Contacts of the helix formed by residues 56 - 74 (chain B) in PDB entry 1NZ0
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 LYS 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY* 1.3 75.8 - - - +
57B ALA* 1.3 66.4 + - - +
58B THR* 3.3 3.6 - - - +
59B ARG* 3.0 9.6 + - + +
60B ARG* 3.0 21.1 + - - +
5011B SO4 3.6 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 1.3 71.1 - - - +
58B THR* 1.3 58.7 + - - +
60B ARG* 3.2 16.9 + - - +
61B ASN* 2.7 45.1 + - - +
5011B SO4 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.2 2.8 + - - +
57B ALA* 1.3 79.1 - - - +
59B ARG* 1.4 58.5 + - - +
61B ASN* 3.4 13.4 + - + +
62B LYS* 3.0 27.6 + - + +
65B ARG* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 2.8 31.4 + - + -
55B GLY* 3.9 6.5 - - - -
56B LYS* 3.0 14.6 + - + +
58B THR* 1.4 76.1 - - - +
60B ARG* 1.3 64.0 + - - +
62B LYS* 3.2 7.7 + - + +
63B LEU* 3.1 22.3 + - - +
93B SER* 2.7 52.1 + - - +
96B PHE* 3.8 23.4 - - + +
97B GLU* 3.0 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.7 29.0 - - + +
51B LYS 3.9 11.0 - - - -
52B ARG* 3.3 20.6 - - - +
54B PHE* 4.4 7.2 - - + -
55B GLY 2.8 48.5 + - - +
56B LYS 3.0 6.0 + - - +
57B ALA* 3.5 21.8 - - - +
59B ARG* 1.3 75.3 - - - +
61B ASN* 1.3 62.5 + - - +
63B LEU* 3.3 4.1 + - - +
64B LYS* 3.0 32.4 + - - +
5008B SO4 2.8 44.4 + - - +
5011B SO4 2.9 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 2.7 37.9 + - - +
58B THR* 3.4 13.4 + - + +
60B ARG* 1.3 75.5 - - - +
62B LYS* 1.3 57.3 + - - +
64B LYS* 3.4 19.3 + - - +
65B ARG* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 3.0 16.7 + - + +
59B ARG* 3.2 7.4 + - - +
61B ASN* 1.3 72.9 - - - +
63B LEU* 1.3 68.6 + - - +
65B ARG* 3.2 25.9 + - - +
66B TRP* 3.0 60.8 + - - +
96B PHE* 3.7 27.2 + - + -
97B GLU* 6.0 1.4 - - - +
5006B SO4 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.7 1.8 - - + -
48B ILE* 4.2 5.4 - - + -
50B VAL* 3.8 14.1 - - + -
54B PHE* 3.8 30.5 - - + -
59B ARG 3.1 6.1 + - - -
60B ARG* 3.6 7.9 - - - +
62B LYS* 1.3 78.8 - - - +
64B LYS* 1.3 64.5 + - - +
66B TRP* 3.2 4.5 + - + +
67B VAL* 2.9 46.9 + - + +
88B PRO* 3.7 26.7 - - + -
92B LEU* 4.0 26.2 - - + -
96B PHE* 3.6 19.8 - - + -
104B VAL* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.6 37.4 - - + +
50B VAL* 3.9 25.8 - - + +
60B ARG* 3.0 22.9 + - - +
61B ASN* 3.7 19.3 + - - +
63B LEU* 1.3 77.9 - - - +
65B ARG* 1.3 58.7 + - - +
67B VAL 3.3 0.7 + - - -
68B ARG* 2.8 27.0 + - - -
5008B SO4 2.6 46.9 + - - -
22D LYS* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR 5.5 0.4 + - - -
61B ASN* 2.9 34.8 + - - +
62B LYS* 3.2 25.2 + - - +
64B LYS* 1.3 76.4 - - - +
66B TRP* 1.3 62.0 + - - +
68B ARG* 3.8 1.0 - - - +
69B GLU* 2.9 51.9 + - + +
