Contacts of the strand formed by residues 63 - 71 (chain A) in PDB entry 2CWE
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 VAL 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 5.4 0.2 - - + -
26A LEU* 3.7 21.8 - - + -
29A LEU* 4.0 21.3 - - + -
54A ILE* 3.9 9.9 - - + +
57A LEU* 3.6 15.0 - - + -
58A LYS* 3.4 43.6 - - - +
61A GLY* 3.3 2.3 - - - -
62A LEU* 1.3 84.9 - - - +
64A GLU* 1.3 63.7 + - - +
79A TYR* 4.2 18.4 - - + -
80A GLY 3.1 13.2 - - - +
81A ARG* 4.4 1.3 - - - -
82A THR* 4.1 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 5.1 3.8 - - - +
63A VAL* 1.3 75.6 - - - +
65A VAL* 1.3 68.0 + - - +
66A LYS* 2.8 45.1 + - + +
79A TYR* 3.3 11.3 - - - -
80A GLY 2.9 30.6 + - - -
82A THR* 3.6 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 3.8 22.2 - - - +
64A GLU* 1.3 76.8 - - - +
66A LYS* 1.3 66.9 + - - +
67A ARG* 3.7 22.2 - - - +
68A THR* 3.8 20.2 - - + -
77A LYS* 3.9 18.2 - - + -
78A TYR 3.5 4.3 - - - +
79A TYR* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.2 28.5 - - + +
64A GLU* 2.8 45.6 + - + +
65A VAL* 1.3 73.9 - - - +
67A ARG* 1.3 62.2 + - - +
78A TYR 2.6 15.3 + - - +
79A TYR 4.1 0.2 - - - -
80A GLY* 3.0 45.8 + - - +
81A ARG 3.3 11.6 + - - -
82A THR* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.3 42.8 + - - +
65A VAL* 3.4 4.9 - - - +
66A LYS* 1.3 81.4 - - - +
68A THR* 1.3 67.1 + - - +
69A GLU* 2.7 33.2 + - - -
77A LYS* 3.7 1.0 - - - -
78A TYR* 2.8 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.8 18.8 - - + -
67A ARG* 1.3 82.3 - - - +
69A GLU* 1.3 60.2 + - - +
70A MET 4.2 0.5 + - - -
75A VAL* 4.4 14.8 - - - +
76A GLU 3.4 8.5 - - - -
77A LYS* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 2.7 39.5 + - - +
68A THR* 1.3 73.9 - - - +
70A MET* 1.3 60.1 + - - +
71A LYS* 3.3 22.7 + - + +
75A VAL* 4.3 3.4 - - - -
76A GLU* 2.7 44.6 + - - +
78A TYR* 3.8 23.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR 4.2 1.0 + - - -
69A GLU* 1.3 74.2 - - - +
71A LYS* 1.3 59.1 + - - +
72A GLY 2.9 32.7 + - - +
73A ASN* 3.4 5.8 - - - +
74A LEU 3.2 41.3 - - - +
75A VAL* 3.5 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 4.1 10.2 + - - +
38A GLN* 3.1 19.6 - - - +
69A GLU* 3.3 24.6 + - + +
70A MET* 1.3 71.4 - - - +
72A GLY* 1.3 59.1 + - - +
73A ASN* 3.4 4.9 + - - +
74A LEU* 2.7 25.0 + - + +
76A GLU* 4.0 17.4 + - + +
78A TYR* 2.8 43.7 + - - -
----------------------------------------------------------
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