Contacts of the helix formed by residues 70 - 95 (chain A) in PDB entry 1TBX
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 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY* 2.8 28.1 + - - +
55A PHE* 2.9 20.9 + - - +
56A VAL* 4.0 1.9 + - - -
57A LYS* 4.3 23.6 - - - +
69A LEU* 1.3 77.1 - - - +
71A GLU* 1.3 56.9 + - - +
72A LYS* 3.2 10.5 - - + +
73A GLY 3.0 21.1 - - - +
74A LYS* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 1.3 75.8 + - + +
72A LYS* 1.3 61.3 + - - +
74A LYS* 3.3 9.1 + - + +
75A LEU* 3.2 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 2.9 29.8 + - - +
54A GLY* 3.5 17.7 - - - +
55A PHE* 3.6 25.9 - - + -
70A THR* 3.2 4.3 - - + +
71A GLU* 1.3 76.1 - - - +
73A GLY* 1.3 64.9 + - - +
75A LEU* 3.7 7.6 + - - -
76A PHE* 3.2 24.4 + - - +
90B ILE* 3.7 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.6 2.5 - - - +
55A PHE* 3.4 34.3 - - - -
69A LEU* 4.0 9.4 - - - +
70A THR* 3.0 11.7 - - - +
72A LYS* 1.3 74.0 - - - +
74A LYS* 1.3 57.1 + - - +
76A PHE* 4.7 0.9 - - - -
77A ALA* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 4.1 12.5 - - + -
21A GLU* 3.2 41.4 + - - +
69A LEU* 3.9 26.0 + - + +
70A THR 2.7 21.5 + - - +
71A GLU* 3.6 7.9 - - + +
73A GLY* 1.3 73.5 - - - +
75A LEU* 1.3 65.0 + - + +
77A ALA* 4.0 1.4 - - - +
78A ILE* 3.3 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.2 30.7 + - - +
72A LYS* 4.0 6.7 - - - +
74A LYS* 1.3 79.9 - - + +
76A PHE* 1.3 63.6 + - - +
78A ILE* 3.5 23.7 + - + +
79A SER* 3.8 5.2 + - - -
86B THR* 4.4 8.4 - - + +
90B ILE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.7 20.6 - - + -
55A PHE* 4.0 13.7 - + + -
72A LYS 3.2 16.9 + - - +
73A GLY 3.9 1.3 - - - +
75A LEU* 1.3 77.3 - - - +
77A ALA* 1.3 67.0 + - - +
78A ILE 3.0 0.2 + - - -
79A SER* 3.0 16.7 + - - -
80A LEU* 3.0 37.7 + - + +
6B PHE* 3.7 28.9 - + - -
7B PHE* 3.6 15.9 - + - -
83B ALA 3.3 23.3 - - - -
86B THR* 3.9 9.0 - - + -
87B TYR* 3.6 33.7 - + + -
90B ILE* 3.6 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.6 34.6 - - + +
15A ALA* 4.2 2.9 - - - +
18A TYR* 3.7 21.3 - - + -
69A LEU* 4.2 5.2 - - + -
73A GLY 2.7 23.7 + - - +
74A LYS 4.0 4.0 - - - +
76A PHE* 1.3 72.2 - - - +
78A ILE* 1.3 55.6 + - - +
80A LEU* 3.3 5.7 + - - +
81A LYS* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.4 37.9 - - + +
74A LYS* 3.3 20.4 + - + +
75A LEU* 3.7 18.4 - - + +
76A PHE 3.0 1.2 + - - -
77A ALA* 1.3 75.4 - - - +
79A SER* 1.3 65.7 + - - +
81A LYS* 3.3 8.4 + - - +
82A THR* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 3.8 2.1 + - - -
76A PHE* 3.0 18.4 + - - -
78A ILE* 1.3 79.5 - - - +
80A LEU* 1.3 63.0 + - - +
82A THR* 2.8 24.6 - - - +
83A ALA* 3.3 10.2 + - - +
79B SER 4.5 0.5 - - - +
82B THR* 3.8 18.2 - - - -
83B ALA* 3.8 11.3 - - - +
86B THR* 3.5 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 5.2 4.9 - - + -
11A ALA* 3.8 35.9 - - + +
14A LEU* 3.7 33.4 - - + -
15A ALA* 4.3 8.5 - - + -
76A PHE* 3.0 40.9 + - + +
77A ALA* 3.7 6.3 - - - +
79A SER* 1.3 75.9 + - - +
81A LYS* 1.3 65.2 + - - +
83A ALA* 3.2 5.9 + - - +
84A ILE* 2.9 30.3 + - + +
6B PHE* 4.1 2.0 - - + -
7B PHE* 3.7 31.0 - - + -
83B ALA* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.6 35.6 + - + +
16A TYR* 4.1 24.6 - - - +
18A TYR* 5.1 15.9 - - + +
77A ALA 2.8 21.0 + - - +
78A ILE* 3.3 9.2 + - - +
80A LEU* 1.3 72.4 - - - +
82A THR* 1.3 54.0 + - - +
84A ILE* 3.9 3.6 - - - +
85A GLU* 2.7 63.9 + - + +
88A LYS* 3.6 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.2 7.4 + - + +
79A SER* 2.8 40.2 - - - +
81A LYS* 1.3 79.9 - - - +
83A ALA* 1.3 52.6 + - - +
