Contacts of the strand formed by residues 20 - 26 (chain A) in PDB entry 1NTN
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 LEU 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ILE* 4.0 2.2 - - - +
3A CYS* 3.4 9.3 - - - -
14A CYS* 4.2 2.6 - - - -
18A GLN* 4.9 0.2 - - - +
19A ASN* 1.3 86.8 - - + +
21A CYS* 1.3 61.3 + - - +
42A CYS* 3.4 6.2 - - - -
43A ALA* 2.8 35.6 + - + +
44A ALA 3.9 7.2 - - - +
45A THR* 3.8 14.1 - - - +
46A CYS* 3.5 36.6 - - + +
57A CYS* 4.7 8.5 - - + -
58A CYS 3.2 20.4 - - - +
59A SER* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ILE* 3.7 7.2 - - - -
2A THR 3.4 11.9 - - - -
3A CYS* 2.1 48.2 - - - -
20A LEU* 1.3 74.3 - - - +
22A TYR* 1.3 61.7 - - - +
41A GLY 3.4 2.9 - - - -
43A ALA 5.3 0.2 - - - -
57A CYS* 3.2 7.6 - - - +
58A CYS* 2.7 30.8 + - - +
60A THR 4.3 0.2 - - - -
63A CYS* 3.5 32.1 - - - -
64A ASN* 3.7 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A CYS* 1.3 76.1 - - - +
23A THR* 1.3 61.0 + - - +
24A LYS* 4.0 15.0 - - + -
39A GLU* 2.3 57.8 + - + +
40A LEU* 3.2 5.9 - - - -
41A GLY* 3.1 52.6 + - - -
42A CYS 3.3 23.6 - - - -
43A ALA* 3.8 14.1 - - + -
47A PRO* 4.0 12.8 - - + -
55A ILE* 4.1 10.5 - - + -
56A LYS 3.4 6.3 - - - +
57A CYS* 3.8 19.7 - - - -
64A ASN* 3.3 8.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 1.3 71.7 - - - +
24A LYS* 1.3 65.0 - - - +
25A THR* 4.2 19.7 - - + -
38A ILE* 5.0 4.9 - - + -
39A GLU 3.4 3.6 - - - +
40A LEU* 3.4 22.5 - - + +
54A ASP 4.0 0.3 - - - +
55A ILE* 3.3 4.3 - - - +
56A LYS* 3.0 40.4 + - + +
64A ASN* 3.6 15.1 - - - +
65A PRO 5.0 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.0 15.5 - - + -
23A THR* 1.3 77.7 - - - +
25A THR* 1.3 64.0 + - - +
26A TRP* 3.3 24.2 - - + -
38A ILE* 3.3 2.9 - - - -
39A GLU* 2.6 63.5 + - - +
47A PRO* 5.7 3.8 - - - -
48A THR 5.2 1.6 + - - -
49A VAL* 3.4 27.2 - - + +
53A GLN* 3.0 36.2 + - + +
54A ASP 3.4 5.2 - - - +
55A ILE* 4.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 4.2 13.7 - - + -
24A LYS* 1.3 78.1 - - - +
26A TRP* 1.3 74.9 + - - +
36A LYS* 3.0 29.6 + - + -
37A VAL 3.2 6.7 - - - -
38A ILE* 3.5 31.6 - - + -
53A GLN* 3.4 2.3 - - - +
54A ASP* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.3 39.9 - - + -
25A THR* 1.3 97.1 - - - +
27A CYS* 1.3 85.8 - - - +
28A ASP* 3.3 14.6 + - - -
36A LYS* 3.3 13.6 - - - +
37A VAL* 2.7 57.4 + - + +
39A GLU* 3.9 19.3 - - + -
52A TYR* 3.8 23.5 - + + +
53A GLN* 3.6 26.7 - - + -
----------------------------------------------------------
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