Contacts of the helix formed by residues 66 - 81 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F TYR* 3.9 15.9 - - + -
64F LEU 3.8 0.4 + - - -
65F LYS* 1.3 75.4 - - - +
67F PRO* 1.3 78.4 - - + +
68F ASP* 3.7 12.5 + - - +
69F THR* 3.1 22.7 + - - -
70F GLN* 3.0 18.9 + - - +
221F SER* 4.9 1.2 - - - -
222F SER* 4.2 17.0 + - - -
223F GLN* 3.2 29.1 + - - +
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Residues in contact with PRO 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PRO* 3.3 39.4 - - + +
68C ASP* 4.1 10.8 - - - +
71C ALA* 4.0 11.9 - - + -
56F TYR* 3.3 42.6 - - + +
66F ASP* 1.3 90.7 - - + +
68F ASP* 1.3 58.5 + - - +
70F GLN* 3.2 20.1 - - - +
71F ALA 2.8 22.9 + - - -
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Residues in contact with ASP 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 4.2 10.9 + - - -
67C PRO* 4.0 17.0 - - - +
68C ASP* 5.4 4.3 - - - +
66F ASP* 3.2 13.4 - - - +
67F PRO* 1.3 76.2 - - - +
69F THR* 1.3 65.6 + - - +
71F ALA* 3.0 9.6 + - - +
72F VAL* 3.0 25.6 + - - +
220F ALA 4.3 7.3 - - - +
221F SER* 3.9 16.6 - - - -
222F SER 5.3 1.3 - - - +
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Residues in contact with THR 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F LYS* 3.5 20.0 - - + -
66F ASP* 3.1 11.1 + - - -
68F ASP* 1.3 79.3 - - - +
70F GLN* 1.3 60.1 + - - +
72F VAL* 3.3 2.1 + - - +
73F TYR* 3.0 50.9 + - + -
186F GLU* 4.8 0.7 - - - +
221F SER* 2.9 23.0 + - - -
223F GLN* 2.7 32.2 + - + +
224F LEU* 3.9 9.5 - - + +
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Residues in contact with GLN 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ALA* 5.7 3.1 - - - +
56F TYR* 5.2 3.6 - - - +
57F GLN 5.6 0.8 + - - -
63F MET* 3.1 35.2 - - + +
65F LYS* 3.0 26.4 + - + +
66F ASP 3.0 9.6 + - - +
67F PRO* 3.2 19.4 - - - +
68F ASP 3.1 0.2 - - - -
69F THR* 1.3 75.7 - - - +
71F ALA* 1.3 65.6 + - - +
72F VAL 3.1 0.2 + - - -
73F TYR* 3.2 1.1 + - - -
74F HIS* 2.9 24.4 + - - +
98F TRP* 3.4 43.7 - - + -
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 4.6 14.4 - - + -
67C PRO* 3.7 22.9 - - + -
70C GLN* 6.2 0.4 - - - +
67F PRO 2.8 13.5 + - - +
68F ASP* 3.0 10.7 + - - +
70F GLN* 1.3 77.2 - - - +
72F VAL* 1.3 63.8 + - + +
74F HIS* 3.6 6.2 + - - +
75F ASP* 3.2 30.2 + - - +
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ASP 3.0 13.4 + - - +
69F THR 3.6 1.8 - - - +
71F ALA* 1.3 73.3 - - + +
73F TYR* 1.3 67.2 + - - +
75F ASP* 2.9 20.5 + - - +
76F MET* 2.9 19.5 + - + +
217F TYR* 3.8 32.0 - - + +
220F ALA* 3.7 36.3 - - + +
221F SER* 4.1 0.4 - - - -
224F LEU* 3.3 35.7 - - + -
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Residues in contact with TYR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F LYS* 3.8 10.5 - - + -
69F THR* 3.0 39.7 + - + +
72F VAL* 1.3 79.4 - - - +
74F HIS* 1.3 58.1 + - - +
76F MET* 3.7 17.9 - - + +
77F LEU* 2.9 38.7 + - + +
98F TRP* 3.6 23.8 - + + -
99F PHE* 3.8 20.0 - + + -
156F ILE* 4.9 2.2 - - + -
158F ILE* 3.6 29.6 - - + +
184F ILE* 3.8 24.9 - - + +
186F GLU* 2.4 30.9 + - - +
224F LEU* 3.4 19.3 - - + +
