Contacts of the helix formed by residues 71 - 83 (chain B) in PDB entry 1BJW
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 PRO 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PRO* 4.3 13.0 - - + -
69B GLY 3.4 5.7 - - - +
70B ILE* 1.3 85.2 - - + +
72B GLU* 1.3 80.2 + - - +
74B ARG* 3.1 11.4 + - + +
75B GLU* 3.0 32.1 + - + +
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Residues in contact with GLU 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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70B ILE* 3.7 15.5 - - + +
71B PRO* 1.3 93.7 - - - +
73B LEU* 1.3 57.8 + - - +
75B GLU* 3.4 15.4 + - - +
76B ALA* 3.0 26.9 + - - +
273B TRP* 3.6 28.5 - - + -
276B LEU* 3.7 22.5 - - + +
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Residues in contact with LEU 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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70B ILE* 3.1 19.1 + - + +
72B GLU* 1.3 76.8 - - - +
74B ARG* 1.3 60.1 + - - +
76B ALA* 3.2 1.1 + - + -
77B LEU* 2.8 35.7 + - + +
96B VAL* 3.6 34.8 - - + -
243B ILE* 4.9 1.3 - - + -
245B TYR* 5.5 0.7 - - + -
272B GLN* 3.7 36.1 - - + +
275B THR* 4.3 12.6 - - + -
276B LEU* 4.0 22.0 - - + +
279B LEU* 3.5 28.9 - - + -
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Residues in contact with ARG 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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68B ALA* 3.4 41.6 + - - +
69B GLY 3.7 13.4 + - - -
70B ILE 3.1 10.1 + - - +
71B PRO* 3.1 13.4 + - + +
73B LEU* 1.3 76.5 - - - +
75B GLU* 1.3 62.2 + - - +
77B LEU* 3.4 0.6 + - - -
78B ALA* 3.0 22.0 + - - +
91B PRO* 3.4 20.0 + - + +
92B GLU* 3.2 29.9 + - - +
94B THR* 2.8 49.9 + - + +
96B VAL* 4.6 4.7 - - + -
253B ILE* 4.4 4.2 - - - +
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Residues in contact with GLU 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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71B PRO* 3.0 21.8 + - + +
72B GLU* 3.6 15.1 - - - +
74B ARG* 1.3 76.8 - - - +
76B ALA* 1.3 63.9 + - - +
78B ALA* 3.3 1.9 + - - +
79B GLU* 3.2 30.3 + - + +
91B PRO* 4.3 23.8 - - + +
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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
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72B GLU 3.0 17.6 + - - +
73B LEU 3.2 4.5 + - - +
75B GLU* 1.3 77.0 - - - +
77B LEU* 1.3 56.3 + - - +
79B GLU* 3.3 10.1 + - - +
80B LYS* 3.0 28.6 + - - +
83B ARG* 5.2 0.2 + - - -
276B LEU* 3.7 20.6 - - + -
279B LEU* 4.1 23.6 - - + +
280B THR* 4.5 8.3 - - + -
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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 LEU* 2.8 22.5 + - + +
74B ARG 3.5 5.8 - - - +
76B ALA* 1.3 76.6 - - - +
78B ALA* 1.3 65.1 + - - +
80B LYS* 3.2 5.1 + - + +
81B PHE* 3.0 41.3 + - + -
94B THR* 3.5 23.1 - - + +
95B ILE 4.4 1.3 - - - +
96B VAL* 3.7 29.8 - - + -
245B TYR* 3.7 43.3 - - + -
279B LEU* 3.4 27.8 - - + -
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Residues in contact with ALA 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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74B ARG 3.0 13.6 + - - +
75B GLU 3.3 8.3 + - - +
77B LEU* 1.3 75.4 - - - +
79B GLU* 1.3 70.4 + - - +
81B PHE* 3.7 1.7 + - - +
82B ARG* 3.2 26.4 + - - +
89B VAL* 3.8 26.7 - - - +
90B THR 3.9 2.7 - - - +
91B PRO* 3.8 29.6 - - + -
94B THR* 3.9 2.8 + - - +
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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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75B GLU* 3.2 18.2 + - - +
76B ALA* 3.5 9.6 - - - +
77B LEU 3.2 0.4 - - - -
78B ALA* 1.3 81.8 - - - +
80B LYS* 1.3 55.6 + - - +
82B ARG* 3.1 37.6 + - - +
83B ARG* 2.8 53.8 + - + +
91B PRO* 5.7 1.2 - - - +
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Residues in contact with LYS 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 ALA 3.0 15.9 + - - +
77B LEU* 3.2 6.3 + - + +
79B GLU* 1.3 75.8 - - - +
81B PHE* 1.3 78.0 + - + +
83B ARG* 3.7 17.5 - - - +
84B GLU* 2.8 67.7 + - - +
85B ASN* 3.0 22.3 + - - -
207B GLU* 2.7 30.6 + - - -
208B HIS* 5.3 1.6 - - - -
230B ASN* 4.1 9.9 - - - +
245B TYR* 4.3 17.0 - - + -
279B LEU* 4.0 24.0 - - + -
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Residues in contact with PHE 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 LEU* 3.0 40.6 + - + +
80B LYS* 1.3 89.0 - - + +
82B ARG* 1.3 60.8 + - - +
85B ASN* 3.2 33.2 + - - +
87B LEU* 3.0 36.1 + - + -
89B VAL* 3.8 17.9 - - + -
94B THR* 4.0 9.9 - - - -
228B THR* 4.2 13.9 - - + -
230B ASN* 4.3 10.5 - - + -
245B TYR* 4.0 19.3 - + - -
246B ALA* 4.1 18.4 - - - -
247B CYS* 3.7 32.3 - - + -
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Residues in contact with ARG 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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78B ALA* 3.2 14.6 + - - +
79B GLU* 3.1 44.1 + - - +
81B PHE* 1.3 77.5 - - - +
83B ARG* 1.3 65.3 + - - +
86B GLY* 2.9 26.7 + - - -
87B LEU 3.2 21.7 + - - +
88B SER* 5.2 4.7 - - - +
89B VAL 5.4 6.2 + - - +
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Residues in contact with ARG 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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76B ALA 5.2 0.4 + - - -
79B GLU* 2.8 50.8 + - - +
80B LYS* 3.7 21.8 - - - +
82B ARG* 1.3 82.0 - - - +
84B GLU* 1.3 82.8 + - + +
86B GLY 4.8 0.3 + - - -
279B LEU* 4.2 13.1 + - - +
282B GLN* 3.2 44.2 - - - +
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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