Contacts of the helix formed by residues 66 - 80 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B TYR* 3.7 19.1 - - + -
64B LEU 3.3 3.0 + - - +
65B LYS* 1.3 69.9 - - - +
67B PRO* 1.3 79.1 - - + +
68B ASP* 3.5 13.3 + - - +
69B THR* 2.9 28.1 + - - -
70B GLN* 3.1 14.8 + - - -
221B SER* 5.4 0.5 - - - -
222B SER* 4.5 9.0 + - - -
223B GLN* 2.9 29.3 + - - +
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Residues in contact with PRO 67 (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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67A PRO* 3.5 42.0 - - + +
68A ASP* 4.1 7.4 - - - +
71A ALA* 3.9 8.1 - - + -
56B TYR* 3.2 49.1 - - + +
66B ASP* 1.3 83.9 - - + -
68B ASP* 1.3 65.4 + - - +
70B GLN* 3.0 28.5 + - + +
71B ALA 3.1 9.9 + - - -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 4.2 15.2 + - - -
67A PRO* 4.4 12.3 - - - +
68A ASP* 4.3 17.4 - - - +
66B ASP* 3.0 12.3 + - - +
67B PRO* 1.3 76.8 - - - +
69B THR* 1.3 61.4 + - - +
71B ALA* 3.5 5.2 + - - +
72B VAL* 3.4 24.6 + - - +
220B ALA 4.1 5.8 - - - +
221B SER* 4.2 15.5 - - - -
222B SER 5.5 1.8 - - - +
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Residues in contact with THR 69 (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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65B LYS* 4.0 13.0 - - + -
66B ASP* 2.9 11.3 + - - -
68B ASP* 1.3 77.2 - - - +
70B GLN* 1.3 64.3 + - - +
72B VAL* 3.1 4.5 + - - +
73B TYR* 3.0 38.6 + - + -
186B GLU* 4.8 1.6 - - - +
221B SER* 3.5 14.2 + - - -
223B GLN* 2.8 42.9 + - + +
224B LEU* 3.6 21.8 - - + -
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Residues in contact with GLN 70 (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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56B TYR* 5.3 3.2 - - - +
58B TRP* 5.2 5.4 - - - -
63B MET* 3.9 24.1 - - + +
65B LYS* 3.3 16.2 + - + -
66B ASP* 3.1 28.9 + - - +
67B PRO* 3.0 18.7 + - - +
69B THR* 1.3 76.5 - - - +
71B ALA* 1.3 57.0 + - - +
73B TYR* 3.3 0.6 + - - -
74B HIS* 2.9 31.4 + - - +
98B TRP* 3.4 41.5 + - + -
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Residues in contact with ALA 71 (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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56A TYR* 4.3 18.8 - - + -
67A PRO* 3.8 27.1 - - + -
67B PRO 3.1 3.2 + - - +
68B ASP* 3.6 10.3 - - - +
69B THR 3.2 0.4 - - - -
70B GLN* 1.3 79.6 - - - +
72B VAL* 1.3 63.9 + - + +
74B HIS* 3.6 6.2 - - - +
75B ASP* 3.1 28.9 + - - +
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Residues in contact with VAL 72 (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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68B ASP 3.4 15.5 + - - +
69B THR 3.1 7.5 + - - +
71B ALA* 1.3 77.6 - - + +
73B TYR* 1.3 60.8 + - - +
75B ASP* 3.1 9.5 + - - +
76B MET* 2.9 32.5 + - + +
217B TYR* 3.9 37.1 - - + +
220B ALA* 3.5 34.5 - - + +
221B SER* 4.4 0.7 - - - -
224B LEU* 3.9 23.1 - - + -
228B VAL* 5.7 0.2 - - + -
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Residues in contact with TYR 73 (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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65B LYS* 3.7 15.5 - - + -
69B THR* 3.0 31.2 + - + +
72B VAL* 1.3 76.8 - - - +
74B HIS* 1.3 52.0 + - - +
76B MET* 3.1 21.1 + - + +
77B LEU* 2.7 44.0 + - + +
98B TRP* 3.7 24.0 - + + -
99B PHE* 3.8 20.9 - + + -
156B ILE* 4.6 2.9 - - + -
158B ILE* 3.2 30.3 - - + +
184B ILE* 3.6 24.3 - - + +
186B GLU* 2.6 32.2 + - - +
224B LEU* 3.6 17.3 - - + +