72B ARG* 6.1 0.4 - - - +
5006B SO4 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.0 46.5 + - + +
63B LEU* 3.6 10.5 - - + +
65B ARG* 1.3 77.2 - - + +
67B VAL* 1.3 59.9 + - + +
69B GLU* 3.3 6.8 + - - +
70B ILE* 2.9 37.5 + - + +
96B PHE* 3.8 25.6 - + - -
99B VAL* 3.7 15.7 - - + -
100B ASP 4.0 0.9 - - - -
101B PHE* 3.5 61.2 - + + -
104B VAL* 3.8 26.9 - - + -
5006B SO4 2.8 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.9 26.0 - - + -
46B LEU* 4.3 7.6 - - + -
48B ILE* 3.7 24.7 - - + -
63B LEU* 2.9 40.2 + - + +
64B LYS 3.8 2.7 - - - +
66B TRP* 1.3 74.7 - - + +
68B ARG* 1.3 64.6 + - - +
70B ILE* 3.2 10.6 + - + +
71B PHE* 3.0 23.1 + - + +
86B VAL* 4.0 15.7 - - + -
104B VAL* 5.5 0.9 - - + -
108B LEU* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.1 16.6 - - - -
48B ILE* 4.3 1.7 - - - +
64B LYS 2.8 17.1 + - - -
65B ARG* 3.9 1.6 - - - +
67B VAL* 1.3 76.6 - - - +
69B GLU* 1.3 57.3 + - - +
71B PHE* 3.7 1.2 - - - +
72B ARG* 2.9 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 2.9 43.1 + - + +
66B TRP* 3.6 7.8 - - - +
68B ARG* 1.3 76.8 - - - +
70B ILE* 1.3 63.9 + - - +
72B ARG* 3.6 24.9 + - - +
73B ARG* 2.9 69.2 + - - +
101B PHE* 4.0 17.8 - - + -
5006B SO4 4.3 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TRP 2.9 24.8 + - - +
67B VAL* 3.2 4.9 + - - +
69B GLU* 1.3 77.6 - - - +
71B PHE* 1.3 62.1 + - - +
73B ARG* 5.1 0.2 - - - -
74B ASN* 2.8 35.5 + - - +
101B PHE* 3.6 25.1 - - + -
104B VAL* 4.0 19.5 - - + +
105B ARG* 3.6 33.0 - - + +
108B LEU* 3.9 24.5 - - + -
109B LEU* 3.7 30.8 - - + +
112B LEU* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 4.0 25.4 - - - -
45B ARG* 4.2 2.2 - - - -
46B LEU* 3.8 51.8 - - + -
67B VAL* 3.0 16.3 + - + +
68B ARG 3.7 4.0 - - - +
70B ILE* 1.3 80.1 - - - +
72B ARG* 1.3 60.3 + - + +
75B LYS* 3.1 62.5 + - + +
78B ILE* 3.4 29.3 - - + +
84B ILE* 4.0 23.1 - - + -
108B LEU* 5.9 1.1 - - + -
112B LEU* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 2.9 28.8 + - - +
69B GLU* 3.6 29.7 + - - +
71B PHE* 1.3 81.9 - - + +
73B ARG* 1.3 75.5 + - + +
74B ASN 3.4 0.5 + - - -
75B LYS* 3.7 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 2.9 63.7 + - - +
70B ILE* 5.6 0.2 - - - +
72B ARG* 1.3 90.2 - - + +
74B ASN* 1.3 71.5 + - - +
75B LYS 3.6 0.6 + - - -
101B PHE* 4.8 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 2.8 33.2 + - - +
71B PHE 3.6 3.1 - - - -
73B ARG* 1.3 92.7 - - - +
75B LYS* 1.3 63.2 + - - +
76B GLY 3.0 4.8 + - - -
77B VAL* 3.1 22.8 + - + +
78B ILE* 3.5 6.4 - - - +
101B PHE* 6.1 0.2 - - - -
105B ARG* 2.9 36.7 + - - +
109B LEU* 3.8 28.5 - - + +
----------------------------------------------------------
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