Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 4BSX
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B LEU* 5.2 4.0 - - - +
64B LEU* 2.9 15.2 - - + +
66B MSE 1.3 77.4 + - - +
68B ALA* 1.3 60.3 + - - +
69B VAL* 3.2 14.9 + - - +
70B ALA* 2.8 32.4 + - + +
71B ARG* 2.9 29.5 - - - +
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Residues in contact with ALA 68 (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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66B MSE 3.8 1.4 + - - -
67B ASP* 1.3 75.0 + - - +
69B VAL* 1.3 59.8 + - + +
71B ARG* 3.3 32.3 + - - +
72B LEU* 3.0 27.2 + - - +
87B GLU* 4.6 6.4 - - - +
90B PRO* 3.8 24.9 - - + +
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Residues in contact with VAL 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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8B LEU* 4.9 7.2 - - + -
42B LEU* 4.0 15.9 - - + -
67B ASP* 3.2 13.4 + - - +
68B ALA* 1.3 77.9 - - + +
70B ALA* 1.3 65.2 + - - +
72B LEU* 3.3 3.8 + - + +
73B VAL* 3.0 28.9 + - + +
90B PRO* 4.2 13.0 - - + -
91B ASP 3.9 21.1 - - - +
92B VAL* 4.2 17.5 - - + -
95B ALA* 3.9 31.2 - - + -
96B VAL* 6.3 0.2 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.1 16.3 - - + +
61B LEU* 3.9 9.5 - - + +
64B LEU* 3.4 44.0 - - + +
67B ASP* 2.8 23.3 + - + +
69B VAL* 1.3 77.7 - - - +
71B ARG* 1.3 56.1 + - - +
73B VAL* 3.6 1.6 + - - +
74B ALA* 2.9 28.6 + - - +
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Residues in contact with ARG 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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65B LYS* 2.7 54.9 + - + +
66B MSE 3.0 24.4 + - - +
67B ASP 2.9 9.3 - - - +
68B ALA* 3.4 28.2 - - - +
69B VAL 3.1 0.2 - - - -
70B ALA* 1.3 74.5 - - - +
72B LEU* 1.3 64.7 + - - +
74B ALA* 3.2 7.8 + - - +
75B ARG* 3.1 51.0 + - - +
87B GLU* 2.8 40.0 + - - +
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Residues in contact with LEU 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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8B LEU* 4.4 15.0 - - + -
68B ALA 3.0 12.8 + - - +
69B VAL* 3.3 7.6 + - - +
71B ARG* 1.3 76.3 - - - +
73B VAL* 1.3 57.3 + - - +
75B ARG* 3.3 9.5 + - - +
76B GLN* 2.8 69.6 + - + +
77B TRP* 4.6 4.7 - - + -
89B PRO* 4.4 13.9 - - + -
90B PRO* 3.6 23.3 - - + +
92B VAL* 4.0 26.9 - - + -
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Residues in contact with VAL 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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8B LEU* 4.1 31.9 - - + -
12B PHE* 4.5 1.1 - - + -
42B LEU* 4.0 20.0 - - + -
46B MSE 4.4 11.9 - - + -
49B LEU* 4.2 15.0 - - + -
61B LEU* 4.0 21.5 - - + -
69B VAL* 3.0 22.3 + - + +
70B ALA 3.8 3.8 - - - +
72B LEU* 1.3 72.7 - - - +
74B ALA* 1.3 65.9 + - - +
77B TRP* 3.0 32.6 + - + -
78B ALA* 3.1 6.4 + - - +
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Residues in contact with ALA 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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61B LEU* 3.8 21.0 - - + +
70B ALA 2.9 18.1 + - - +
71B ARG* 3.2 11.9 + - - +
73B VAL* 1.3 72.6 - - - +
75B ARG* 1.3 60.7 + - + +
78B ALA* 3.0 15.6 - - - +
79B GLY 2.9 24.3 + - - -
80B VAL* 3.1 23.4 + - + +
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Residues in contact with ARG 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 ARG* 3.1 39.5 + - - +
72B LEU* 3.8 8.3 - - - +
74B ALA* 1.3 78.9 - - + +
76B GLN* 1.3 70.2 + - + +
79B GLY* 3.4 18.4 + - - -
80B VAL* 3.3 23.0 + - + +
81B ASP* 5.1 0.2 - - - -
82B SER* 3.3 41.1 + - - +
83B THR 5.4 0.2 - - - +
84B GLU* 5.2 8.3 - - - +
87B GLU* 3.0 41.2 + - - +
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Residues in contact with GLN 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 LEU* 2.8 52.4 + - + +
75B ARG* 1.3 83.1 - - + +
77B TRP* 1.3 78.9 + - + +
79B GLY 4.8 0.7 - - - -
89B PRO* 5.7 4.6 - - - +
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Residues in contact with TRP 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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8B LEU* 3.8 35.2 - - + -
9B PRO* 4.2 26.4 - - + +
12B PHE* 3.3 52.0 - + + +
49B LEU* 3.8 17.5 - - + +
54B GLU* 4.9 5.4 - - - +
72B LEU* 4.6 9.6 - - + -
73B VAL* 3.0 21.8 + - + +
76B GLN* 1.3 104.0 - - + +
78B ALA* 1.3 61.9 + - - +
79B GLY 3.6 0.7 - - - -
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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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49B LEU* 4.0 16.8 - - + -
54B GLU* 4.4 5.4 - - - -
58B ARG* 2.9 44.1 + - + -
61B LEU* 3.8 17.9 - - + -
73B VAL 3.1 3.8 + - - +
74B ALA* 3.0 24.9 - - - +
77B TRP* 1.3 77.7 - - - +
79B GLY* 1.3 59.2 + - - +
80B VAL* 3.4 1.6 + - + -
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Residues in contact with GLY 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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58B ARG* 3.6 11.7 + - - -
74B ALA 2.9 3.0 + - - -
75B ARG 3.4 13.0 + - - -
76B GLN 4.8 0.2 - - - -
77B TRP 3.6 1.8 - - - +
78B ALA* 1.3 78.7 - - - +
80B VAL* 1.3 61.0 + - - +
81B ASP* 3.7 7.0 + - - +
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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