Contacts of the helix formed by residues 74 - 104 (chain B) in PDB entry 2BTP
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 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 1.3 74.2 + - + +
76B LEU* 3.2 10.7 + - - +
77B GLN* 3.6 15.6 + - - +
78B LEU* 4.0 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 3.9 33.2 - - - +
74B LYS* 1.3 81.2 - - + +
76B LEU* 1.3 56.9 + - - +
78B LEU* 3.1 24.4 + - + +
79B ILE* 3.1 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.5 48.1 - - + +
69B THR* 3.9 32.8 - - - +
74B LYS 3.2 7.5 - - - +
75B LYS* 1.3 75.5 - - - +
77B GLN* 1.3 65.9 + - - +
79B ILE* 3.9 11.7 - - + +
80B LYS* 3.1 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
74B LYS* 3.6 11.0 + - - +
75B LYS 3.4 0.6 - - - -
76B LEU* 1.3 76.6 - - - +
78B LEU* 1.3 56.6 + - - +
80B LYS* 3.3 6.5 + - + +
81B ASP* 2.9 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-20A HIS* 5.3 0.6 - - + -
5A GLU* 4.2 25.4 - - + +
8A GLN* 3.2 42.2 - - + +
9A LYS* 3.6 42.2 - - + +
12A LEU* 5.3 6.5 - - + -
74B LYS 4.0 2.8 + - - +
75B LYS* 3.1 15.7 + - + +
77B GLN* 1.3 76.2 - - - +
79B ILE* 1.3 66.1 + - + +
81B ASP* 3.5 13.7 + - - +
82B TYR* 3.2 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 23.6 - - + -
62B ILE* 3.7 24.6 - - + +
65B ILE* 4.0 25.4 - - + +
66B GLU* 3.9 24.0 - - + +
69B THR* 5.2 3.8 - - - -
75B LYS* 3.1 18.6 + - + +
76B LEU* 3.9 24.2 - - + +
78B LEU* 1.3 75.3 - - + +
80B LYS* 1.3 60.9 + - - +
82B TYR* 3.0 4.2 + - - +
83B ARG* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.4 21.1 + - - +
76B LEU 3.1 17.2 + - - +
77B GLN* 3.6 7.0 - - + +
78B LEU 3.3 0.2 - - - -
79B ILE* 1.3 78.7 - - - +
81B ASP* 1.3 65.8 + - - +
83B ARG* 3.2 14.8 + - - +
84B GLU* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-20A HIS* 3.8 37.1 + - + +
77B GLN* 2.9 45.0 + - - +
78B LEU* 3.6 11.4 - - - +
79B ILE 3.3 0.2 - - - -
80B LYS* 1.3 77.9 - - - +
82B TYR* 1.3 55.8 + - - +
84B GLU* 3.3 15.5 + - - +
85B LYS* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-21A MET* 3.6 22.2 - - + -
-20A HIS* 5.1 4.9 - - - -
9A LYS* 4.9 7.6 - - + -
12A LEU* 4.2 19.7 - - + -
13A ALA* 3.5 28.1 - - + +
16A ALA* 4.7 0.7 - - + -
18A ARG* 3.0 23.1 + - - -
21A ASP* 2.5 39.0 + - - +
62B ILE* 3.3 33.9 - - + -
78B LEU* 3.2 9.5 + - + +
79B ILE 3.0 9.9 + - - +
81B ASP* 1.3 77.0 - - - +
83B ARG* 1.3 67.0 + - - +
85B LYS* 3.2 24.9 + - + +
86B VAL* 3.2 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 3.7 26.1 - - + +
62B ILE* 3.8 25.2 - - + +
63B SER* 4.0 16.2 - - - +
66B GLU* 2.9 41.0 + - - +
79B ILE 2.9 11.6 + - - +
80B LYS* 3.4 20.2 - - - +
82B TYR* 1.3 78.2 - - - +
84B GLU* 1.3 77.1 + - - +
86B VAL* 3.3 5.4 + - - +
87B GLU* 2.9 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LYS* 3.0 18.2 + - - +
81B ASP* 3.7 16.3 - - - +
82B TYR 3.2 0.2 - - - -
