Contacts of the strand formed by residues 70 - 75 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65T LYS* 3.9 8.1 - - - +
66T GLU* 3.7 20.6 + - + +
67T ARG* 3.1 66.4 + - + +
68T VAL 4.2 2.4 - - - +
69T GLY* 1.3 84.8 - - - +
71T TYR* 1.3 64.4 + - - +
81T THR* 4.3 16.8 - - + +
82T SER 3.6 3.8 - - - -
83T LYS* 3.5 37.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T LEU* 4.4 9.0 - - + -
63T VAL* 5.3 1.8 - - + -
64T TYR 4.1 2.2 - - - -
65T LYS* 3.5 33.3 + - + -
70T GLU* 1.3 75.5 - - - +
72T SER* 1.3 62.6 + - - +
81T THR* 3.4 2.4 - - - +
82T SER 2.9 35.1 + - - +
84T VAL* 3.6 18.6 - - + -
86T GLU* 2.6 34.1 + - - -
92T VAL* 3.8 19.9 - - - +
94T ILE* 3.6 26.0 - - + -
107T PHE* 3.6 33.4 - + + -
109T ILE* 3.6 27.8 - - + -
114T LEU* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62T LEU 3.6 0.2 - - - +
63T VAL* 3.5 5.2 - - - -
64T TYR* 2.9 39.6 + - - -
66T GLU* 2.8 29.6 + - - +
70T GLU 4.2 0.4 - - - -
71T TYR* 1.3 74.4 - - - +
73T LEU* 1.3 59.4 + - - +
74T TYR* 4.2 15.9 - - - -
79T LYS* 4.2 2.7 + - - -
80T VAL 3.2 6.1 - - - -
81T THR* 2.5 25.1 + - - -
107T PHE* 3.5 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T PHE* 4.2 5.2 - - + -
61T LEU* 3.9 20.4 - - + -
62T LEU 3.3 12.6 - - - +
63T VAL* 4.3 8.3 - - + -
72T SER* 1.3 74.3 - - - +
74T TYR* 1.3 72.2 + - - +
75T ILE* 4.0 21.5 - - + -
78T HIS 3.8 0.5 - - - +
79T LYS* 3.5 1.4 - - - -
80T VAL* 2.8 47.0 + - + +
96T VAL* 4.0 19.5 - - + -
98T TRP* 4.2 11.0 - - + -
105T ALA* 3.7 27.4 - - + -
107T PHE* 3.8 17.6 - - + -
119T LEU* 4.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L CPJ 3.3 42.6 - - + +
59T ASN* 3.9 20.4 - - + +
61T LEU* 3.2 6.9 - - - -
62T LEU* 2.8 63.1 + - + -
64T TYR* 3.9 23.4 - + + -
66T GLU* 3.8 4.9 + - - -
72T SER* 4.2 6.5 - - - -
73T LEU* 1.3 79.3 - - - +
75T ILE* 1.3 65.9 + - - +
76T GLY 4.2 0.2 - - - -
77T ARG 3.8 20.4 - - - -
78T HIS 3.0 7.9 - - - +
79T LYS* 3.2 41.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T PHE* 3.7 35.9 - - + -
60T GLU 3.4 3.6 - - - +
61T LEU* 4.4 9.0 - - + -
73T LEU* 4.0 19.7 - - + -
74T TYR* 1.3 82.6 - - - +
76T GLY* 1.3 69.4 + - - +
77T ARG 3.3 0.9 - - - -
78T HIS 2.9 15.7 + - - +
98T TRP* 3.9 35.7 - - + -
119T LEU* 3.7 14.6 - - + +
120T ARG* 3.1 17.8 - - + +
123T TYR* 3.8 25.1 - - + -
125T VAL* 4.9 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