Contacts of the helix formed by residues 66 - 81 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A TYR* 3.5 22.4 - - + -
64A LEU 3.5 2.6 + - - +
65A LYS* 1.3 75.4 - - - +
67A PRO* 1.3 76.8 - - + +
68A ASP* 3.3 12.8 + - - +
69A THR* 2.9 23.4 + - - -
70A GLN* 2.9 18.1 + - - +
221A SER* 5.1 0.3 - - - -
222A SER* 5.2 8.3 + - - -
223A GLN* 3.2 28.8 + - - +
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.6 36.3 - - + +
65A LYS 4.0 0.2 - - - -
66A ASP* 1.3 90.5 - - + +
68A ASP* 1.3 61.8 + - - +
70A GLN* 3.5 19.2 - - + +
71A ALA* 3.0 20.1 + - - +
67B PRO* 3.5 39.4 - - + +
68B ASP* 4.2 11.2 - - - +
71B ALA* 3.8 17.5 - - + -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.1 12.2 + - - +
67A PRO* 1.3 81.7 - - - +
69A THR* 1.3 62.6 + - - +
71A ALA* 3.4 9.6 + - - +
72A VAL* 3.5 16.5 + - - +
220A ALA 4.7 6.6 - - - +
221A SER* 3.7 16.8 - - - -
222A SER* 5.3 2.0 - - - +
56B TYR* 4.0 16.7 + - - -
67B PRO* 4.1 9.3 - - - +
68B ASP* 4.3 18.7 - - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 4.1 14.1 - - + -
66A ASP* 2.9 14.6 + - - -
68A ASP* 1.3 78.2 - - - +
70A GLN* 1.3 62.3 + - - +
72A VAL* 3.5 4.5 + - - +
73A TYR* 3.2 45.5 + - + -
186A GLU* 4.6 3.8 - - - +
221A SER* 3.2 13.1 + - - -
223A GLN* 2.7 39.5 + - + +
224A LEU* 4.1 13.0 - - + -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR* 5.1 4.0 - - - +
57A GLN 5.2 2.8 + - - -
58A TRP* 5.3 4.1 - - - -
63A MET* 3.8 25.2 - - + +
65A LYS* 2.9 26.4 + - + +
66A ASP* 2.9 14.0 + - - +
67A PRO* 3.1 20.1 + - + +
69A THR* 1.3 74.4 - - - +
71A ALA* 1.3 55.3 + - - +
73A TYR* 3.1 2.6 + - - -
74A HIS* 2.8 33.9 + - - +
98A TRP* 3.4 48.2 + - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 3.0 12.1 + - - +
68A ASP* 3.6 9.0 - - - +
70A GLN* 1.3 74.0 - - - +
72A VAL* 1.3 62.5 + - + +
74A HIS* 3.0 9.1 + - - +
75A ASP* 2.7 34.7 + - - +
56B TYR* 4.0 18.8 - - + -
67B PRO* 3.9 20.0 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP 3.5 14.3 + - - +
69A THR 3.6 7.6 - - - +
71A ALA* 1.3 79.5 - - + +
73A TYR* 1.3 62.5 + - - +
75A ASP* 3.1 5.9 + - - +
76A MET* 3.0 25.5 + - + +
217A TYR* 3.8 33.6 - - + +
220A ALA* 3.5 36.6 - - + +
221A SER* 4.1 6.3 - - - +
224A LEU* 3.2 26.2 - - + -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.6 20.4 - - + -
69A THR* 3.2 31.5 + - + -
70A GLN 3.1 8.5 + - - +
72A VAL* 1.3 78.8 - - - +
74A HIS* 1.3 63.2 + - - +
76A MET* 3.3 19.2 + - + -
77A LEU* 2.9 34.7 + - + +
98A TRP* 3.6 18.6 - + + -
99A PHE* 3.8 16.2 - + + -
156A ILE* 4.7 1.8 - - + -
158A ILE* 3.5 26.7 - - + +
184A ILE* 3.5 34.7 - - + +
186A GLU* 2.4 32.6 + - - -
224A LEU* 3.5 8.7 - - + +
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN 2.8 17.0 + - - +
71A ALA* 3.3 12.6 - - - +
73A TYR* 1.3 73.7 - - - +
75A ASP* 1.3 61.9 + - - +
