Contacts of the strand formed by residues 55 - 60 (chain A) in PDB entry 2BYE
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 TYR 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 5.5 4.0 - - - -
18A PRO* 5.1 18.7 - - + +
38A LEU* 3.6 34.5 - - + +
42A LEU* 4.0 25.6 - - + -
51A VAL 4.8 2.5 - - - -
53A THR* 2.8 32.1 + - + +
54A ASP* 1.3 81.2 - - - +
56A PHE* 1.3 61.7 + - - +
105A LEU* 4.1 19.7 - - + -
106A LYS 3.2 17.0 - - - +
107A THR* 3.4 24.9 - - + -
108A GLN* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.6 0.4 - - - -
54A ASP 3.7 1.6 - - - -
55A TYR* 1.3 74.5 - - - +
57A LEU* 1.3 87.9 + - - +
58A MET* 3.6 25.6 - - + -
79A ALA* 4.0 15.0 - - + -
80A ILE 3.7 12.1 - - - +
81A GLY* 5.7 0.9 - - - -
105A LEU* 3.2 5.7 - - - -
106A LYS* 2.7 45.1 + - + -
107A THR 3.0 29.8 - - - -
108A GLN* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 5.6 0.9 - - + -
14A VAL* 5.2 6.3 - - + -
34A ALA* 3.8 27.6 - - + +
37A LEU* 4.8 9.6 - - + -
38A LEU* 4.0 10.1 - - + +
41A ILE* 5.8 1.1 - - + -
56A PHE* 1.3 88.6 - - - +
58A MET* 1.3 67.5 + - - +
80A ILE* 2.7 42.4 + - + +
86A ILE* 3.4 33.4 - - + -
103A ILE* 4.1 19.3 - - + -
104A VAL 3.0 8.1 - - - +
105A LEU* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.6 14.8 - - + -
57A LEU* 1.3 86.2 - - - +
59A GLU* 1.3 59.2 + - - +
60A GLU* 3.6 5.5 + - + +
77A GLN* 3.3 44.6 - - + +
78A ARG 3.1 8.5 - - - +
79A ALA* 3.6 17.9 - - + -
80A ILE* 3.8 6.3 - - - -
102A ARG 3.1 4.9 - - - +
103A ILE* 3.4 2.3 - - - -
104A VAL* 2.8 44.2 + - + +
106A LYS* 3.2 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 1.3 72.5 - - - +
60A GLU* 1.3 61.0 + - - +
61A LYS* 2.8 42.4 + - - +
77A GLN* 3.4 4.7 - - - +
78A ARG* 2.9 52.0 + - + +
80A ILE* 4.1 4.4 - - + +
89A ILE* 3.3 45.0 - - + +
92A SER* 5.7 2.9 - - - -
93A TRP* 5.9 3.1 - - + -
102A ARG 3.5 7.9 - - - +
103A ILE* 5.0 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 3.9 8.1 - - + -
59A GLU* 1.3 73.2 - - - +
61A LYS* 1.3 57.9 + - - +
62A TYR* 5.6 2.5 - - + -
77A GLN* 3.3 28.6 + - - +
100A MET* 5.4 0.5 - - - +
101A GLY* 3.4 21.8 + - - -
102A ARG* 2.7 63.6 + - - +
104A VAL* 3.4 28.8 - - + +
106A LYS* 2.8 29.5 + - - -
----------------------------------------------------------
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