Contacts of the helix formed by residues 79 - 94 (chain B) in PDB entry 2BTU
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 THR 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 4.0 19.3 + - - +
77B HIS 3.2 0.6 - - - -
78B ASP* 1.3 102.1 + - - +
80B ILE* 1.3 66.4 + - - +
81B GLY 3.1 4.1 + - - -
82B ILE* 3.5 23.5 + - + +
83B ASP* 3.7 11.6 + - - +
222B LEU* 3.7 22.7 + - - +
224B PRO* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.8 41.7 - - + +
68B LEU* 3.3 27.6 - - + -
71B ALA* 4.4 8.7 - - + -
76B LYS 5.2 1.5 + - - +
77B HIS* 3.8 14.4 + - - +
78B ASP 3.8 0.4 - - - -
79B THR* 1.3 80.3 + - - +
81B GLY* 1.3 59.6 + - - +
82B ILE 3.4 0.2 - - - -
83B ASP* 3.7 21.1 - - + +
84B ALA* 3.8 6.6 + - - +
119B ILE* 4.8 2.7 - - + -
151B TYR* 3.5 24.7 - - + +
153B LEU* 4.3 15.4 - - + +
222B LEU* 4.7 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS 4.8 2.0 + - - -
79B THR* 3.1 2.0 - - - +
80B ILE* 1.3 77.6 - - - +
82B ILE* 1.3 59.1 + - - +
83B ASP 3.5 0.2 - - - -
84B ALA* 3.7 3.9 - - - +
85B VAL* 2.9 31.5 + - - +
119B ILE 4.6 2.7 + - - -
122B GLY* 3.6 16.9 - - - -
123B ILE* 3.7 10.1 - - - +
153B LEU* 3.9 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP 5.1 1.1 - - - +
79B THR* 3.5 24.2 - - + +
81B GLY* 1.3 75.9 - - - +
83B ASP* 1.3 55.0 + - - +
84B ALA 3.2 0.2 - - - -
85B VAL* 3.1 1.1 + - - +
86B ALA* 2.5 38.3 + - - +
122B GLY* 3.5 16.8 - - - +
125B GLU* 3.8 24.7 - - + -
126B GLY* 4.0 8.7 - - - -
129B GLN* 4.1 11.4 - - - +
224B PRO* 4.1 20.6 - - + -
225B THR 4.1 11.9 - - - +
227B ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 2.9 32.8 + - + +
79B THR 3.7 6.9 - - - +
80B ILE* 3.7 15.0 - - + +
82B ILE* 1.3 78.1 - - - +
84B ALA* 1.3 51.9 + - - +
86B ALA* 2.8 8.6 - - - +
87B MET* 2.5 41.2 + - - +
187B HIS 3.7 0.3 - - - +
188B SER* 4.0 5.5 + - - +
222B LEU 5.1 0.7 - - - +
224B PRO* 3.1 21.7 - - - +
225B THR* 2.4 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 5.0 10.2 - - - +
80B ILE 3.8 8.1 + - - +
81B GLY* 3.7 15.3 - - - +
83B ASP* 1.3 74.9 - - - +
85B VAL* 1.3 68.2 + - + +
87B MET* 3.0 15.3 + - - +
88B CYS* 3.1 18.3 + - - +
102B PHE* 4.5 8.5 - - + -
123B ILE* 5.7 1.1 - - + -
153B LEU* 4.4 21.1 - - + +
154B ALA 5.6 3.6 - - - -
155B GLY* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY 2.9 22.9 + - - +
82B ILE 3.1 6.1 + - - +
84B ALA* 1.3 73.8 - - - +
86B ALA* 1.3 59.2 + - - +
88B CYS* 3.0 4.2 + - - +
89B VAL* 2.9 33.5 + - + +
102B PHE* 3.7 38.1 - - + -
123B ILE* 3.5 24.0 - - + +
126B GLY* 3.6 30.5 - - - +
127B CYS* 3.9 5.8 - - - +
130B ALA* 4.1 13.7 - - + -
132B CYS* 4.7 1.3 - - - -
227B ILE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 2.5 17.6 + - - +
83B ASP 2.8 15.9 - - - +
85B VAL* 1.3 72.5 - - - +
87B MET* 1.3 58.8 + - - +
89B VAL* 4.2 2.2 - - - -
90B ASN* 3.0 34.1 + - - +
225B THR* 3.5 37.5 - - + +
226B LYS 4.2 1.3 - - - +
227B ILE* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.0 35.9 - - + +
