.5 - - + -
119F LEU* 4.0 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E CPJ 3.2 37.9 + - + +
59F ASN* 3.9 22.7 - - + +
61F LEU* 3.2 7.2 - - - -
62F LEU* 2.7 62.7 + - + -
64F TYR* 4.1 21.0 - + + -
66F GLU* 3.6 9.5 + - - -
72F SER* 4.1 7.4 - - - -
73F LEU* 1.3 78.0 - - - +
75F ILE* 1.3 66.1 + - - +
76F GLY 4.1 0.4 - - - -
77F ARG 3.7 19.7 - - - -
78F HIS 3.0 4.7 - - - +
79F LYS* 3.4 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 3.7 35.9 - - + -
60F GLU 3.5 4.0 - - - +
61F LEU* 4.5 3.6 - - + -
73F LEU* 3.8 20.9 - - + -
74F TYR* 1.3 80.5 - - - +
76F GLY* 1.3 68.2 + - - +
77F ARG 3.2 0.2 - - - -
78F HIS 2.8 17.2 + - - +
98F TRP* 3.8 34.8 - - + -
119F LEU* 3.6 13.7 - - + +
120F ARG* 3.0 19.1 - - + +
123F TYR* 3.7 25.4 - - + -
125F VAL* 4.2 9.6 - - + -
----------------------------------------------------------
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