Contacts of the helix formed by residues 66 - 81 (chain C) in PDB entry 2BM9
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 ASP 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C TYR* 3.7 17.5 - - + +
64C LEU 3.7 1.9 + - - +
65C LYS* 1.3 75.5 - - - +
67C PRO* 1.3 77.0 - - + +
68C ASP* 3.1 14.4 - - - +
69C THR* 2.8 33.4 + - - -
70C GLN* 2.9 10.9 + - - +
221C SER* 4.5 0.2 + - - -
222C SER* 4.3 9.4 + - - -
223C GLN* 3.0 29.4 + - - +
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Residues in contact with PRO 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.5 31.0 - - + +
66C ASP* 1.3 91.3 - - + +
68C ASP* 1.3 60.6 + - - +
70C GLN* 3.4 21.0 + - - +
71C ALA* 3.0 18.4 + - - +
67F PRO* 3.3 40.3 - - + +
68F ASP* 4.0 11.7 - - - +
71F ALA* 3.7 23.8 - - + -
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 2.9 12.8 + - - +
67C PRO* 1.3 78.8 - - - +
69C THR* 1.3 63.4 + - - +
71C ALA* 3.0 17.2 + - - +
72C VAL* 3.1 16.7 + - - +
220C ALA 4.3 6.7 - - - +
221C SER* 4.4 16.0 - - - +
222C SER* 5.1 3.8 + - - +
56F TYR* 4.0 15.9 + - - -
67F PRO* 4.1 9.6 - - - +
68F ASP* 5.4 4.0 - - - +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LYS* 4.0 11.2 - - + -
66C ASP* 2.8 20.0 + - - -
68C ASP* 1.3 74.4 - - - +
70C GLN* 1.3 54.9 + - - -
72C VAL* 3.2 3.8 + - - +
73C TYR* 3.0 44.4 + - + -
186C GLU* 4.4 1.3 - - - +
221C SER* 2.7 24.5 + - - -
223C GLN* 2.8 30.6 + - + +
224C LEU* 3.8 23.8 - - + -
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 4.8 5.5 - - - +
57C GLN 5.0 4.1 + - - +
58C TRP* 5.6 3.9 - - - -
63C MET* 3.5 33.2 - - + +
65C LYS* 3.2 24.2 + - + +
66C ASP 2.9 9.4 + - - +
67C PRO* 3.6 27.6 - - + +
69C THR* 1.3 72.8 - - - +
71C ALA* 1.3 60.4 + - - +
73C TYR* 3.9 1.1 - - - -
74C HIS* 3.2 22.7 + - - +
98C TRP* 3.5 41.4 + - + -
71F ALA* 6.2 0.2 - - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PRO 3.0 12.2 + - - +
68C ASP* 3.0 11.5 + - - +
70C GLN* 1.3 76.5 - - - +
72C VAL* 1.3 63.8 + - + +
74C HIS* 3.3 4.8 + - - +
75C ASP* 3.1 32.9 + - - +
56F TYR* 4.1 17.9 - - + -
67F PRO* 4.0 19.3 - - + -
70F GLN* 5.7 2.9 - - - +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP 3.1 10.2 + - - +
69C THR 3.2 2.0 + - - +
71C ALA* 1.3 76.3 - - + +
73C TYR* 1.3 62.8 + - - +
75C ASP* 3.5 5.7 + - - +
76C MET* 3.1 24.9 + - + +
217C TYR* 3.5 38.5 - - + +
220C ALA* 3.1 37.2 - - + +
221C SER* 3.6 13.0 - - - -
224C LEU* 3.3 25.8 - - + -
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LYS* 3.6 21.5 - - + -
69C THR* 3.0 27.5 + - + +
71C ALA 3.3 0.2 - - - -
72C VAL* 1.3 73.6 - - - +
74C HIS* 1.3 70.4 + - - +
76C MET* 3.7 17.7 - - + +
77C LEU* 3.1 29.4 + - + +
98C TRP* 3.5 25.4 - + + -
99C PHE* 3.9 15.7 - + + -
156C ILE* 4.8 1.8 - - + -
158C ILE* 3.2 35.6 - - + +
184C ILE* 3.6 23.1 - - + +
186C GLU* 2.7 34.3 + - - +
224C LEU* 3.6 15.5 - - + +
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Residues in contact with HIS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLN 3.2 19.2 + - - +