83B ASP 2.5 18.3 + - - +
84B ALA* 3.0 6.5 + - - +
86B ALA* 1.3 72.9 - - - +
88B CYS* 1.3 59.4 + - - +
90B ASN 4.6 0.9 - - - -
91B ASP* 3.5 14.7 - - - +
188B SER* 3.1 36.3 - - - +
189B ASN* 4.4 5.2 - - - +
225B THR* 5.0 1.8 - - + +
246B HIS* 2.4 42.8 - - + +
248B THR* 2.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY* 5.3 4.6 - - - +
61B THR* 4.0 6.7 - - - +
62B ASP* 3.6 35.9 - - - -
84B ALA 3.1 10.0 + - - +
85B VAL 3.0 8.3 + - - +
87B MET* 1.3 77.7 - - - +
89B VAL* 1.3 65.3 + - - +
90B ASN 3.3 0.4 - - - -
91B ASP* 3.4 14.9 + - - +
92B ILE* 3.6 14.2 + - - +
102B PHE* 3.9 7.9 - - + -
155B GLY* 3.7 20.4 - - - -
157B THR* 3.0 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 2.9 21.3 + - + +
86B ALA* 3.9 1.3 - - - +
88B CYS* 1.3 75.9 - - + +
90B ASN* 1.3 77.0 + - - +
91B ASP 3.1 2.5 - - - -
92B ILE* 2.8 32.0 - - + +
93B VAL* 3.2 5.7 + - - +
99B PRO* 3.3 43.1 - - + -
130B ALA* 3.7 22.4 - - + -
132B CYS* 4.9 1.1 - - - -
157B THR* 4.8 8.5 - - + -
227B ILE* 3.9 5.2 - - + -
229B VAL* 3.3 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 3.0 20.9 + - - +
89B VAL* 1.3 88.7 - - - +
91B ASP* 1.3 62.4 + - - +
93B VAL* 3.5 6.1 - - - +
94B VAL* 3.3 29.6 + - - +
225B THR* 4.3 0.7 - - - +
226B LYS 3.0 21.2 - - - +
227B ILE* 3.6 7.3 - - - +
228B TYR* 3.1 36.5 - - - +
229B VAL* 4.1 3.4 - - - +
246B HIS* 3.1 36.3 - - + +
303B MET* 4.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.8 28.5 - - + +
62B ASP* 4.5 4.2 - - - +
87B MET* 3.5 16.1 - - - +
88B CYS 3.4 10.4 + - - +
89B VAL 3.1 0.8 - - - -
90B ASN* 1.3 77.7 - - - +
92B ILE* 1.3 55.7 + - - +
94B VAL* 4.1 7.1 - - - +
95B GLN* 2.5 36.8 + - - +
246B HIS* 2.8 36.1 - - - +
248B THR* 4.9 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 5.3 3.1 - - - +
58B VAL* 4.1 30.1 - - + +
59B SER 4.5 14.1 - - - +
60B GLY* 4.6 4.0 - - - +
88B CYS 3.6 7.6 + - - +
89B VAL* 2.8 39.9 - - + +
91B ASP* 1.3 81.1 - - - +
93B VAL* 1.3 68.8 + - + +
94B VAL 3.3 0.2 - - - -
95B GLN* 3.2 21.2 + - - +
97B ALA* 3.1 24.9 - - + +
99B PRO* 3.3 47.8 - - + -
157B THR* 4.9 10.5 - - + -
159B GLY* 4.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 3.2 11.2 + - - +
90B ASN* 3.5 16.8 - - - +
92B ILE* 1.3 81.1 - - + +
94B VAL* 1.3 59.9 + - + +
95B GLN 3.0 5.2 - - - -
96B GLY* 2.9 24.6 + - - -
97B ALA 3.4 19.1 - - - +
229B VAL* 3.9 35.9 - - + +
232B ILE* 3.7 37.7 - - + +
233B LEU* 4.0 10.3 - - + -
244B MET* 3.9 1.2 - - - +
303B MET* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 5.8 3.8 - - + -
90B ASN 3.3 19.0 + - - +
91B ASP* 4.1 7.4 - - - +
93B VAL* 1.3 76.8 - - - +
95B GLN* 1.3 65.2 + - + +
96B GLY 3.2 3.1 - - - -
167B VAL* 3.8 8.5 - - - +
244B MET* 3.5 49.4 - - + +
245B ALA* 3.9 19.7 - - - +
246B HIS* 4.0 6.1 - - + +
303B MET* 3.8 30.3 - - + -
----------------------------------------------------------
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