Contacts of the helix formed by residues 50 - 62 (chain B) in PDB entry 5BMU
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ASN 5.5 0.7 - - - -
49B THR* 1.3 80.4 - - - +
51B VAL* 1.3 79.1 + - - +
52B ASN* 3.5 9.6 + - - +
53B SER* 3.6 26.2 + - - +
54B ILE* 3.2 24.6 + - - +
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Residues in contact with VAL 51 (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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14B PRO* 4.6 23.1 - - + -
15B LEU 5.2 5.8 - - - +
17B ALA* 5.1 2.5 - - + -
50B ASP* 1.3 84.8 - - - +
52B ASN* 1.3 67.6 - - - +
54B ILE* 3.2 15.4 + - - +
55B LEU* 3.3 37.3 + - + +
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Residues in contact with ASN 52 (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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50B ASP* 3.5 9.0 + - - +
51B VAL* 1.3 79.4 - - - +
53B SER* 1.3 63.5 + - - +
55B LEU* 3.9 10.3 - - - +
56B ARG* 3.1 47.9 + - - +
82B LEU* 3.2 51.2 + - + +
83B GLU* 4.4 1.8 - - - +
85B SER* 5.3 0.2 + - - -
86B ALA* 3.4 18.8 - - - +
123B SER* 4.7 3.6 + - - -
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Residues in contact with SER 53 (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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48B PHE* 3.7 34.3 - - - -
49B THR 5.1 0.4 - - - -
50B ASP* 3.6 27.2 + - - +
51B VAL 3.3 0.6 - - - -
52B ASN* 1.3 78.6 - - - +
54B ILE* 1.3 57.2 + - - +
56B ARG* 3.3 7.6 + - - +
57B TYR* 2.9 30.4 + - - +
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Residues in contact with ILE 54 (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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6B LEU* 4.9 13.9 - - + -
17B ALA* 5.0 10.5 - - + +
38B ASN* 4.3 6.7 - - + +
39B ILE* 4.3 13.5 - - - +
40B LEU* 3.8 37.7 - - + -
48B PHE* 4.0 19.3 - - + +
50B ASP 3.2 28.0 - - - +
51B VAL* 3.2 7.9 + - - +
53B SER* 1.3 75.9 - - - +
55B LEU* 1.3 63.0 + - + +
57B TYR* 3.3 1.6 + - - +
58B LEU* 3.0 49.3 + - + +
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Residues in contact with LEU 55 (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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16B GLY 3.7 10.8 - - - +
17B ALA* 3.6 36.8 - - + +
20B ALA* 4.8 5.7 - - + +
51B VAL* 3.3 23.1 + - + +
52B ASN* 3.9 24.2 - - - +
54B ILE* 1.3 81.3 - - + +
56B ARG* 1.3 61.5 + - - +
58B LEU* 4.0 3.5 - - - +
59B ALA* 3.0 26.5 + - - +
82B LEU* 4.1 8.5 - - + -
119B LEU* 3.5 24.5 - - + +
122B LEU* 6.0 0.4 - - + -
123B SER* 4.0 28.9 - - - +
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Residues in contact with ARG 56 (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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52B ASN* 3.1 40.9 + - - +
53B SER* 3.3 6.5 + - - +
55B LEU* 1.3 79.6 - - - +
57B TYR* 1.3 59.5 + - - +
59B ALA* 3.7 1.4 - - - +
60B ARG* 2.8 53.0 + - - +
68B TYR* 3.4 22.5 - - + +
79B ASP* 3.1 49.5 + - - +
82B LEU* 4.2 18.3 - - + +
83B GLU* 4.5 13.1 + - - +
119B LEU* 3.9 8.1 - - + -
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Residues in contact with TYR 57 (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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4B LEU* 5.0 4.7 - - + -
40B LEU* 4.3 7.9 - - + -
42B VAL* 3.5 42.4 - - + +
48B PHE* 3.7 33.4 - + + -
53B SER 2.9 17.1 + - - +
54B ILE 3.3 3.8 + - - +
56B ARG* 1.3 76.8 - - - +
58B LEU* 1.3 61.9 + - + +
60B ARG* 3.2 11.5 + - + +
61B VAL* 2.9 54.1 + - + +
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Residues in contact with LEU 58 (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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4B LEU* 3.7 25.8 - - + -
17B ALA 4.7 4.5 - - - +
20B ALA* 4.7 10.3 - - + -
21B VAL* 3.9 30.7 - - + +
24B VAL* 4.3 12.3 - - + +
28B VAL* 5.1 1.3 - - + -
30B ILE* 3.5 28.9 - - + -
40B LEU* 4.5 9.0 - - + -
54B ILE* 3.0 39.0 + - + +
55B LEU* 4.1 3.1 - - - +
57B TYR* 1.3 78.1 - - + +
59B ALA* 1.3 56.8 + - - +
61B VAL* 4.2 3.3 - - + +
62B ALA* 3.0 35.3 + - - +
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Residues in contact with ALA 59 (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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20B ALA* 6.2 0.2 - - - +
24B VAL* 5.4 0.9 - - - +
55B LEU 3.0 18.8 + - - +
56B ARG 3.8 0.4 - - - +
58B LEU* 1.3 77.3 - - - +
60B ARG* 1.3 61.2 + - - +
62B ALA 4.1 13.6 - - - +
63B THR* 4.4 5.0 + - - +
65B ALA 5.5 0.2 - - - +
67B LEU* 4.1 22.0 + - + +
68B TYR* 3.6 24.4 + - + +
119B LEU* 3.3 32.1 - - + +
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Residues in contact with ARG 60 (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 ARG* 2.8 37.9 + - - +
57B TYR* 3.2 12.7 + - + +
59B ALA* 1.3 75.9 - - - +
61B VAL* 1.3 64.4 + - + +
63B THR* 3.4 21.1 - - - +
68B TYR* 3.5 36.7 + - + -
79B ASP* 4.8 5.7 + - - -
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Residues in contact with VAL 61 (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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4B LEU* 5.0 11.0 - - + -
28B VAL* 3.9 23.3 - - + +
57B TYR* 2.9 62.6 + - + +
58B LEU* 4.2 4.3 - - + +
60B ARG* 1.3 75.1 - - + +
62B ALA* 1.3 59.3 + - - +
63B THR* 3.1 10.8 + - - -
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Residues in contact with ALA 62 (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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24B VAL* 3.1 41.5 - - + -
27B ASP* 3.7 18.2 - - + +
28B VAL* 4.0 9.4 - - + -
58B LEU 3.0 10.7 + - - +
59B ALA* 4.1 7.4 - - - +
61B VAL* 1.3 73.2 - - - +
63B THR* 1.3 58.3 + - - +
64B THR* 3.1 3.6 - - - +
65B ALA* 2.8 26.2 + - - +
67B LEU 5.3 0.2 + - - -
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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