Contacts of the helix formed by residues 68 - 89 (chain B) in PDB entry 1BT6
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 PHE 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 3.9 22.4 - - + -
80A ILE* 3.8 35.9 - - + -
83A ASN* 3.4 44.4 - - + +
11B MET 4.2 2.0 - - - -
12B MET* 4.0 19.1 - - + -
15B PHE* 3.4 51.4 - + + -
23B GLY 5.4 0.2 + - - -
67B GLY* 1.3 71.8 - - - -
69B GLN* 1.3 58.3 + - - +
71B PHE* 3.2 10.0 - + - +
72B PHE* 2.9 36.1 + + - +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.9 37.7 - - + +
67B GLY 3.0 1.2 + - - -
68B PHE* 1.3 81.0 - - - +
70B SER* 1.3 59.9 + - - +
72B PHE* 3.3 9.5 - - - +
73B SER* 3.0 23.7 + - - -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.2 38.7 + - - +
60B GLN* 5.3 5.4 + - - -
66B VAL* 4.7 7.0 - - - -
67B GLY 3.0 17.0 + - - -
69B GLN* 1.3 79.1 - - - +
71B PHE* 1.3 61.9 + - - +
73B SER* 2.9 18.7 + - - -
74B LEU* 2.9 12.8 + - - +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MET* 4.7 5.8 - - + -
11B MET* 3.4 29.8 - - + -
14B THR* 4.7 8.5 - - + -
15B PHE* 3.7 39.5 - + + -
25B LEU* 4.7 9.0 - - + -
30B LEU* 5.6 5.4 - - + -
33B LEU* 4.4 23.3 - - + -
58B LEU* 5.5 0.9 - - - -
66B VAL* 4.2 11.7 - - + +
67B GLY 3.0 12.5 + - - +
68B PHE* 3.2 21.5 - + - +
70B SER* 1.3 72.5 - - - +
72B PHE* 1.3 57.4 + + - +
74B LEU* 2.7 32.7 + - + +
75B ILE* 3.0 42.0 + - + +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.3 31.9 - + - -
75A ILE* 4.4 5.2 - - + -
76A ALA* 3.3 42.6 - - + -
79A THR* 3.8 26.0 - - + -
80A ILE* 4.4 9.9 - - + -
11B MET* 4.2 25.4 - - + -
68B PHE* 2.9 31.8 + + - +
69B GLN* 3.3 13.2 - - - +
71B PHE* 1.3 81.5 - + - +
73B SER* 1.3 58.6 + - - +
75B ILE* 4.5 4.7 - - + +
76B ALA* 2.8 29.4 + - + +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 5.3 5.4 - - - -
69B GLN* 3.0 13.7 + - - -
70B SER* 2.9 16.8 + - - -
72B PHE* 1.3 75.6 - - - +
74B LEU* 1.3 67.1 + - - +
76B ALA* 3.8 6.7 - - - +
77B GLY* 3.1 16.3 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.9 27.6 - - + -
33B LEU* 6.4 1.1 - - + -
34B MET* 4.2 15.0 - - - -
38B PHE* 5.9 0.7 - - + -
54B ILE* 4.0 32.3 - - + -
58B LEU* 4.2 16.1 - - + +
70B SER 2.9 8.6 + - - +
71B PHE* 2.7 23.1 + - + +
73B SER* 1.3 70.7 - - - +
75B ILE* 1.3 74.6 + - + +
77B GLY* 3.0 5.2 + - - -
78B LEU* 2.9 40.4 + - + +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A MET* 4.0 12.1 - - + -
8A MET* 4.3 5.6 - - + -
72A PHE* 4.7 4.3 - - + -
11B MET* 3.8 32.1 - - + -
38B PHE* 3.8 31.4 - - + -
71B PHE* 3.0 45.2 + - + +
72B PHE* 4.0 9.2 - - + +
74B LEU* 1.3 84.5 - - + +
76B ALA* 1.3 62.7 + - - +
78B LEU* 3.0 5.7 + - + +
79B THR* 2.8 39.3 + - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.5 33.5 - - + -
76A ALA* 6.3 0.4 - - + -
72B PHE* 2.8 26.3 + - + +
73B SER* 3.8 8.7 - - - +
75B ILE* 1.3 72.3 - - - +
77B GLY* 1.4 63.7 + - - +
79B THR* 3.4 0.7 + - - -
80B ILE* 2.9 37.3 + - + +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 3.1 8.5 + - - -
74B LEU* 3.0 7.5 + - - -
76B ALA* 1.4 76.7 - - - +
78B LEU* 1.3 64.3 + - - +
80B ILE* 4.0 6.4 - - - +
81B ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 4.1 12.8 - - + -
34B MET* 5.4 2.5 - - - -
38B PHE* 4.0 38.6 - - + -
41B PHE* 4.1 34.8 - - + -
74B LEU* 2.9 38.7 + - + +
75B ILE* 3.8 7.2 - - + +
77B GLY* 1.3 75.8 - - - +
