Contacts of the strand formed by residues 71 - 75 (chain A) in PDB entry 3BDW
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 ASN 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A CYS 5.3 0.7 - - - +
61A CYS* 3.9 1.0 - - - -
67A GLY* 3.2 5.2 - - - -
68A TYR 2.9 31.1 + - - +
69A ARG* 3.1 13.6 + - - +
70A CYS* 1.3 87.2 - - - +
72A CYS* 1.3 66.6 + - - +
73A TYR* 3.2 29.6 + - + +
104A GLU* 4.6 3.0 + - - +
175A LYS* 3.3 23.6 - - + +
176A GLN 3.5 12.5 - - - +
177A GLN* 3.3 22.2 + - - +
178A LEU* 4.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.3 1.1 - - - -
61A CYS* 2.0 61.9 - - + -
65A TRP* 3.9 14.0 - - + -
66A VAL 3.3 4.7 - - - -
71A ASN* 1.3 76.6 - - - +
73A TYR* 1.3 63.7 + - - +
175A LYS* 3.3 6.6 - - - +
176A GLN* 3.0 44.9 + - + +
178A LEU* 4.1 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.2 9.9 - - - -
66A VAL* 2.6 59.1 + - + +
68A TYR* 3.8 20.4 + - + -
69A ARG* 5.8 0.9 - - - +
71A ASN* 3.2 32.9 + - + -
72A CYS* 1.3 75.7 - - - +
74A PHE* 1.3 61.4 + - - +
75A ILE* 4.0 13.5 - - + -
97A LEU* 4.0 3.8 - - + -
104A GLU* 2.9 41.9 + - + +
105A LEU* 3.8 18.6 - - + -
107A PHE* 4.1 17.9 - + + -
173A ILE* 4.2 7.0 - - + -
174A CYS 3.5 10.3 - - - -
175A LYS* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS 4.6 8.5 - - - -
65A TRP* 3.5 48.9 - + + +
66A VAL* 5.6 0.2 - - - -
73A TYR* 1.3 73.0 - - - +
75A ILE* 1.3 66.0 + - - +
76A SER* 4.1 15.0 - - - -
77A SER 5.7 0.2 - - - -
78A GLU* 6.1 0.2 - - - -
92A GLN* 5.9 6.3 - - + -
172A TYR* 3.7 38.8 - + - -
173A ILE* 3.3 5.9 - - - -
174A CYS* 3.1 37.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 4.6 16.0 - - + +
73A TYR* 4.0 16.6 + - + -
74A PHE* 1.3 84.3 - - - +
76A SER* 1.3 64.3 + - - +
77A SER* 3.9 1.7 + - - -
107A PHE* 4.8 1.3 - - + -
108A MET* 4.0 26.9 - - + -
115A TYR* 3.3 42.6 - - + +
172A TYR 4.1 1.6 - - - -
173A ILE* 3.8 23.1 - - + -
165B PHE* 5.7 2.9 - - + -
168B ILE* 3.9 23.1 - - + +
169B ILE* 4.7 8.5 - - + -
----------------------------------------------------------
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