Contacts of the strand formed by residues 70 - 75 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 3.6 9.8 - - - +
66D GLU* 3.6 22.2 + - + +
67D ARG* 2.9 66.8 + - + +
68D VAL 4.9 1.7 - - - +
69D GLY* 1.3 77.7 - - - +
71D TYR* 1.3 63.8 + - - +
81D THR* 4.1 18.6 - - + +
82D SER 3.7 1.6 - - - -
83D LYS* 3.7 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 4.5 8.7 - - + -
63D VAL* 5.3 2.5 - - + -
64D TYR 4.1 1.3 - - - -
65D LYS* 3.3 35.0 + - + -
70D GLU* 1.3 77.3 - - - +
72D SER* 1.3 62.5 + - - +
81D THR* 3.3 2.6 - - - +
82D SER 2.9 40.5 + - - +
84D VAL* 3.7 21.8 - - + -
86D GLU* 2.6 31.7 + - - -
92D VAL* 3.8 19.8 - - - +
94D ILE* 3.7 26.2 - - + -
107D PHE* 3.6 33.2 - + + -
109D ILE* 3.8 22.9 - - + -
114D LEU* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU 3.6 0.7 - - - +
63D VAL* 3.4 5.4 - - - +
64D TYR 2.9 40.8 + - - -
66D GLU* 2.8 26.2 + - - +
70D GLU 4.3 0.2 - - - -
71D TYR* 1.3 71.8 - - - +
73D LEU* 1.3 59.5 + - - +
74D TYR* 4.2 15.7 - - - -
79D LYS* 4.6 1.8 - - - -
80D VAL 3.2 8.1 - - - -
81D THR* 2.7 27.9 + - - +
107D PHE* 3.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 4.3 3.6 - - + -
61D LEU* 4.0 19.7 - - + -
62D LEU 3.4 11.7 - - - +
63D VAL* 4.2 8.3 - - + -
72D SER* 1.3 73.4 - - - +
74D TYR* 1.3 70.9 + - - +
75D ILE* 3.8 26.5 - - + -
79D LYS* 3.1 3.3 - - - +
80D VAL* 2.9 38.8 + - + +
96D VAL* 3.9 20.9 - - + -
98D TRP* 4.2 9.2 - - + -
105D ALA* 3.7 26.9 - - + -
107D PHE* 3.7 16.8 - - + -
119D LEU* 4.1 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASN* 4.0 24.2 - - + +
61D LEU* 3.2 6.5 - - - -
62D LEU* 2.8 63.3 + - + +
64D TYR* 4.0 23.3 - + + -
66D GLU* 3.9 4.5 + - - -
72D SER* 4.2 9.4 - - - -
73D LEU* 1.3 76.1 - - - +
75D ILE* 1.3 66.3 + - - +
76D GLY 4.1 0.2 - - - -
77D ARG 4.0 13.9 - - - -
78D HIS 2.9 9.0 - - - +
79D LYS* 3.6 44.7 + - + +
344D CPJ 3.3 41.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 3.6 35.7 - - + -
60D GLU 3.5 4.3 - - - +
61D LEU* 4.4 4.0 - - + -
73D LEU* 3.8 20.4 - - + -
74D TYR* 1.3 80.2 - - - +
76D GLY* 1.3 69.6 + - - +
77D ARG 3.3 0.2 - - - -
78D HIS* 2.8 17.7 + - - +
98D TRP* 3.9 31.2 - - + -
119D LEU* 3.6 13.9 - - + +
120D ARG* 3.1 17.0 - - + +
123D TYR* 3.8 23.8 - - + -
125D VAL* 4.0 14.8 - - + -
----------------------------------------------------------
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