77A LEU 3.3 0.2 + - - -
78A TRP* 3.1 19.6 + - + +
98A TRP* 4.3 3.5 - - + -
102A LEU* 3.7 19.7 - - + -
106A MET* 3.3 34.0 - - + +
57B GLN* 3.1 44.3 + - - -
58B TRP* 3.5 29.6 - + - -
59B ARG* 3.3 27.4 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 2.7 33.0 + - - +
72A VAL* 3.7 6.7 - - - +
74A HIS* 1.3 77.4 + - - +
76A MET* 1.3 57.9 + - - +
78A TRP* 3.7 2.6 - - - +
79A GLU* 3.2 21.7 + - - +
217A TYR* 3.3 25.3 + - + +
24B TYR* 3.4 13.0 + - - -
56B TYR* 5.6 4.0 - - - -
57B GLN* 2.8 42.8 + - - +
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 3.0 23.2 + - + +
73A TYR* 3.8 18.6 - - + +
75A ASP* 1.3 76.8 - - - +
77A LEU* 1.3 61.2 + - + +
79A GLU* 4.0 1.0 - - - +
80A LEU* 3.1 30.7 + - - +
156A ILE* 4.1 21.3 - - + +
182A TYR* 4.0 26.7 - - + +
184A ILE* 3.8 30.7 - - + -
217A TYR* 3.7 32.1 + - + -
224A LEU* 4.8 0.4 - - + -
228A VAL* 4.0 20.4 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 2.9 24.8 + - + +
74A HIS 3.7 4.5 - - - +
76A MET* 1.3 77.1 - - + +
78A TRP* 1.3 56.0 + - - +
81A ARG* 2.8 30.0 + - - -
82A PRO* 3.2 17.7 - - + +
85A ILE* 3.6 17.5 - - + -
98A TRP* 5.1 2.2 - - + -
99A PHE* 4.2 30.7 - - + +
102A LEU* 4.2 27.1 - - + -
103A THR* 4.5 7.6 - - + -
106A MET* 3.9 11.4 - - - -
108A ILE* 4.0 4.0 - - + +
156A ILE* 3.6 28.3 - - + -
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Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS 3.1 16.4 + - - +
75A ASP 3.7 6.3 - - - +
77A LEU* 1.3 76.3 - - - +
79A GLU* 1.3 68.3 + - - +
81A ARG* 3.5 29.9 + - - +
106A MET* 3.8 43.9 - - + -
24B TYR* 5.4 6.6 - + - -
57B GLN* 3.8 20.6 - - - +
59B ARG* 3.1 48.2 - - + -
60B GLY* 3.5 20.4 - - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP 3.2 14.8 + - - +
76A MET* 4.2 3.4 - - - +
78A TRP* 1.3 84.8 - - - +
80A LEU* 1.3 65.7 + - + +
81A ARG* 3.7 3.3 + - - +
182A TYR* 4.6 4.7 + - - +
216A LEU* 4.4 2.5 - - - +
217A TYR* 2.5 30.0 + - - +
230A ARG* 5.4 1.3 + - - -
34B ARG* 3.0 36.6 + - - -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET 3.1 18.6 + - - +
79A GLU* 1.3 83.4 - - + +
81A ARG* 1.3 72.6 + - - +
82A PRO* 3.9 22.0 - - + -
154A PRO* 3.2 48.2 - - + +
155A LEU 4.1 4.5 - - - +
156A ILE* 4.0 16.8 - - + -
180A GLY* 4.3 14.4 - - - +
182A TYR* 3.9 23.6 - - + +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU 2.8 12.3 + - - -
78A TRP* 3.5 34.2 + - - +
79A GLU 4.4 3.1 - - - +
80A LEU* 1.3 82.0 - - - +
82A PRO* 1.3 69.6 - - - +
83A ARG* 4.7 2.3 - - - +
106A MET 3.4 20.6 + - - -
107A GLY 3.0 27.5 + - - -
108A ILE* 3.4 29.8 - - + +
154A PRO* 3.6 11.6 - - - +
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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
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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