Contacts of the helix formed by residues 47 - 64 (chain A) in PDB entry 2NS8
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 ASN 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.5 2.5 - - - +
46A LYS* 1.3 88.6 - - - +
48A LYS* 1.3 63.0 + - - +
49A ARG* 3.4 10.1 + - - +
50A ALA* 2.6 42.5 + - - +
51A LEU 3.3 13.3 + - - -
157B GLU* 4.5 14.2 + - - +
1Z TRP* 3.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.1 39.9 + - - -
23A GLU* 4.3 5.0 + - - +
25A LEU* 2.7 35.1 + - - +
26A THR* 4.6 2.4 - - - +
47A ASN* 1.3 72.0 - - - +
49A ARG* 1.3 55.1 + - - +
51A LEU* 3.0 9.6 + - + +
52A LEU* 2.8 53.4 + - + +
1Z TRP* 3.5 48.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.6 8.9 - - + +
48A LYS* 1.3 77.5 - - - +
50A ALA* 1.3 56.2 + - - +
52A LEU* 3.2 19.7 + - - +
53A ASP* 2.8 43.1 + - - +
101A LEU 4.2 15.4 + - - -
102A GLY 4.5 3.4 + - - -
150B GLU* 3.0 30.1 + - - +
153B VAL* 3.9 11.5 - - - +
154B ALA* 3.8 18.7 - - - +
157B GLU* 2.7 52.1 + - + +
158B ARG* 3.9 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.6 3.4 - - + +
45A VAL* 3.9 13.8 - - + +
46A LYS* 4.8 3.4 - - + +
47A ASN* 2.6 33.5 + - - +
49A ARG* 1.3 74.8 - - - +
51A LEU* 1.3 63.7 + - - +
53A ASP* 3.4 13.1 - - - +
54A ALA* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.2 0.7 - - + -
9A VAL* 4.3 12.8 - - + -
10A ILE* 4.7 6.1 - - + -
13A ALA* 4.0 22.0 - - + -
25A LEU* 3.6 37.0 - - + +
30A LEU* 4.2 15.0 - - + -
45A VAL* 3.6 19.2 - - + +
47A ASN 3.3 6.4 + - - +
48A LYS* 3.0 11.3 + - + +
50A ALA* 1.3 78.1 - - - +
52A LEU* 1.3 60.4 + - + +
54A ALA* 2.9 8.7 + - - +
55A LEU* 2.9 38.5 + - + +
1Z TRP* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.8 38.1 - - + -
25A LEU* 4.4 9.0 - - + -
48A LYS* 2.8 39.5 + - + +
49A ARG* 3.2 19.5 + - - +
51A LEU* 1.3 76.0 - - + +
53A ASP* 1.3 57.2 + - - +
55A LEU* 3.3 16.9 + - + -
56A ALA* 2.8 33.2 + - - +
98A LYS 5.3 2.2 - - - +
99A VAL* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.8 35.3 + - - +
50A ALA* 3.4 13.1 - - - +
52A LEU* 1.3 73.5 - - - +
54A ALA* 1.3 61.4 + - - +
56A ALA* 3.4 5.8 + - - +
57A ILE* 3.2 33.1 + - + +
102A GLY 4.5 0.5 - - - +
103A THR* 5.0 2.9 - - - -
104A ARG* 4.8 6.3 + - - +
158B ARG* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 20.6 - - + -
5A ASP* 5.9 2.0 - - - +
10A ILE* 3.5 28.6 - - + +
50A ALA 3.2 3.9 + - - +
51A LEU 2.9 11.1 + - - +
53A ASP* 1.3 77.4 - - - +
55A LEU* 1.3 58.6 + - - +
57A ILE* 3.4 11.3 + - + +
58A GLU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.8 27.8 - - + +
13A ALA* 3.7 26.7 - - + +
14A LEU* 3.4 21.3 - - + +
17A LEU* 4.8 8.7 - - + -
25A LEU* 3.7 30.1 - - + -
51A LEU* 2.9 26.7 + - + +
52A LEU* 3.7 13.0 - - + +
54A ALA* 1.3 74.0 - - - +
56A ALA* 1.3 58.7 + - - +
58A GLU* 3.3 5.3 + - - +
59A MET* 2.9 33.7 + - - +
99A VAL* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 2.8 20.3 + - - +
