Contacts of the helix formed by residues 58 - 80 (chain B) in PDB entry 1KO1
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 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 3.7 1.5 + - - +
57B LEU 1.3 69.2 - - - -
59B ASP* 1.3 64.6 + - - +
60B ASP* 2.9 12.5 + - - +
61B ASP* 2.3 90.7 + - - +
62B ARG* 3.1 16.9 + - - +
91B LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 1.3 74.3 - - - +
60B ASP* 1.3 57.7 + - - +
62B ARG* 3.1 4.5 + - - +
63B LYS* 3.0 26.7 + - - +
91B LYS* 2.7 26.9 + - - +
93B HIS* 6.1 1.6 - - - -
94B TYR* 2.3 46.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 2.9 12.9 + - - +
59B ASP* 1.3 72.5 - - - +
61B ASP* 1.3 68.2 + - - +
62B ARG 3.5 0.2 + - - -
63B LYS* 3.8 13.1 - - - +
64B PRO* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 3.3 24.2 + - - +
50B LYS* 6.0 2.1 - - - +
57B LEU* 3.2 33.6 - - + +
58B ASN* 2.3 81.7 + - - +
60B ASP* 1.3 73.7 - - - +
62B ARG* 1.3 60.9 + - - +
63B LYS 3.4 0.3 + - - -
64B PRO* 3.4 12.3 - - - +
65B TRP 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 5.5 0.2 - - - -
47B ASN* 5.0 0.9 - - - -
56B PRO* 5.0 1.8 - - - +
57B LEU* 3.0 50.4 + - + +
58B ASN* 3.3 9.7 + - - +
59B ASP* 3.1 7.8 + - - +
61B ASP* 1.3 81.9 - - + +
63B LYS* 1.3 65.3 + - - +
64B PRO* 3.5 0.4 - - - -
65B TRP* 3.1 29.8 + - + +
66B LEU* 2.8 39.4 + - + +
88B SER* 5.6 3.4 + - - -
90B LEU* 5.0 10.1 - - - +
91B LYS* 4.7 3.2 - - - +
94B TYR* 2.9 47.2 + - + -
137B GLN* 5.0 8.1 - - - +
140B THR* 4.7 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP 3.0 11.6 + - - +
60B ASP* 3.8 17.0 - - - +
61B ASP 3.3 0.2 - - - -
62B ARG* 1.3 77.5 - - - +
64B PRO* 1.3 73.6 - - + +
66B LEU* 3.1 8.3 + - - +
67B GLN* 3.0 21.0 + - + +
97B LEU* 5.4 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO* 4.2 18.6 - - + -
46B ARG* 4.4 23.1 - - - +
47B ASN* 5.3 1.3 - - - +
60B ASP 3.5 6.7 - - - +
61B ASP 3.4 15.7 - - - +
63B LYS* 1.3 103.7 - - + +
65B TRP* 1.3 56.6 + - - +
67B GLN* 3.4 8.7 + - + +
68B ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 2.9 23.6 + - - -
40B ASP* 3.9 15.7 - - - -
42B LEU* 3.8 7.2 - - + -
43B HIS* 3.1 64.8 + + + -
44B PRO* 4.1 10.2 - - + +
61B ASP 4.7 0.9 - - - +
62B ARG* 3.1 37.4 + - + +
64B PRO* 1.3 79.1 - - - +
66B LEU* 1.3 76.1 + - + +
68B ALA* 3.1 7.3 + - - +
69B LEU* 2.9 44.1 + - + +
87B CYS* 3.8 25.1 - - - -
88B SER* 4.2 16.8 - - - -
89B ALA 5.5 0.7 - - - -
94B TYR* 5.9 1.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.8 32.2 + - + +
63B LYS 3.1 3.8 + - - +
65B TRP* 1.3 86.2 - - + +
67B GLN* 1.3 59.0 + - - +
69B LEU* 3.2 5.3 + - + +
70B ASN* 2.8 29.6 + - - +
87B CYS* 3.7 29.8 - - - -
94B TYR* 3.5 47.6 - - + +
97B LEU* 4.0 28.1 - - + +
98B LEU* 3.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 4.5 1.8 - - - +
63B LYS* 3.0 14.2 + - + +
64B PRO* 3.6 12.1 - - + +
65B TRP 3.2 0.2 - - - -
66B LEU* 1.3 75.7 - - - +
68B ALA* 1.3 63.3 + - - +
70B ASN* 3.2 17.7 + - - +
71B ASP* 2.9 44.9 + - - +
97B LEU* 5.5 5.5 - - - +
100B GLU* 4.6 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.0 28.9 - - + +
64B PRO 3.0 14.7 + - - +
65B TRP* 3.4 10.5 - - - +
67B GLN* 1.3 77.6 - - - +
69B LEU* 1.3 57.3 + - - +
71B ASP* 3.3 9.3 + - - +
72B ALA* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 5.6 - - + -
39B GLY* 3.5 25.4 - - - -
42B LEU* 3.8 20.4 - - + -
65B TRP* 2.9 39.9 + - + +
66B LEU* 3.6 7.9 - - + +
67B GLN 3.2 0.2 - - - -
68B ALA* 1.3 79.5 - - - +
70B ASN* 1.3 57.0 + - - +
72B ALA* 3.7 2.6 - - - +
73B ALA* 2.9 29.3 + - - +
85B ILE* 3.9 21.4 - - + +
87B CYS* 3.6 39.3 - - + -
98B LEU* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 2.9 29.3 + - - -