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Residues in contact with HIS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 3.4 39.9 + - + +
58C TRP* 3.5 36.7 - + + -
59C ARG* 3.1 19.3 + - - +
70F GLN 2.9 17.0 + - - +
71F ALA* 3.6 6.7 + - - +
73F TYR* 1.3 74.0 - - - +
75F ASP* 1.3 81.6 + - - +
77F LEU* 3.4 0.7 + - - -
78F TRP* 3.1 24.0 + - + +
98F TRP* 4.1 2.1 - - + -
102F LEU* 4.6 13.2 - - + -
106F MET* 3.1 35.0 - - + +
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Residues in contact with ASP 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 4.9 4.3 + - - +
55C PRO 4.8 8.7 - - - +
56C TYR* 5.7 4.2 - - - -
57C GLN* 3.2 30.6 + - - +
71F ALA* 3.2 16.3 + - - +
72F VAL* 2.9 12.2 + - - +
74F HIS* 1.3 98.1 + - - +
76F MET* 1.3 64.6 + - - +
78F TRP* 3.1 11.4 + - - +
79F GLU* 3.2 10.9 + - - +
217F TYR* 3.6 25.2 + - + +
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Residues in contact with MET 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F VAL* 2.9 23.5 + - + +
73F TYR* 3.7 21.5 - - + +
75F ASP* 1.3 76.7 - - - +
77F LEU* 1.3 62.3 + - + +
79F GLU* 3.4 2.9 + - - +
80F LEU* 3.1 24.1 + - + +
156F ILE* 3.9 23.3 - - + -
182F TYR* 3.8 27.4 - - + -
184F ILE* 3.8 26.7 - - + -
217F TYR* 3.5 39.2 + - + -
224F LEU* 5.6 0.7 - - + -
228F VAL* 4.2 12.8 - - + -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F TYR* 2.9 32.1 + - + +
74F HIS 3.8 3.6 - - - +
76F MET* 1.3 77.1 - - + +
78F TRP* 1.3 58.9 + - - +
79F GLU 3.1 0.2 - - - -
81F ARG* 2.9 29.5 + - - -
82F PRO* 3.3 22.0 - - + +
85F ILE* 4.0 13.0 - - + -
99F PHE* 3.9 36.3 - - + +
102F LEU* 4.5 24.9 - - + -
103F THR* 3.7 24.9 - - + +
106F MET* 4.0 11.9 - - + -
108F ILE* 3.9 3.2 - - - +
156F ILE* 4.3 9.2 - - + -
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Residues in contact with TRP 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 5.5 3.4 - + - -
57C GLN* 3.9 21.1 - - - +
59C ARG* 3.2 56.8 - - + -
60C GLY* 3.4 18.4 - - - +
74F HIS* 3.1 20.9 + - - +
75F ASP* 3.5 5.8 - - - +
77F LEU* 1.3 75.5 - - - +
79F GLU* 1.3 61.2 + - + +
81F ARG* 4.3 24.0 + - - +
106F MET* 3.8 32.5 - - + -
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 2.8 41.0 + - - -
75F ASP 3.2 10.0 + - - +
76F MET* 3.7 6.9 - - - +
77F LEU 3.1 0.4 - - - -
78F TRP* 1.3 82.4 - - + +
80F LEU* 1.3 66.4 + - + +
81F ARG* 3.4 6.0 + - - +
182F TYR* 4.2 3.7 + - - -
216F LEU* 4.4 3.5 - - - +
217F TYR* 2.7 28.2 + - - +
230F ARG* 5.5 1.1 - - - -
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F MET 3.1 15.8 + - - +
79F GLU* 1.3 81.2 - - + +
81F ARG* 1.3 73.6 + - - +
82F PRO* 4.1 8.5 - - + -
154F PRO* 3.4 38.7 - - + +
155F LEU 4.6 2.5 - - - +
156F ILE* 3.8 19.3 - - + -
180F GLY 3.8 16.4 - - - +
182F TYR* 3.5 38.4 - - + -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU 2.9 10.1 + - - -
78F TRP* 4.3 26.1 + - - +
79F GLU 4.0 10.5 - - - +
80F LEU* 1.3 81.7 - - - +
82F PRO* 1.3 69.6 - - - +
83F ARG* 3.3 6.8 + - - +
106F MET 3.3 23.8 + - - -
107F GLY 4.1 8.9 + - - -
108F ILE* 3.3 43.0 - - + +
154F PRO* 3.7 8.8 - - - +
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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