Contacts of the helix formed by residues 50 - 58 (chain B) in PDB entry 1R9G
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B GLU* 2.6 19.7 + - - -
49B SER* 1.3 83.1 - - - +
51B THR* 1.3 61.3 + - - +
52B MSE 3.1 3.2 + - - -
53B ARG* 3.4 36.6 + - + +
54B ARG* 3.8 8.0 + - - +
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Residues in contact with THR 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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10B GLN* 2.8 28.9 + - + +
49B SER* 2.4 23.8 + - - +
50B THR* 1.3 78.9 - - - +
52B MSE 1.3 52.3 + - - +
53B ARG 3.3 0.2 - - - -
54B ARG* 3.1 29.9 - - + +
55B LEU* 2.8 34.2 - - + +
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Residues in contact with MSE 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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7B LEU* 4.1 28.3 - - + +
8B GLY* 5.5 1.3 - - - -
10B GLN 5.8 2.5 - - - +
44B LEU* 5.0 4.3 - - + -
45B PRO* 5.6 1.1 - - + -
46B GLY* 3.8 35.0 - - - +
47B GLY 4.8 1.6 - - - +
48B GLU* 3.0 25.2 + - - +
50B THR 3.1 1.0 - - - -
51B THR* 1.3 76.5 - - - +
53B ARG* 1.3 64.5 + - + +
55B LEU* 3.5 14.1 - - + +
56B ILE* 2.9 53.3 + - + +
81B GLY* 4.9 1.6 - - - -
84B ILE* 3.3 41.5 - - + -
95B PRO* 6.3 0.4 - - - -
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Residues in contact with ARG 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 GLU* 5.6 2.0 - - - +
50B THR* 3.4 30.7 + - + +
51B THR 3.3 0.2 - - - -
52B MSE 1.3 76.9 - - + +
54B ARG* 1.3 68.4 + - + +
56B ILE* 4.9 1.8 - - - -
57B ASP* 2.9 42.1 + - - +
93B ASP 5.3 3.0 + - - -
94B ASN* 3.1 34.3 + - - +
95B PRO* 3.4 31.5 - - - +
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Residues in contact with ARG 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 THR 4.0 10.3 - - - +
51B THR* 3.1 24.9 - - + +
53B ARG* 1.3 83.6 - - + +
55B LEU* 1.3 56.6 + - - +
56B ILE 2.9 0.3 + - - -
58B THR* 2.7 49.4 + - - +
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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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7B LEU* 4.4 13.7 - - + -
8B GLY* 3.3 36.3 - - - +
9B LEU 4.7 2.2 - - - +
30B VAL 5.1 0.2 - - - +
31B LYS* 5.0 9.0 - - - +
51B THR* 2.8 39.5 - - + +
52B MSE 3.5 21.5 - - + +
54B ARG* 1.3 76.9 - - - +
56B ILE* 1.3 62.0 + - + +
58B THR* 4.1 0.2 - - - -
59B TYR* 3.4 25.9 - - + +
61B PHE* 2.8 31.1 - - + -
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Residues in contact with ILE 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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7B LEU* 4.6 11.2 - - + -
52B MSE 2.9 53.4 - - + +
53B ARG* 3.4 2.2 + - - +
54B ARG 2.9 1.4 + - - -
55B LEU* 1.3 87.7 - - + +
57B ASP* 1.3 65.1 + - - +
60B GLN* 2.8 24.1 + - - -
61B PHE* 2.8 30.9 + - + -
62B MSE 3.9 30.3 + - + +
65B LEU* 5.1 1.3 - - + -
84B ILE* 4.6 16.8 - - + -
95B PRO* 4.3 14.1 - - + -
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Residues in contact with ASP 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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53B ARG* 2.9 41.0 + - - +
56B ILE* 1.3 79.1 - - - +
58B THR* 1.3 60.2 + - + +
59B TYR 3.1 8.3 + - - -
60B GLN* 3.6 15.2 + - - +
62B MSE 5.0 4.5 - - - +
95B PRO* 3.6 21.2 - - - +
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Residues in contact with THR 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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54B ARG* 2.7 39.0 + - - +
57B ASP* 1.3 79.0 - - + +
59B TYR* 1.3 84.6 + - - +
60B GLN* 5.8 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