Contacts of the strand formed by residues 71 - 76 (chain S) in PDB entry 2D3O
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 GLN 71 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S ASN* 2.7 35.9 - - - +
54S ILE* 4.2 15.7 - - + +
70S GLU* 1.3 76.2 - - - +
72S ARG* 1.3 67.3 + - - +
73S GLU* 5.1 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4910 A 5.3 6.5 + - - -
52S ASN* 3.0 14.7 - - - +
53S VAL 3.2 16.8 + - - +
55S THR* 3.5 30.1 - - + +
57S ASN* 2.6 38.3 - - - +
70S GLU* 3.0 30.1 + - - +
71S GLN* 1.3 79.1 - - - +
73S GLU* 1.3 80.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S LEU* 4.6 6.5 - - + -
47S VAL* 3.7 29.4 - - + -
48S VAL 3.2 6.0 - - - +
49S GLU* 3.2 40.6 - - - +
51S VAL 4.0 6.5 - - - +
52S ASN* 3.6 21.2 + - - +
53S VAL* 4.8 4.1 - - - +
71S GLN* 5.1 1.4 + - - +
72S ARG* 1.3 102.5 - - - +
74S LEU* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4880 A 6.3 1.1 - - + -
4890 A 4.1 38.1 - - + +
4900 A 4.9 4.7 - - - +
4910 A 4.3 27.4 - - + +
46S VAL 3.3 8.8 - - - +
47S VAL* 4.3 8.9 - - - -
48S VAL 4.8 2.3 + - - +
51S VAL* 4.2 16.6 + - + +
53S VAL* 3.9 30.5 - - + -
73S GLU* 1.3 78.3 - - - +
75S ALA* 1.3 76.3 + - - +
76S LEU* 3.6 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4890 A 3.9 14.4 + - - +
45S LYS* 2.9 42.6 - - + -
46S VAL 3.2 7.9 - - - +
47S VAL* 4.4 9.5 - - + +
74S LEU* 1.3 86.1 - - + +
76S LEU* 1.3 68.3 - - - +
77S HIS* 5.3 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S VAL* 4.9 18.6 - - + -
44S GLN 3.0 12.3 - - - +
45S LYS* 3.1 1.4 - - - -
46S VAL* 2.9 39.7 + - + +
48S VAL* 5.2 11.9 - - + +
51S VAL* 4.7 25.1 - - + -
74S LEU* 3.6 25.4 - - + +
75S ALA* 1.3 94.3 - - - +
77S HIS* 1.3 75.4 + - - +
79S SER* 4.6 9.4 - - - +
80S LYS* 5.7 6.5 - - + -
----------------------------------------------------------
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