66B LEU 2.8 17.0 + - - +
67B GLN* 3.2 19.7 + - - +
69B LEU* 1.3 74.6 - - - +
71B ASP* 1.3 62.0 + - - +
73B ALA* 3.4 2.7 + - - -
74B PHE* 3.1 18.9 + - - +
97B LEU 2.8 28.0 + - - +
98B LEU* 3.2 17.2 + - - +
100B GLU* 2.9 32.2 + - - +
102B ASN* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 5.1 0.2 - - - -
43A HIS 5.6 6.9 - - - +
44A PRO* 6.5 0.4 - - + -
45A ARG* 2.5 52.6 + - + +
48A ILE* 5.6 0.7 - - - +
67B GLN* 2.9 33.3 + - - +
68B ALA* 3.6 10.3 - - - +
70B ASN* 1.3 73.2 - - - +
72B ALA* 1.3 65.4 + - - +
74B PHE* 3.1 4.6 + - - +
75B ALA* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 21.5 - - + +
42A LEU* 5.1 0.4 - - + -
37B LEU* 3.4 32.5 - - + -
42B LEU* 4.0 8.7 - - + -
68B ALA 2.8 20.2 + - - +
69B LEU 3.7 4.7 - - - +
71B ASP* 1.3 73.4 - - - +
73B ALA* 1.3 56.7 + - - +
75B ALA* 3.1 2.4 + - - +
76B MET* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.5 26.1 - - + +
69B LEU 2.9 14.8 + - - +
70B ASN* 3.7 5.4 - - - +
71B ASP 3.3 0.2 - - - -
72B ALA* 1.3 76.3 - - - +
74B PHE* 1.3 63.1 + - - +
76B MET* 3.8 4.2 - - - +
77B GLN* 3.1 26.2 + - - +
85B ILE* 3.4 26.6 - - + +
102B ASN* 4.1 9.9 - - - +
105B LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 4.0 39.5 - - + +
48A ILE* 4.4 20.6 - - + -
49A GLU* 5.1 10.1 - - - -
3B THR* 3.8 41.7 - - - -
4B THR* 4.2 7.4 - - - -
70B ASN 3.1 14.2 + - - +
71B ASP 3.4 8.5 - - - +
73B ALA* 1.3 79.2 - - - +
75B ALA* 1.3 65.5 + - - +
77B GLN* 3.0 35.5 + - - +
78B ARG* 3.6 12.3 + - + +
101B GLY 4.6 5.8 - - - -
102B ASN* 4.0 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 4.7 4.7 - - - +
41A PHE* 3.8 32.8 - - + +
43A HIS 4.8 4.5 - - - +
48A ILE* 4.0 26.2 - - + -
71B ASP 2.9 13.3 + - - +
72B ALA 3.5 7.0 - - - +
74B PHE* 1.3 78.2 - - - +
76B MET* 1.3 62.3 + - - +
78B ARG* 3.3 18.1 + - - +
79B THR* 4.3 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.6 33.0 - - + -
35B ALA* 3.8 17.3 - - + -
36B PHE 3.9 1.8 - - - +
37B LEU* 3.7 29.4 - - + +
72B ALA 2.8 20.4 + - - +
73B ALA* 3.3 4.9 + - - +
75B ALA* 1.3 74.6 - - - +
77B GLN* 1.3 57.1 + - - +
78B ARG 3.2 0.4 + - - -
79B THR 3.5 0.9 + - - -
80B ASN* 3.0 35.7 + - - +
83B SER* 3.2 31.9 - - - +
84B LEU 3.7 22.9 - - - +
85B ILE* 3.7 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR 3.5 20.6 + - - -
4B THR* 3.5 5.0 - - - -
5B ASN* 2.6 31.1 + - - +
8B HIS* 2.6 38.5 + - + +
9B HIS 5.1 1.3 - - - +
10B ILE* 3.7 28.0 - - + +
73B ALA 3.1 16.2 + - - +
74B PHE* 3.0 29.3 + - + +
76B MET* 1.3 73.8 - - - +
78B ARG* 1.3 69.8 + - - +
79B THR 3.3 0.2 - - - -
80B ASN 4.0 7.0 - - - -
83B SER* 4.6 2.0 - - - -
102B ASN* 5.2 0.9 - - - +
104B ASN* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.4 38.1 - - - +
51A MET* 6.0 3.4 - - - +
52A ALA* 5.1 16.7 - - - +
3B THR 4.4 11.7 + - - +
5B ASN* 4.7 6.3 + - - -
8B HIS* 3.4 14.7 - - - -
74B PHE* 3.7 20.2 - - + +
75B ALA* 3.3 9.8 + - - +
76B MET 3.2 1.2 - - - -
77B GLN* 1.3 95.0 - - - +
79B THR* 1.3 77.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.5 7.6 - - - -
8B HIS* 4.4 5.2 - - - -
75B ALA 4.3 2.4 + - - +
76B MET 3.5 2.1 + - - -
78B ARG* 1.3 101.3 - - + +
80B ASN* 1.3 79.4 + - - +
81B LYS 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.3 26.4 - - - -
8B HIS* 3.1 21.6 + - - +
9B HIS 4.5 0.9 + - - +
33B HIS 5.5 1.9 - - - +
34B ALA* 5.1 0.6 - - - -
35B ALA* 3.5 18.3 + - - +
76B MET 3.0 24.4 + - - +
77B GLN* 3.8 4.5 - - - +
78B ARG 3.7 0.6 - - - -
79B THR* 1.3 96.8 + - - +
81B LYS* 1.3 65.1 + - - +
82B VAL* 3.4 10.6 + - - +
83B SER* 3.6 12.7 + - - +
----------------------------------------------------------
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