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Residues in contact with HIS 74 (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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57A GLN* 3.8 12.7 + - - -
58A TRP* 3.2 55.7 - + - -
59A ARG* 3.4 22.0 + - + -
70B GLN 2.9 18.3 + - - +
71B ALA* 3.6 8.7 - - - +
73B TYR* 1.3 75.2 - - - +
75B ASP* 1.3 72.1 + - - +
77B LEU* 3.1 3.4 + - - +
78B TRP* 2.9 33.5 + - + +
98B TRP* 4.2 2.5 - - + -
102B LEU* 4.2 21.6 - - + +
106B MET* 4.6 10.9 - - + +
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Residues in contact with ASP 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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24A TYR* 4.8 5.1 + - - -
50A TYR* 5.7 1.2 + - - -
55A PRO 4.9 7.3 - - - +
56A TYR* 5.7 3.8 - - - -
57A GLN* 2.9 43.6 + - - +
71B ALA* 3.1 18.3 + - - +
72B VAL* 3.5 9.5 - - - +
74B HIS* 1.3 81.2 - - - +
76B MET* 1.3 58.5 + - - +
78B TRP* 3.8 1.4 - - - +
79B GLU* 3.0 26.0 + - - +
217B TYR* 3.2 25.7 + - + +
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Residues in contact with MET 76 (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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72B VAL* 2.9 25.9 + - + +
73B TYR* 3.5 30.3 - - + +
75B ASP* 1.3 76.4 - - - +
77B LEU* 1.3 64.9 + - + +
79B GLU* 4.1 0.2 - - - +
80B LEU* 3.1 25.9 + - + +
156B ILE* 3.5 28.4 - - + +
182B TYR* 3.9 33.4 - - + -
184B ILE* 4.0 13.5 - - + -
217B TYR* 3.4 34.5 - - + -
224B LEU* 5.5 1.6 - - + -
228B VAL* 4.6 6.3 - - + -
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Residues in contact with LEU 77 (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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73B TYR* 2.7 29.4 + - + +
74B HIS* 3.7 2.2 - - - +
76B MET* 1.3 73.3 - - + +
78B TRP* 1.3 65.5 + - - +
80B LEU 3.2 1.0 - - - -
81B ARG* 3.1 29.1 + - - +
82B PRO* 3.7 19.0 - - + +
85B ILE* 4.0 15.0 - - + -
99B PHE* 4.0 20.4 - - + +
102B LEU* 4.1 26.9 - - + -
103B THR* 3.6 26.9 - - + +
106B MET* 3.6 13.0 - - + +
108B ILE* 4.4 1.3 - - + +
156B ILE* 4.0 20.4 - - + -
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Residues in contact with TRP 78 (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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24A TYR* 5.2 5.0 - + - -
57A GLN* 3.8 20.8 - - - +
59A ARG* 3.2 52.0 - - + -
60A GLY* 3.8 14.4 - - - +
74B HIS* 2.9 24.0 + - + +
75B ASP 3.8 3.4 - - - +
77B LEU* 1.3 78.0 - - - +
79B GLU* 1.3 65.1 + - + +
81B ARG* 3.6 37.6 + - - +
106B MET* 3.0 33.9 - - + +
108B ILE* 5.4 1.3 - - - -
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Residues in contact with GLU 79 (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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34A ARG* 3.3 33.1 + - - -
75B ASP 3.0 18.4 + - - +
76B MET 4.1 1.1 - - - +
77B LEU 3.2 0.2 - - - -
78B TRP* 1.3 82.6 - - + +
80B LEU* 1.3 65.3 + - - +
81B ARG* 3.6 4.6 + - - +
182B TYR* 4.7 1.9 + - - -
216B LEU* 4.9 2.7 - - - +
217B TYR* 2.8 24.6 + - - +
230B ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 80 (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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76B MET 3.1 12.6 + - - +
77B LEU 3.2 3.3 - - - +
79B GLU* 1.3 85.4 - - + +
81B ARG* 1.3 67.7 + - - +
82B PRO* 2.6 12.4 - - + +
154B PRO* 3.2 40.6 - - + -
155B LEU 5.1 1.8 - - - +
156B ILE* 4.4 15.3 - - + -
180B GLY 3.9 23.1 - - - +
181B ASP* 5.1 0.9 - - - -
182B TYR* 3.9 23.8 - - + -
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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
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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