83B ARG* 1.3 92.7 + - - +
85B LYS* 1.3 66.5 + - - +
87B GLU* 3.5 21.0 - - + +
88B SER* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-21A MET* 3.0 30.3 - - + +
-20A HIS* 3.5 27.5 - - - +
-18A HIS 5.1 5.8 - - - +
18A ARG* 4.3 11.0 - - - +
21A ASP* 4.7 7.2 - - - +
81B ASP 3.0 12.0 + - - +
82B TYR* 3.2 17.8 + - + +
84B GLU* 1.3 77.3 - - - +
86B VAL* 1.3 64.3 + - + +
88B SER* 3.3 8.2 + - - -
89B GLU* 3.2 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.1 28.0 - - - +
55B ARG* 3.5 38.1 - - + +
58B ALA* 4.4 2.5 - - + -
59B TRP* 4.1 16.8 - - + +
62B ILE* 4.0 19.7 - - + -
82B TYR* 3.2 15.5 + - + +
83B ARG* 3.6 8.1 - - - +
84B GLU 3.2 0.2 - - - -
85B LYS* 1.3 76.1 - - + +
87B GLU* 1.3 63.6 + - - +
89B GLU* 3.0 11.3 + - - +
90B LEU* 2.8 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 3.0 36.6 + - + +
83B ARG* 2.9 36.2 + - - +
84B GLU* 3.5 21.7 - - - +
86B VAL* 1.3 75.6 - - - +
88B SER* 1.3 64.0 + - - +
90B LEU* 2.9 19.2 + - - +
91B ARG* 2.9 45.9 + - - +
132B VAL* 4.0 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 2.9 17.1 + - - -
85B LYS* 3.5 12.0 - - - -
87B GLU* 1.3 73.4 - - - +
89B GLU* 1.3 63.0 - - - +
91B ARG* 3.3 9.8 + - - +
92B SER* 3.1 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.8 43.7 + - - -
55B ARG* 3.0 34.7 + - + +
85B LYS* 3.2 22.9 + - + +
86B VAL* 3.0 9.9 + - - +
88B SER* 1.3 77.4 - - - +
90B LEU* 1.3 67.3 + - - +
92B SER* 3.3 6.8 + - - -
93B ILE* 3.2 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.0 12.5 - - + +
55B ARG* 3.3 32.3 - - + +
56B ARG* 3.7 28.7 - - + +
59B TRP* 5.7 2.9 - - + -
86B VAL* 2.8 11.8 + - + +
87B GLU* 3.2 11.4 - - - +
89B GLU* 1.3 76.2 - - - +
91B ARG* 1.3 59.7 + - + +
93B ILE* 3.5 5.1 + - - +
94B CYS* 3.0 35.7 + - - -
128B TYR 3.7 16.4 - - - +
129B LEU* 5.0 2.9 - - + -
131B GLU* 5.5 0.2 - - - +
132B VAL* 3.6 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.9 50.2 + - - +
88B SER* 3.7 11.2 - - - +
90B LEU* 1.3 77.4 - - + +
92B SER* 1.3 53.7 + - - +
94B CYS* 3.6 0.5 - - - +
95B THR* 2.6 46.5 + - - +
129B LEU* 3.5 27.1 + - + +
132B VAL* 3.6 28.1 + - + +
133B ALA* 4.4 9.3 - - - +
134B CYS* 6.4 0.2 - - - -
137B ASP* 4.7 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B SER 3.1 17.4 + - - -
89B GLU* 3.3 7.4 + - - -
91B ARG* 1.3 75.5 - - - +
93B ILE* 1.3 55.7 + - - +
95B THR* 3.5 6.8 - - - -
96B THR* 2.7 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 4.4 16.6 - - + -
51B VAL* 3.8 28.3 - - + +
52B VAL* 3.8 28.5 - - + +
55B ARG* 3.7 38.8 - - + +
89B GLU 3.2 16.8 + - - +
90B LEU* 3.6 7.4 - - - +
91B ARG 3.2 0.2 - - - -
92B SER* 1.3 80.3 - - - +
94B CYS* 1.3 62.7 + - - +
96B THR* 3.3 8.0 + - - +
97B VAL* 3.0 26.2 + - + +
125B TYR* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.4 7.0 - - - -
90B LEU* 3.0 22.7 + - - +
91B ARG 3.6 3.1 - - - +
93B ILE* 1.3 75.9 - - - +