53A ASP* 3.6 7.4 - - - +
55A LEU* 1.3 69.3 - - - +
57A ILE* 1.3 67.2 + - + +
59A MET 3.0 2.4 + - - -
60A LEU* 3.0 20.4 + - - +
99A VAL* 3.8 11.8 - - - +
100A HIS* 3.0 41.2 + - + -
103A THR* 3.9 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 3.2 24.0 + - + +
54A ALA* 3.7 9.2 - - + +
56A ALA* 1.3 79.0 - - + +
58A GLU* 1.3 65.3 + - - +
60A LEU* 3.2 11.8 + - + +
61A ASP* 2.9 47.0 + - - +
103A THR* 6.0 5.2 - - + -
104A ARG 5.6 2.7 - - - +
106A THR* 4.3 17.7 - - + -
108A LYS* 4.0 19.5 - - - +
109A GLN* 4.1 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.5 29.4 - - + +
14A LEU* 3.6 17.5 - - + -
54A ALA 2.9 18.4 + - - +
55A LEU 3.7 4.3 - - - +
57A ILE* 1.3 77.7 - - - +
59A MET* 1.3 57.5 + - - +
61A ASP* 3.3 11.6 + - - +
62A ARG* 2.5 59.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
14A LEU* 4.4 12.8 - - + -
17A LEU* 4.9 4.9 - - - -
55A LEU 2.9 16.7 + - - +
56A ALA 3.0 8.7 + - - +
58A GLU* 1.3 74.3 - - - +
60A LEU* 1.3 64.9 + - - +
62A ARG* 3.3 4.8 + - - +
63A HIS* 3.0 30.3 + - - +
89A ALA* 2.6 36.1 - - - +
90A LEU* 4.2 6.7 - - - +
92A SER* 2.9 13.9 - - - +
93A HIS* 3.7 41.1 - - + +
96A GLY* 4.3 9.0 - - - +
99A VAL* 5.1 5.6 - - - -
100A HIS* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 3.0 11.3 + - - +
57A ILE* 3.6 13.2 - - + +
59A MET* 1.3 76.9 - - - +
61A ASP* 1.3 64.3 + - - +
64A HIS* 2.8 57.5 + - + +
86A PHE* 4.1 17.9 - - + -
89A ALA* 4.1 7.9 - - + -
100A HIS* 3.1 35.7 - - + +
103A THR* 5.5 6.7 - - + -
109A GLN* 6.1 6.5 - - + +
0H ACE 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 2.9 35.0 + - - +
58A GLU* 3.7 15.7 - - - +
60A LEU* 1.3 83.5 - - - +
62A ARG* 1.3 58.8 + - - +
64A HIS 5.6 0.5 - - - +
65A THR* 5.9 1.6 - - - +
108A LYS* 5.4 4.9 + - - -
109A GLN* 5.7 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.2 0.2 - - - +
11A ASN* 2.5 35.7 + - - +
14A LEU* 3.5 32.4 - - - +
58A GLU* 2.5 44.1 + - - +
59A MET* 3.3 1.3 + - - +
60A LEU 3.2 0.2 - - - -
61A ASP* 1.3 80.3 - - - +
63A HIS* 1.3 88.3 + - + +
64A HIS 3.9 0.2 - - - -
65A THR* 4.9 8.9 - - - +
93A HIS* 4.5 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MET* 3.0 11.0 + - - +
62A ARG* 1.3 114.8 + - + +
64A HIS* 1.3 62.2 + - - +
65A THR* 3.4 12.2 + - - -
85A SER* 3.5 12.8 + - - +
88A ASN* 4.3 8.8 + - + +
89A ALA* 3.6 23.8 + - - +
92A SER* 3.5 32.4 - - - -
93A HIS* 4.2 11.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 2.8 43.0 + - + +
61A ASP 5.9 0.4 - - - -
62A ARG 3.9 0.2 - - - -
63A HIS* 1.3 75.2 - - - +
65A THR* 1.3 62.3 - - - +
66A HIS 3.9 4.3 - - - -
67A PHE* 3.4 33.1 - - + +
82A ASN* 3.2 48.9 + - - -
85A SER* 2.8 23.9 + - - -
86A PHE* 3.3 13.5 + - - -
89A ALA* 4.0 8.5 - - + -
116A GLN* 5.6 1.0 + - - -
0H ACE 3.3 22.6 + - - -
----------------------------------------------------------
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