Contacts of the helix formed by residues 51 - 65 (chain A) in PDB entry 3NSO
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 ARG 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 4.2 1.8 - - - -
48A THR* 3.0 15.4 + - - +
50A PHE* 1.3 98.8 + - + +
52A GLU* 1.3 65.4 + - - +
53A CYS 3.3 3.1 - - - -
54A ASP* 2.7 38.7 + - - +
55A TYR* 2.9 23.6 + - - +
84A LEU* 3.8 20.5 + - - +
85A TYR* 3.6 37.9 - - - +
90A PHE 5.2 4.7 + - - +
91A LYS 5.2 6.9 + - - +
93A CYS 3.1 26.3 + - - -
94A PRO* 4.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.9 23.1 - - + +
48A THR 3.8 13.1 + - - +
49A GLU* 4.4 13.7 - - - +
50A PHE 3.8 1.4 - - - -
51A ARG* 1.3 76.3 - - - +
53A CYS* 1.3 63.7 + - - +
55A TYR* 3.5 0.9 - - - +
56A ASN* 2.8 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG 3.3 0.2 - - - -
52A GLU* 1.3 81.7 - - - +
54A ASP* 1.3 65.2 + - - +
56A ASN* 4.2 8.8 - - - +
57A LYS* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE 5.3 0.4 - - - -
51A ARG* 2.7 43.3 + - - +
53A CYS* 1.3 78.1 - - - +
55A TYR* 1.3 59.0 + - - +
57A LYS* 3.5 11.6 + - - +
58A PHE* 2.9 29.6 + - - +
85A TYR* 3.5 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 5.9 0.5 + - - -
45A TRP 4.0 11.7 + - - -
46A THR* 5.1 0.7 - - - +
47A PRO* 3.6 31.2 - - + -
51A ARG 2.9 17.8 + - - +
52A GLU 3.5 2.7 - - - +
54A ASP* 1.3 75.1 - - - +
56A ASN* 1.3 77.0 + - - +
58A PHE* 3.1 4.2 + + - +
59A MET* 2.9 59.3 + - + +
82A LEU* 3.7 24.2 - - + +
85A TYR* 3.9 25.1 - + + -
86A CYS* 3.7 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 5.4 1.5 - - - +
52A GLU* 2.8 33.1 + - - +
53A CYS* 4.2 8.6 - - - +
55A TYR* 1.3 93.4 - - - +
57A LYS* 1.3 57.0 + - + +
59A MET* 3.2 5.9 + - - +
60A SER* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 3.0 35.0 + - - +
54A ASP* 3.8 11.0 - - - +
56A ASN* 1.3 73.8 - - + +
58A PHE* 1.3 65.9 + - - +
60A SER* 2.9 21.0 + - - +
61A VAL* 3.0 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 13.5 - - + -
54A ASP 2.9 14.7 + - - +
55A TYR* 3.3 9.4 - + - +
57A LYS* 1.3 78.0 - - - +
59A MET* 1.3 71.9 + - + +
61A VAL* 3.4 13.0 + - - +
62A LEU* 3.5 29.7 + - + +
78A SER* 3.7 29.4 - - - -
81A CYS* 4.0 17.0 - - + -
82A LEU* 2.9 35.7 - - + -
85A TYR* 3.5 26.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.8 51.1 + - - +
38A LEU* 4.3 20.0 - - + -
39A GLN* 5.0 12.6 - - + +
55A TYR* 2.9 55.8 + - + +
56A ASN* 3.7 6.7 - - - +
58A PHE* 1.3 89.9 - - + +
60A SER* 1.3 62.2 + - - +
62A LEU* 3.4 10.2 + - - +
63A ASP 3.3 8.8 + - - -
82A LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 4.6 1.1 - - - +
56A ASN 2.9 15.3 + - - -
57A LYS* 2.9 19.9 + - - -
59A MET* 1.3 75.3 - - - +
61A VAL* 1.3 64.9 + - - +
63A ASP* 3.3 6.3 + - - +
64A THR* 3.0 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 4.0 12.1 - - - +
57A LYS* 3.0 22.9 + - + +
58A PHE* 3.8 7.0 - - - +
59A MET 3.3 0.2 - - - -
60A SER* 1.3 77.2 + - - +
62A LEU* 1.3 63.4 + - + +
64A THR* 4.7 0.9 - - - -
65A ASN* 2.8 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 3.3 49.5 - - + +
32A ALA* 4.9 0.5 - - - -
34A LEU* 4.0 13.9 - - + -
35A LYS* 3.9 31.9 - - + +
38A LEU* 3.9 27.6 - - + -
58A PHE* 3.5 30.0 + - + +
59A MET* 3.4 10.7 + - - +
60A SER 3.3 0.6 - - - -
61A VAL* 1.3 82.1 - - + +
63A ASP* 1.3 62.2 + - - +
64A THR 3.5 0.2 + - - -
65A ASN 3.5 14.9 + - - +
66A LYS* 4.3 3.8 + - - -
78A SER* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 6.3 0.2 - - - +
35A LYS* 3.4 36.7 + - - +
59A MET 3.3 4.5 + - - +
60A SER* 3.7 6.1 - - - +
61A VAL 3.2 0.4 - - - -
62A LEU* 1.3 76.8 - - - +
64A THR* 1.3 61.4 + - - +
66A LYS* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.0 17.6 + - - -
61A VAL* 4.0 2.0 - - - -
63A ASP* 1.3 80.0 - - - +
65A ASN* 1.3 83.2 + - - +
66A LYS* 3.3 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 2.8 38.7 - - - +
61A VAL* 2.8 38.1 + - + +
62A LEU 3.5 3.6 + - - -
63A ASP 3.5 1.0 - - - -
64A THR* 1.3 101.0 + - - +
66A LYS* 1.3 56.9 + - - +
67A ASP* 2.9 20.8 + - - +
----------------------------------------------------------
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