95B THR* 1.3 51.8 + - - +
97B VAL* 3.1 2.6 + - - +
98B LEU* 2.7 43.6 + - + +
125B TYR* 3.6 43.7 - - + +
128B TYR* 4.1 13.2 - - - -
129B LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 2.6 30.2 + - - +
92B SER* 3.5 7.3 - - - -
94B CYS* 1.3 72.5 - - - +
96B THR* 1.3 64.4 + - - +
98B LEU* 3.9 8.3 - - - +
99B GLU* 2.9 40.7 + - + +
129B LEU* 5.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.4 22.3 + - + +
48B TYR* 3.6 32.8 - - + +
92B SER* 2.7 26.9 + - - -
93B ILE* 3.4 7.1 - - - -
95B THR* 1.3 75.9 - - - +
97B VAL* 1.3 57.7 + - - +
99B GLU* 3.3 11.1 + - - +
100B LEU* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.4 44.9 - - + -
93B ILE 3.0 17.9 + - - +
94B CYS 3.6 3.4 - - - +
96B THR* 1.3 74.4 - - - +
98B LEU* 1.3 60.0 + - - +
100B LEU* 3.1 11.0 + - + +
101B LEU* 2.9 41.7 + - + +
121B MET* 4.8 6.3 - - - -
125B TYR* 3.7 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B CYS* 2.7 26.8 + - + +
95B THR* 3.9 6.7 - - - +
97B VAL* 1.3 71.7 - - - +
99B GLU* 1.3 57.3 + - - +
101B LEU* 3.4 6.9 + - + +
102B ASP* 2.9 41.8 + - - +
122B LYS* 3.9 28.3 - - + +
125B TYR* 4.2 11.9 - - + -
126B PHE* 3.7 54.1 - - + +
129B LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 2.9 33.9 + - + +
96B THR* 3.3 10.5 + - - +
98B LEU* 1.3 77.3 - - - +
100B LEU* 1.3 53.3 + - - +
102B ASP* 3.1 5.5 + - - +
103B LYS* 2.8 46.8 + - + +
104B TYR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.2 31.4 - - + +
30B THR* 3.7 29.6 - - + +
31B GLU* 4.4 7.4 - - + +
44B LEU* 4.4 11.7 - - + -
48B TYR* 4.1 32.1 - - + +
96B THR 3.0 16.0 + - - +
97B VAL* 3.4 11.7 - - + +
99B GLU* 1.3 76.3 - - - +
101B LEU* 1.3 61.8 + - - +
104B TYR* 3.0 38.2 + - + +
105B LEU* 3.1 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 2.9 37.3 + - + +
98B LEU* 3.6 10.5 - - + +
100B LEU* 1.3 76.0 - - - +
102B ASP* 1.3 63.1 + - - +
105B LEU* 3.4 23.9 + - + -
106B ILE* 3.1 41.4 + - + +
118B TYR* 3.6 37.0 - - + +
121B MET* 4.0 12.8 - - + -
122B LYS* 3.4 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 2.9 26.0 + - - +
99B GLU* 3.1 4.4 + - - +
101B LEU* 1.3 78.2 - - - +
103B LYS* 1.3 63.7 + - - +
104B TYR 3.5 0.5 + - - -
106B ILE* 4.7 4.1 - - - +
107B ALA* 4.0 13.3 + - - +
122B LYS* 2.6 34.3 + - - +
126B PHE* 5.9 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 2.8 29.1 + - + +
102B ASP* 1.3 75.3 - - - +
104B TYR* 1.3 96.7 + - + +
107B ALA* 4.0 8.8 - - - +
108B ASN* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.6 28.5 - - + +
31B GLU* 3.6 47.4 + - + +
33B GLY* 4.2 12.1 - - - -
100B LEU* 3.0 31.3 + - + +
102B ASP 3.3 0.8 - - - -
103B LYS* 1.3 115.3 - - + +
105B LEU* 1.3 66.0 + - + +
106B ILE 3.6 1.1 - - - -
107B ALA* 3.6 3.6 - - - +
108B ASN* 3.2 36.3 + - - +
----------------------------------------------------------
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