85A GLU* 3.7 4.5 - - - +
86A THR* 2.6 42.0 + - - -
79B SER* 4.3 9.0 - - - +
82B THR* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.8 20.9 - - + -
79A SER 3.3 12.5 + - - +
80A LEU* 3.2 9.6 + - - +
82A THR* 1.3 76.2 - - - +
84A ILE* 1.3 55.6 + - - +
86A THR* 3.2 3.6 + - - -
87A TYR* 2.8 28.2 + - - +
76B PHE* 3.6 4.7 - - - -
79B SER* 3.5 30.0 - - - +
80B LEU* 4.3 7.0 - - + -
83B ALA* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.8 34.1 - - + -
11A ALA 3.9 13.2 - - - +
12A ILE* 4.1 13.2 - - + -
15A ALA* 3.4 30.7 - - + -
16A TYR* 4.5 4.9 - - + -
36A PHE* 3.5 35.0 - - + -
80A LEU* 2.9 24.1 + - + +
81A LYS* 4.0 4.7 - - - +
83A ALA* 1.3 71.2 - - - +
85A GLU* 1.3 57.8 - - - +
87A TYR* 3.1 4.1 - - - +
88A LYS* 2.8 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 2.7 42.8 + - + +
82A THR* 3.7 5.8 - - - +
84A ILE* 1.3 74.1 - - - +
86A THR* 1.3 58.6 + - - +
88A LYS* 2.7 41.1 + - - +
89A GLN* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 2.6 25.4 + - - -
83A ALA 3.2 4.9 + - - -
85A GLU* 1.3 75.4 - - - +
87A TYR* 1.3 60.1 + - - +
89A GLN* 3.2 8.0 + - + +
90A ILE* 2.9 43.5 + - + +
75B LEU* 4.1 20.0 - - + +
76B PHE* 4.4 1.8 - - + -
79B SER* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 5.1 1.1 - - + -
5A PRO* 3.6 35.4 - - + +
6A PHE* 3.8 19.6 - + - -
7A PHE* 3.8 20.0 - + + -
36A PHE* 4.5 21.3 - + - -
83A ALA 2.8 14.2 + - - +
84A ILE 3.1 9.9 - - - +
86A THR* 1.3 76.2 - - - +
88A LYS* 1.3 66.1 + - - +
90A ILE* 2.9 9.2 + - + +
91A LYS* 2.9 70.8 + - + +
55B PHE* 4.4 3.4 - + - -
76B PHE* 3.8 27.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.1 29.0 + - - -
35A GLU* 3.4 20.0 + - - +
36A PHE* 3.9 20.6 - - + -
81A LYS* 3.6 11.5 - - - +
84A ILE* 2.8 21.8 + - - +
85A GLU* 2.7 47.3 + - - +
87A TYR* 1.3 73.3 - - + +
89A GLN* 1.3 65.9 + - - +
91A LYS* 3.4 7.5 + - - +
92A LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 3.0 29.0 + - + +
86A THR* 3.2 10.0 + - + +
88A LYS* 1.3 82.0 - - - +
90A ILE* 1.3 59.2 + - + +
92A LYS* 3.7 35.7 + - - +
93A ARG* 3.0 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 2.9 23.7 + - + +
87A TYR* 2.9 14.3 + - + +
89A GLN* 1.3 75.8 - - + +
91A LYS* 1.3 70.6 + - - +
93A ARG* 3.2 7.1 + - - -
94A HIS* 3.1 28.8 + - + +
55B PHE* 4.3 9.6 - - + -
72B LYS* 3.5 42.8 - - + +
75B LEU* 4.1 19.7 - - + -
76B PHE* 3.3 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 5.3 3.0 - - - +
6A PHE* 5.1 0.8 - - - -
87A TYR* 2.9 64.4 + - + +
88A LYS* 3.7 8.7 - - - +
90A ILE* 1.3 72.9 - - - +
92A LYS* 1.3 66.1 + - - +
94A HIS* 2.8 14.0 + - - -
95A HIS* 3.2 21.5 + - + -
49B PHE* 5.5 0.2 - - - -
53B GLU* 4.0 25.1 + - - +
55B PHE* 4.0 8.8 - - - -
72B LYS* 3.8 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 2.9 20.1 + - - +
89A GLN* 3.7 34.7 + - - +
91A LYS* 1.3 70.9 - - - +
93A ARG* 1.3 69.2 + - + +
94A HIS 2.9 1.4 + - - -
95A HIS* 3.5 16.5 + - - +
96A HIS* 5.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 3.0 32.5 + - - +
90A ILE* 3.5 9.9 - - - +
91A LYS 3.1 0.2 + - - -
92A LYS* 1.3 77.1 - - + +
94A HIS* 1.3 82.3 + - + +
96A HIS* 3.9 16.1 + - - -
75B LEU* 4.6 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.1 26.2 + - + +
91A LYS 2.8 7.8 + - - +
93A ARG* 1.3 102.0 + - + +
95A HIS* 1.3 49.4 + - - -
96A HIS* 2.4 31.6 + - - +
72B LYS* 3.7 58.8 - - + +
75B LEU* 5.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.2 21.4 + - + -
92A LYS* 3.5 12.1 + - - +
94A HIS* 1.3 68.4 - - - +
96A HIS* 1.3 69.9 + - + +
----------------------------------------------------------
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