Contacts of the strand formed by residues 53 - 59 (chain A) in PDB entry 1BMA
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 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.8 7.9 - - - +
52A GLN* 1.3 82.9 - - - +
54A TRP* 1.3 78.4 + - - +
113A ARG* 3.5 23.1 + - + +
114A LEU* 2.9 43.1 + - - +
116A GLN* 4.2 8.5 - - - +
117A SER* 3.8 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.8 4.0 - - - +
50A ILE* 3.0 30.5 + - + -
51A ARG* 3.0 36.2 + - + +
52A GLN 3.8 0.2 - - - -
53A ASN* 1.3 105.4 + - - +
55A VAL* 1.3 60.1 + - - +
91A LYS* 5.0 0.7 - - + -
93A VAL* 4.3 7.9 - - + -
111A LEU* 3.8 30.5 - - + -
112A LEU 3.3 20.4 - - - -
113A ARG* 3.3 53.8 - - + +
114A LEU* 4.3 0.4 - - - +
251A VAL* 3.9 21.3 - - + -
252A ILE* 4.0 27.0 + - + +
255A ASN* 3.5 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.8 38.6 - - + -
47A GLY* 4.6 1.1 - - - -
48A THR 3.4 6.7 - - - +
49A LEU* 4.0 17.7 - - + -
50A ILE* 4.6 3.1 - - - -
54A TRP* 1.3 74.6 - - - +
56A MET* 1.3 70.7 + - - +
57A THR* 4.1 2.1 + - - -
70A VAL* 4.2 16.2 - - + -
110A ALA 3.9 0.3 - - - +
111A LEU* 3.4 6.5 - - - +
112A LEU* 2.9 58.0 + - + +
114A LEU* 4.4 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.3 4.2 - - - -
48A THR* 2.9 48.2 + - - +
50A ILE* 4.1 10.5 - - + +
55A VAL* 1.3 73.3 - - - +
57A THR* 1.3 61.5 + - - +
109A ILE* 4.1 19.7 - - + -
110A ALA 3.6 4.7 - - - +
111A LEU* 4.0 16.6 - - + -
129A LEU* 3.9 25.4 - - + -
204A GLY 3.9 1.6 - - - +
217A VAL* 3.9 15.7 - - + -
220A VAL* 3.9 22.8 - - + +
241A VAL* 3.9 21.3 - - + -
248A ILE* 4.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.5 6.4 - - + +
45A CYS* 4.4 1.0 - - - +
46A GLY 2.9 23.7 + - - -
47A GLY* 4.4 1.8 - - - -
55A VAL* 4.6 5.4 - - - -
56A MET* 1.3 74.5 - - - +
58A ALA* 1.3 73.5 + - - +
61A CYS* 4.0 13.2 - - + +
62A VAL* 4.8 2.0 - - + -
109A ILE* 3.5 7.3 - - - +
110A ALA* 2.9 36.5 + - + +
112A LEU* 4.1 30.3 - - + -
204A GLY* 3.5 10.9 - - - -
220A VAL* 3.6 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 1.3 85.8 + - - +
59A ALA* 1.3 64.6 + - - +
60A HIS* 3.8 17.3 - - + +
61A CYS* 3.2 21.5 + - - +
62A VAL* 4.1 1.2 + - - +
108A ASP* 3.4 24.0 - - - +
110A ALA* 4.1 2.2 - - - +
204A GLY* 3.4 23.8 - - - +
220A VAL* 3.9 4.3 - - + -
221A THR 3.9 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 1.3 71.0 - - - +
60A HIS* 1.3 61.3 + - - +
62A VAL* 3.1 19.5 + - - +
63A ASP* 3.4 9.9 + - - +
94A VAL* 3.5 19.1 - - + +
98A TRP* 3.5 35.4 - - + -
108A ASP* 3.0 7.0 + - - +
109A ILE 3.5 20.8 - - - +
110A ALA* 3.8 10.8 - - - -
----------------------------------------------------------
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