79B THR* 1.3 57.8 + - - +
81B ALA* 3.3 5.2 + - + +
82B CYS* 3.0 32.9 + - - -
7C LEU* 4.4 11.1 - - + +
10C LEU* 5.5 4.9 - - + -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 3.7 43.5 - - + +
11A MET* 5.3 0.2 - - + -
12A MET* 4.5 6.6 - - + +
68A PHE* 4.0 13.7 - - + -
72A PHE* 3.8 27.9 - - + -
11B MET* 5.1 0.2 - - - +
75B ILE* 2.8 31.5 + - - +
76B ALA 3.8 2.0 - - - -
78B LEU* 1.3 70.8 - - - +
80B ILE* 1.3 61.8 + - - +
82B CYS* 3.8 3.5 - - - +
83B ASN* 2.9 26.3 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.0 26.9 - - + -
69A GLN* 4.1 41.5 - - + +
72A PHE* 4.5 12.8 - - + -
76B ALA* 2.9 37.0 + - + +
77B GLY* 4.1 4.7 - - - +
79B THR* 1.3 77.5 - - - +
81B ALA* 1.4 58.4 + - - +
83B ASN* 3.2 2.9 + - - +
84B ASP* 2.9 39.1 + - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY 3.0 18.0 + - - +
78B LEU* 3.6 4.9 - - + +
79B THR 3.3 0.2 - - - -
80B ILE* 1.4 73.2 - - - +
82B CYS* 1.3 66.3 + - - +
84B ASP* 3.0 19.3 + - - +
85B TYR* 3.1 14.0 + - - +
10C LEU* 3.4 28.6 - - + +
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Residues in contact with CYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 4.3 7.4 - - - -
12A MET* 3.8 21.1 - - + -
78B LEU 3.0 18.8 + - - +
79B THR* 3.9 2.9 - - - +
81B ALA* 1.3 75.2 - - - +
83B ASN* 1.4 58.4 + - - +
85B TYR* 3.5 0.3 + - - +
86B PHE* 2.9 29.3 + - - +
3C VAL* 4.3 5.4 - - + -
6C ILE* 3.7 30.9 - - + +
7C LEU* 2.9 42.8 - - - -
10C LEU* 4.2 1.5 - - - +
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 3.8 16.5 - - - -
16A HIS* 2.6 40.8 + - - -
68A PHE* 3.6 44.0 - - + +
79B THR 2.9 19.0 + - - +
80B ILE* 3.8 2.3 - - - +
81B ALA 3.1 0.4 - - - -
82B CYS* 1.4 74.3 - - - +
84B ASP* 1.3 76.5 + - - +
86B PHE* 3.1 2.1 + - - +
87B VAL* 2.9 27.2 + - - +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 2.9 26.7 + - - +
81B ALA* 3.0 12.5 + - - +
83B ASN* 1.3 87.1 - - - +
85B TYR* 1.3 61.0 + - - +
87B VAL* 3.3 10.9 + - - +
88B VAL* 3.4 20.3 + - - +
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA 3.1 12.0 + - - +
82B CYS 3.7 0.2 - - - +
84B ASP* 1.3 76.1 - - - +
86B PHE* 1.3 64.2 + - - +
88B VAL* 5.0 0.7 - - - -
89B HIS* 3.1 68.3 + + + +
90B MET* 4.6 9.0 - - + -
6C ILE* 3.6 40.2 - - + -
9C LYS* 3.4 37.9 - - + +
10C LEU* 4.4 16.4 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 4.0 11.9 - - - -
13A PHE* 3.5 33.7 - + - -
16A HIS* 3.9 38.6 - + + -
82B CYS 2.9 18.1 + - - +
83B ASN 3.5 3.1 - - - +
85B TYR* 1.3 77.6 - - - +
87B VAL* 1.3 56.6 + - + +
90B MET* 2.9 36.5 + - + -
91B LYS* 2.6 58.0 + - + -
2C THR* 4.5 8.1 - - - -
6C ILE* 3.8 11.4 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 3.4 36.1 - - + +
83B ASN* 2.9 24.7 + - - +
84B ASP* 3.3 5.6 + - - +
86B PHE* 1.3 80.9 - - + +
88B VAL* 1.3 67.0 + - + +
91B LYS* 2.6 53.7 + - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP 3.4 16.0 + - - +
85B TYR* 5.0 0.2 - - - -
86B PHE 3.3 0.2 - - - -
87B VAL* 1.3 85.6 - - + +
89B HIS* 1.3 90.4 + - + +
90B MET 3.7 0.2 - - - -
91B LYS 6.1 0.2 - - - -
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Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.1 67.5 + + + +
88B VAL* 1.3 96.1 - - + +
90B MET* 1.3 64.6 + - + +
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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