Contacts of the helix formed by residues 70 - 84 (chain B) in PDB entry 2BHT
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 GLY 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.0 5.5 - - - +
69B SER* 1.3 82.6 + - - +
71B ASN* 1.3 63.5 + - - -
72B THR 3.4 1.6 - - - -
73B GLY* 3.2 2.5 + - - +
74B ILE* 2.9 33.0 + - - +
100B ARG* 4.3 16.4 - - - -
103B MET* 3.7 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 3.7 22.4 + - - +
41B LYS* 4.0 8.5 - - + +
68B THR* 5.3 0.2 - - - +
70B GLY* 1.3 68.0 - - - -
72B THR* 1.3 60.9 + - - +
74B ILE* 2.8 22.0 + - - +
75B ALA* 2.8 16.3 + - - +
100B ARG* 3.3 11.6 + - - +
281B ASP* 3.4 20.8 + - - +
285B ARG* 2.7 36.0 + - - -
286B TYR* 4.4 0.8 + - - -
320B PLP 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.3 27.5 - - + +
45B ALA* 6.0 1.3 - - + -
48B MET* 5.1 2.9 - - + -
66B GLU* 4.5 1.1 - - - +
68B THR* 3.5 22.4 - - - +
70B GLY 3.4 0.6 - - - -
71B ASN* 1.3 76.6 - - - +
73B GLY* 1.3 63.3 + - - +
75B ALA* 4.8 0.9 - - - -
76B LEU* 2.9 51.7 + - + +
140B GLN* 3.1 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 3.8 12.5 - - - -
70B GLY 3.2 11.3 + - - -
72B THR* 1.3 79.2 - - - +
74B ILE* 1.3 55.4 + - - +
77B ALA* 2.8 32.6 + - - +
89B LEU* 3.6 27.5 - - - +
103B MET* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 3.9 27.1 - - + +
39B SER* 5.7 0.4 - - - +
70B GLY 2.9 27.2 + - - +
71B ASN* 2.8 33.6 + - - +
73B GLY* 1.3 77.2 - - - +
75B ALA* 1.3 51.9 + - - +
77B ALA* 3.8 3.1 - - - +
78B MET* 2.6 35.7 + - - +
100B ARG* 4.2 6.7 - - + +
102B ALA* 4.4 21.3 - - + +
103B MET* 4.5 8.1 - - + -
106B TYR* 3.9 19.7 - - + -
285B ARG* 3.4 27.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
37B ALA* 4.4 0.4 - - + -
39B SER* 5.0 0.9 - - - +
41B LYS* 2.9 33.4 - - + +
42B ASP* 3.0 27.4 - - - +
45B ALA* 3.4 7.9 - - + -
71B ASN 2.8 15.8 + - - +
72B THR 4.1 1.6 - - - +
74B ILE* 1.3 70.6 - - - +
76B LEU* 1.3 56.0 + - - +
78B MET* 2.8 7.0 - - - +
79B ILE* 2.6 38.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
45B ALA* 3.5 25.1 - - + +
48B MET* 3.4 17.7 - - + -
49B ILE* 4.5 3.4 - - + -
66B GLU* 3.6 39.5 - - + -
72B THR* 2.9 29.8 + - + +
73B GLY* 4.3 2.7 - - - +
75B ALA* 1.3 72.1 - - - +
77B ALA* 1.3 67.2 + - - +
79B ILE* 2.9 13.3 + - - +
80B ALA 2.9 12.0 + - - -
87B MET* 3.1 22.8 - - + +
89B LEU* 4.8 2.2 - - + -
138B LEU* 3.4 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 2.8 21.6 + - - +
74B ILE* 3.8 3.8 - - - +
76B LEU* 1.3 78.9 - - - +
78B MET* 1.3 64.2 + - - +
79B ILE 3.3 0.2 + - - -
80B ALA* 3.5 7.3 + - - +
