Contacts of the helix formed by residues 45 - 56 (chain B) in PDB entry 5M73
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 THR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PRO* 4.7 1.3 - - - -
43B ASN 3.5 15.0 - - - +
44B PRO* 1.3 75.3 - - - +
46B ALA* 1.3 60.7 + - - +
47B THR* 3.5 10.1 + - - -
48B GLU* 2.9 40.8 + - - +
49B ILE* 2.8 32.1 + - - +
76B VAL* 5.0 4.7 - - + +
77B GLN* 3.9 34.1 - - + +
79B ARG 5.5 0.2 - - - -
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Residues in contact with ALA 46 (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 PRO* 4.3 6.4 - - + +
45B THR* 1.3 72.6 - - - +
47B THR* 1.3 64.5 + - - +
49B ILE* 3.2 4.5 + - - -
50B GLN* 2.9 23.6 + - - +
62B LEU* 3.4 23.6 - - + -
64B LYS* 5.9 0.2 - - - -
79B ARG 4.0 7.4 + - - +
80B GLY* 3.5 33.0 - - - -
81B ARG* 4.4 0.4 - - - -
82B VAL* 3.3 19.2 - - + +
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Residues in contact with THR 47 (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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45B THR* 3.1 10.3 + - - -
46B ALA* 1.3 79.1 - - - +
48B GLU* 1.3 64.6 + - + +
50B GLN* 3.5 5.5 + - - +
51B ASP* 3.0 35.5 + - - +
62B LEU* 4.1 22.2 - - + +
116B LYS* 6.3 0.9 - - - +
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Residues in contact with GLU 48 (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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42B GLU 5.3 0.3 - - - +
43B ASN 3.9 1.8 - - - +
44B PRO* 3.2 11.6 - - - +
45B THR* 2.9 43.2 + - - +
47B THR* 1.3 80.0 - - + +
49B ILE* 1.3 62.6 + - - +
51B ASP* 3.2 7.1 + - - +
52B VAL* 3.0 27.9 + - - +
112B ILE* 3.9 27.0 - - + +
115B LEU* 4.5 9.6 - - + +
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Residues in contact with ILE 49 (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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18B ILE* 3.6 30.7 - - + -
19B TYR 5.1 0.2 - - - -
20B PRO* 4.6 15.9 - - + -
23B LEU* 3.8 20.6 - - + -
44B PRO* 4.9 3.1 - - + -
45B THR 2.8 23.2 + - - +
46B ALA* 3.7 4.7 - - - +
48B GLU* 1.3 74.3 - - - +
50B GLN* 1.3 62.9 + - - +
52B VAL* 3.0 10.6 - - - +
53B CYS* 2.9 32.8 + - - -
82B VAL* 3.7 26.0 - - + -
108B ALA* 4.5 6.3 - - + -
112B ILE* 4.0 19.3 - - + -
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Residues in contact with GLN 50 (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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46B ALA 2.9 16.6 + - - +
47B THR* 3.9 6.8 + - - +
49B ILE* 1.3 75.0 - - - +
51B ASP* 1.3 82.9 + - - +
53B CYS* 2.9 2.6 + - - +
54B SER* 2.9 27.5 + - - +
60B VAL* 4.2 17.4 - - + +
61B PHE* 4.1 2.8 - - - -
62B LEU* 2.9 49.5 + - + +
82B VAL* 3.9 15.2 - - + +
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Residues in contact with ASP 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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47B THR* 3.0 29.9 + - - +
48B GLU* 3.2 6.2 + - - +
50B GLN* 1.3 91.4 + - - +
52B VAL* 1.3 63.8 + - - +
54B SER* 3.7 6.0 + - - -
55B ALA* 3.0 25.7 + - - +
115B LEU* 4.6 14.4 - - + +
116B LYS* 4.9 12.5 + - - -
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Residues in contact with VAL 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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48B GLU 3.0 9.0 + - - +
49B ILE* 3.0 24.5 - - - +
51B ASP* 1.3 77.6 - - - +
53B CYS* 1.3 71.0 + - - +
55B ALA* 3.2 7.6 + - - +
56B VAL* 3.0 22.9 + - - +
107B TYR* 4.6 8.1 - - + -
108B ALA* 4.2 19.1 - - + -
111B MET* 4.2 23.8 - - + -
112B ILE* 4.4 11.0 - - + -
115B LEU* 3.5 30.7 - - + -
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Residues in contact with CYS 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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49B ILE* 2.9 34.5 + - - +
50B GLN* 2.9 1.5 + - - +
52B VAL* 1.3 85.4 - - - +
54B SER* 1.3 63.1 + - - +
56B VAL* 3.0 21.6 + - - +
57B GLY 3.2 8.5 + - - -
58B LEU* 3.4 16.8 + - + +
60B VAL* 3.6 23.6 - - + -
82B VAL* 5.6 0.2 - - + -
84B VAL* 4.7 4.9 - - + -
98B PHE* 6.1 0.2 - - - -
104B VAL* 4.3 22.9 - - - -
107B TYR* 5.5 5.4 - - - -
108B ALA* 4.9 6.1 - - - -
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Residues in contact with SER 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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50B GLN* 2.9 16.7 + - - +
51B ASP* 3.7 10.0 + - - -
53B CYS* 1.3 75.5 - - - +
55B ALA* 1.3 65.3 + - - +
57B GLY* 3.2 13.0 + - - -
58B LEU 4.0 8.4 + - - +
60B VAL* 3.7 20.1 - - - +
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Residues in contact with ALA 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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51B ASP 3.0 18.6 + - - +
52B VAL* 3.5 7.6 - - - +
54B SER* 1.3 84.8 + - - +
56B VAL* 1.3 58.9 + - - +
57B GLY 3.7 0.2 + - - -
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Residues in contact with VAL 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 VAL 3.0 11.7 + - - +
53B CYS* 3.0 17.3 + - - +
55B ALA* 1.3 77.2 - - - +
57B GLY* 1.3 58.4 + - - +
58B LEU* 4.0 8.3 - - + -
95B LEU* 4.3 8.5 - - + +
97B GLN* 5.6 5.8 - - - +
98B PHE* 3.6 35.0 - - + -
107B TYR* 3.4 35.7 - - + +
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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