71C ALA* 3.5 6.7 - - - +
72C VAL 3.2 0.2 - - - -
73C TYR* 1.3 75.7 - - - +
75C ASP* 1.3 76.8 + - - +
77C LEU* 2.8 18.2 + - - +
78C TRP* 3.1 14.2 + - + +
98C TRP* 4.2 6.0 - - + -
102C LEU* 5.4 3.4 - - + -
106C MET* 3.2 27.9 - - + +
57F GLN* 3.1 34.8 + - + -
58F TRP* 3.3 43.6 - + + -
59F ARG 3.5 10.8 + - - -
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Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ALA* 3.1 19.4 + - - +
72C VAL* 3.9 3.4 - - - +
74C HIS* 1.3 78.9 + - - +
76C MET* 1.3 64.1 + - - +
78C TRP* 3.4 3.3 + - - +
79C GLU* 3.1 18.7 + - - +
217C TYR* 3.6 25.5 + - + +
24F TYR* 4.3 7.1 + - - +
27F PRO* 6.1 0.5 - - - +
50F TYR* 5.4 4.3 + - - -
55F PRO 4.6 9.7 - - - +
56F TYR* 5.8 3.3 - - - -
57F GLN* 3.5 45.3 + - - +
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C VAL* 3.1 21.5 + - + +
73C TYR* 3.7 19.3 - - + +
74C HIS 2.8 2.6 + - - -
75C ASP* 1.3 73.2 - - - +
77C LEU* 1.3 64.4 + - + +
79C GLU* 3.1 4.4 + - - +
80C LEU* 2.9 26.4 + - + +
156C ILE* 3.7 26.0 - - + -
182C TYR* 3.9 23.6 - - + -
184C ILE* 3.5 31.0 - - + -
217C TYR* 3.7 39.2 - - + -
224C LEU* 5.0 0.7 - - + -
228C VAL* 4.2 19.5 - - + -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 3.1 18.7 + - + +
74C HIS* 2.8 13.5 + - - +
76C MET* 1.3 75.8 - - + +
78C TRP* 1.3 57.0 + - - +
81C ARG* 2.6 36.0 + - - +
82C PRO* 3.8 20.4 - - + -
85C ILE* 4.0 7.6 - - + -
98C TRP* 5.2 1.8 - - + -
99C PHE* 4.0 26.0 - - + -
102C LEU* 4.3 20.0 - - + -
103C THR* 3.9 21.3 - - + +
106C MET* 3.7 15.7 - - + -
108C ILE* 4.1 0.5 - - - +
156C ILE* 3.6 27.1 - - + -
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Residues in contact with TRP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C HIS* 3.1 21.6 + - + -
75C ASP 3.7 7.2 - - - +
77C LEU* 1.3 78.5 - - - +
79C GLU* 1.3 60.7 + - + +
81C ARG* 4.1 22.7 - - - +
106C MET* 3.6 28.2 - - + -
24F TYR* 5.8 3.0 - + - -
57F GLN* 3.6 23.6 + - - +
59F ARG* 3.4 60.3 - - + -
60F GLY* 3.6 15.6 - - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASP 3.1 5.8 + - - +
76C MET* 3.6 4.4 - - - +
77C LEU 3.1 0.6 - - - -
78C TRP* 1.3 81.7 - - + +
80C LEU* 1.3 70.4 + - + +
81C ARG* 4.9 2.3 - - - +
182C TYR* 3.8 4.7 + - - -
216C LEU* 4.6 5.5 - - - +
217C TYR* 2.6 35.7 + - - +
34F ARG* 3.0 34.8 + - - -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C MET 2.9 16.1 + - - +
79C GLU* 1.3 80.9 - - + +
81C ARG* 1.3 74.4 + - - +
82C PRO* 4.1 9.0 - - + -
154C PRO* 3.6 36.6 - - + +
155C LEU 4.5 5.6 - - - +
156C ILE* 3.8 28.9 - - + -
180C GLY* 3.9 17.5 - - - +
182C TYR* 3.8 26.2 - - + -
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU 2.6 19.5 + - - +
78C TRP* 4.1 27.7 + - - +
79C GLU 4.9 2.0 - - - +
80C LEU* 1.3 77.7 - - - +
82C PRO* 1.3 69.5 - - - +
83C ARG* 3.5 5.9 + - - +
106C MET 3.4 17.8 + - - -
107C GLY* 3.1 32.5 + - - -
108C ILE* 3.4 31.4 - - + +
154C PRO* 3.5 11.4 - - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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