Contacts of the helix formed by residues 53 - 65 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.5 24.1 - - + +
49A THR 2.8 12.7 + - - +
52A LEU* 1.3 77.9 - - - +
54A ILE* 1.3 56.9 + - - +
55A ASP* 3.3 19.6 + - - +
56A ARG* 3.3 24.6 + - + +
57A THR* 2.8 31.2 + - - -
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.4 29.8 + - + +
53A ASN* 1.3 71.1 + - - +
55A ASP* 1.3 64.0 + - + +
57A THR* 3.8 2.2 - - - -
58A GLU* 3.0 28.4 + - - +
79A LEU* 4.1 7.2 - - + -
82A ALA* 3.8 26.0 - - + -
83A TYR* 3.4 50.0 - - + +
86A ASN* 3.9 16.8 - - - +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.3 10.6 + - - +
54A ILE* 1.3 84.4 - - + +
56A ARG* 1.3 61.3 + - - +
58A GLU* 3.5 13.6 + - - +
59A MSE 3.3 34.3 + - - +
83A TYR* 4.6 3.4 - - - -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 13.5 - - + -
24A ASP* 3.1 40.6 + - - +
27A LEU* 3.5 22.5 - - + +
53A ASN* 3.3 27.8 + - - +
55A ASP* 1.3 76.7 - - - +
57A THR* 1.3 61.2 + - - +
59A MSE 3.4 24.0 + - - +
60A TYR* 3.1 37.4 + - - +
63A THR* 5.4 1.4 + - - -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 5.6 1.0 - - - +
27A LEU* 4.6 6.0 - - + +
46A PHE* 3.4 32.4 - - + -
49A THR* 3.0 38.8 + - - +
50A ILE* 3.8 14.4 - - + -
53A ASN 2.8 21.8 + - - -
54A ILE* 3.8 7.4 - - - -
56A ARG* 1.3 74.3 - - - +
58A GLU* 1.3 65.3 + - - +
60A TYR* 3.3 9.3 + - - +
61A TYR* 3.2 21.1 + - - +
79A LEU* 4.1 3.1 - - + -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE 3.0 18.2 + - - +
55A ASP* 3.5 14.0 - - - +
56A ARG 3.3 0.2 - - - -
57A THR* 1.3 75.7 - - - +
59A MSE 1.3 62.8 + - - +
61A TYR* 3.2 12.5 + - - +
62A TRP* 3.2 36.3 + - - +
79A LEU* 4.1 13.0 - - + +
83A TYR* 2.6 25.5 + - - +
91A LYS* 2.8 37.9 + - - +
94A LEU* 4.3 2.8 - - - +
95A PHE* 3.5 28.7 - - + -
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Residues in contact with MSE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 3.3 24.6 + - - +
56A ARG* 3.5 28.7 - - - +
57A THR 3.3 0.2 - - - -
58A GLU* 1.3 79.5 - - - +
60A TYR* 1.3 51.6 + - - +
62A TRP* 3.3 7.7 + - - +
63A THR* 2.8 50.0 + - + +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.6 56.5 - - + -
30A VAL* 3.8 19.6 - - + +
31A SER* 2.6 42.9 + - - -
34A ILE* 4.2 6.1 - - - +
46A PHE* 4.0 13.2 - + - -
56A ARG* 3.1 15.5 + - - +
57A THR 3.3 7.4 + - - +
59A MSE 1.3 72.6 - - - +
61A TYR* 1.3 61.3 + - - +
63A THR* 3.6 5.4 - - - -
64A ASN* 2.9 54.5 + - + +
65A VAL* 3.4 26.2 + - + +
75A LEU* 4.8 0.2 - - + -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.7 3.6 - - + -
57A THR 3.2 12.2 + - - +
58A GLU 3.2 8.5 + - - +
60A TYR* 1.3 79.4 - - - +
62A TRP* 1.3 81.0 + + - +
65A VAL* 3.4 26.3 + - + +
67A LYS* 2.9 47.8 + - + +
72A SER* 3.6 36.6 + - - -
75A LEU* 4.2 17.5 - - + -
76A ALA* 3.7 24.0 - - + +
79A LEU* 4.0 13.7 - - + -
95A PHE* 3.7 23.6 - + - -
98A GLU* 4.5 6.9 - - - +
102A LYS* 4.0 10.6 + - - -
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.2 46.6 + - + -
59A MSE 3.3 7.8 + - - +
61A TYR* 1.3 98.1 - + - +
63A THR* 1.3 64.7 + - + +
67A LYS* 3.3 23.9 + - + +
94A LEU* 4.1 24.6 - - + +
95A PHE* 3.5 29.1 - + - -
98A GLU* 4.5 15.7 - - + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 5.4 1.6 + - - -
59A MSE 2.8 38.6 + - + +
60A TYR* 3.6 3.8 + - - -
62A TRP* 1.3 82.1 - - + +
64A ASN* 1.3 79.3 + - - +
65A VAL 5.2 1.0 - - - +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 4.9 3.7 + - - +
60A TYR* 2.9 47.3 + - + +
63A THR* 1.3 93.7 + - - +
65A VAL* 1.3 61.1 + - - +
66A ASP* 3.6 1.9 + - - +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 5.3 5.2 - - + -
60A TYR* 3.4 25.4 + - + +
61A TYR* 3.4 33.2 + - + +
63A THR 5.2 0.7 - - - +
64A ASN* 1.3 77.3 - - - +
66A ASP* 1.3 75.1 + - - +
67A LYS* 2.9 27.2 + - + +
69A SER* 5.0 1.1 - - - +
71A ILE* 5.2 3.6 - - + -
72A SER* 4.1 18.4 - - - +
75A LEU* 3.6 33.4 - - + -
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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