81B ALA* 3.5 11.1 + - - +
87B MET* 3.8 16.5 - - - +
89B LEU* 4.2 13.9 - - + -
103B MET 4.2 7.4 - - - +
106B TYR* 4.0 27.5 - - + +
108B ALA* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLY* 4.2 15.2 - - - +
4B LEU* 4.3 4.5 - - - -
8B ILE* 3.9 23.1 - - + -
36B PRO* 4.1 12.1 - - + -
37B ALA* 3.9 6.5 - - + +
42B ASP* 3.8 28.7 - - - +
74B ILE 2.6 22.6 + - - +
75B ALA* 2.8 16.5 + - - +
77B ALA* 1.3 76.5 - - - +
79B ILE* 1.3 67.6 + - + -
81B ALA* 3.7 4.9 + - - +
82B LEU* 3.6 29.9 + - + +
106B TYR* 3.3 38.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
8B ILE* 4.4 3.4 - - + -
42B ASP 3.6 7.4 - - - +
45B ALA* 3.4 16.4 - - + -
46B LEU* 3.0 50.0 - - + +
49B ILE* 3.3 31.9 - - + -
75B ALA* 2.6 19.5 + - + +
76B LEU 2.9 2.9 + - - +
78B MET* 1.3 90.4 - - + +
80B ALA* 1.3 63.4 + - - +
82B LEU* 2.9 13.6 - - + +
83B LYS* 2.8 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.2 1.1 - - - +
76B LEU 2.9 6.3 + - - +
77B ALA 3.8 5.4 - - - +
79B ILE* 1.3 79.9 - - - +
81B ALA* 1.3 51.4 + - - +
83B LYS 2.8 2.9 + - - -
84B GLY 2.5 33.8 + - - -
85B TYR* 2.7 42.9 + - + +
87B MET* 3.4 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 4.4 0.9 - - - -
18A ARG* 2.5 34.3 + - - +
245A ALA 3.9 21.8 - - - +
246A VAL 4.1 10.5 - - - +
248A GLU 5.1 0.7 - - - +
249A GLY* 4.3 5.8 - - - +
77B ALA 3.5 5.5 + - - +
78B MET 4.0 8.1 - - - +
79B ILE 3.3 0.2 - - - -
80B ALA* 1.3 73.5 - - - +
82B LEU* 1.3 59.7 + - - +
83B LYS 3.0 1.2 + - - -
84B GLY* 3.4 4.6 + - - +
85B TYR 4.3 2.8 + - - -
106B TYR* 4.1 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 2.4 49.7 - - - +
18A ARG* 3.1 5.9 + - - -
248A GLU 4.0 11.9 - - - +
249A GLY* 4.9 2.2 - - - -
3B THR* 4.4 3.4 - - - +
4B LEU* 3.7 26.9 - - + -
5B GLU* 2.8 44.8 - - + +
8B ILE* 5.0 0.7 - - + -
78B MET* 3.6 28.5 + - + +
79B ILE* 2.9 24.0 + - + +
81B ALA* 1.3 77.2 - - - +
83B LYS* 1.3 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.7 6.3 - - - +
5B GLU* 3.3 29.1 + - - +
46B LEU* 3.0 35.2 - - - +
49B ILE* 4.4 9.6 - - + -
50B VAL* 3.2 16.9 - - + +
53B GLU* 4.8 7.5 + - - +
60B PRO* 3.0 27.8 - - + +
79B ILE* 2.8 29.6 - - + +
80B ALA 2.8 3.0 + - - -
82B LEU* 1.3 78.6 - - - +
84B GLY* 1.3 61.1 + - - +
85B TYR* 3.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.5 11.1 - - - +
60B PRO* 2.9 8.3 - - - +
61B GLY* 2.8 25.6 + - - -
80B ALA 2.5 11.0 + - - -
81B ALA* 3.4 8.4 + - - -
83B LYS* 1.3 74.8 - - - +
85B TYR* 1.3 57.1 + - - -
86B ARG* 5.0 1.8 - - - +
----------------------------------------------------------
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