Contacts of the helix formed by residues 53 - 65 (chain B) in PDB entry 3URZ
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 ASN 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.8 21.3 - - + +
49B THR 2.9 13.0 + - - +
50B ILE 3.4 0.4 + - - -
52B LEU* 1.3 77.4 - - - +
54B ILE* 1.3 61.6 + - - +
55B ASP* 3.2 12.3 + - - +
56B ARG* 3.1 28.7 + - + +
57B THR* 2.9 25.6 + - - -
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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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50B ILE* 3.3 23.5 + - + +
53B ASN* 1.3 72.5 + - - +
55B ASP* 1.3 60.2 + - + +
57B THR* 3.4 4.9 + - - -
58B GLU* 2.8 28.2 + - - +
79B LEU* 4.0 9.0 - - + +
82B ALA* 3.6 30.1 - - + -
83B TYR* 3.5 39.9 - - + -
86B ASN* 3.8 13.5 - - - +
300B PG4 3.5 33.4 - - - -
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Residues in contact with ASP 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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53B ASN* 3.2 8.8 + - - +
54B ILE* 1.3 80.3 - - + +
56B ARG* 1.3 64.5 + - - +
58B GLU* 3.5 10.4 + - - +
59B MSE 3.1 35.5 + - - +
83B TYR* 4.2 7.6 - - - +
91B LYS* 6.1 0.3 - - - -
300B PG4 4.9 22.8 + - - +
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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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23B VAL* 3.8 23.8 - - + +
24B ASP* 5.4 9.9 - - - +
27B LEU* 3.9 25.4 - - + +
53B ASN* 3.1 33.1 + - + +
55B ASP* 1.3 73.8 - - - +
57B THR* 1.3 66.2 + - - +
59B MSE 3.2 30.3 + - - +
60B TYR* 3.0 38.1 + - - +
63B THR* 5.3 1.8 + - - -
64B ASN* 5.9 0.4 + - - -
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Residues in contact with THR 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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23B VAL* 5.7 0.9 - - - +
27B LEU* 4.7 4.8 - - + +
46B PHE* 3.2 36.5 - - + -
49B THR* 3.2 34.6 + - - +
50B ILE* 3.6 20.4 - - + -
53B ASN 2.9 14.8 + - - -
54B ILE 3.6 8.3 - - - -
56B ARG* 1.3 77.0 - - - +
58B GLU* 1.3 61.5 + - - +
60B TYR* 3.2 9.9 + - - +
61B TYR* 3.1 20.4 + - - +
79B LEU* 4.0 2.7 - - + -
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Residues in contact with GLU 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 ILE 2.8 17.9 + - - +
55B ASP* 3.7 11.9 - - - +
57B THR* 1.3 75.7 - - - +
59B MSE 1.3 63.1 + - - +
61B TYR* 3.1 12.3 + - - +
62B TRP* 3.0 45.8 + - + +
79B LEU* 4.0 17.2 - - + +
83B TYR* 2.4 30.0 + - - +
91B LYS* 2.8 33.3 + - - +
94B LEU* 4.2 2.1 - - - +
95B PHE* 3.6 21.4 - - + -
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Residues in contact with MSE 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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55B ASP* 3.1 34.2 + - - +
56B ARG* 3.3 34.5 - - - +
58B GLU* 1.3 75.1 - - - +
60B TYR* 1.3 57.0 + - - +
62B TRP* 3.3 9.1 + - - +
63B THR* 2.9 45.9 + - + +
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Residues in contact with TYR 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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27B LEU* 3.9 39.7 - - + -
30B VAL* 3.6 24.0 - - + +
31B SER* 2.7 39.0 + - - -
34B ILE* 4.2 6.4 - - - +
46B PHE* 3.9 17.7 - + - -
56B ARG* 3.0 21.6 + - - +
57B THR 3.2 8.0 + - - +
59B MSE 1.3 72.7 - - - +
61B TYR* 1.3 63.3 + - - +
63B THR* 3.8 5.2 - - - -
64B ASN* 2.8 61.4 + - + +
65B VAL* 3.5 21.9 + - + +
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Residues in contact with TYR 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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46B PHE* 4.5 3.4 - - + -
57B THR 3.1 7.4 + - - +
58B GLU 3.1 8.7 + - - +
60B TYR* 1.3 80.1 - - - +
62B TRP* 1.3 80.5 + + - +
65B VAL* 3.4 24.4 + - + +
67B LYS* 2.9 50.1 + - + +
72B SER* 3.6 25.4 - - - -
75B LEU* 4.2 17.0 - - + -
76B ALA* 3.8 17.1 - - + +
79B LEU* 3.8 20.2 - - + -
95B PHE* 3.6 23.8 - + - -
98B GLU* 4.5 8.6 - - + +
102B LYS* 3.7 21.1 + - - -
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Residues in contact with TRP 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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58B GLU* 3.0 50.4 + - + +
59B MSE 3.8 8.1 - - - +
60B TYR 3.3 0.2 - - - -
61B TYR* 1.3 94.1 - + - +
63B THR* 1.3 64.1 + - + +
67B LYS* 3.2 24.9 + - - +
94B LEU* 4.2 21.8 - - + -
95B PHE* 3.7 19.5 - + - -
98B GLU* 3.9 25.6 - - + -
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Residues in contact with THR 63 (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* 5.3 1.4 + - - -
59B MSE 2.9 32.5 + - + +
60B TYR* 3.7 2.1 + - - -
62B TRP* 1.3 82.6 - - + +
64B ASN* 1.3 77.7 + - - +
65B VAL 3.9 0.7 - - - -
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Residues in contact with ASN 64 (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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31B SER* 5.0 3.8 + - - +
56B ARG* 6.0 0.3 + - - -
60B TYR* 2.8 53.6 + - + +
63B THR* 1.3 102.6 + - - +
65B VAL* 1.3 61.4 + - - +
66B ASP 3.7 2.1 + - - -
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Residues in contact with VAL 65 (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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34B ILE* 5.3 4.7 - - + -
60B TYR* 3.5 31.0 - - + +
61B TYR* 3.4 33.0 + - + +
63B THR 5.4 0.3 - - - -
64B ASN* 1.3 76.5 - - - +
66B ASP* 1.3 75.3 - - - +
67B LYS* 2.9 26.0 + - + +
69B SER* 4.6 2.0 - - - +
71B ILE* 4.7 4.5 - - + -
72B SER* 4.0 24.5 - - - +
75B LEU* 3.6 21.8 - - + -
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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