Contacts of the helix formed by residues 72 - 85 (chain A) in PDB entry 1UEP
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 HIS 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.4 33.7 + - + -
27A LEU* 4.3 12.2 - - + +
28A GLY 3.7 16.8 - - - +
29A GLY* 2.9 12.6 + - - +
30A ASP* 5.6 0.9 - - - -
36A ILE* 4.9 2.7 - - - -
71A THR* 1.3 69.6 - - - +
73A ARG* 1.3 68.0 + - - +
75A VAL* 2.9 21.8 + - + +
76A ILE* 3.1 41.8 + - + +
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Residues in contact with ARG 73 (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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71A THR* 3.4 9.0 + - - +
72A HIS* 1.3 81.0 + - - +
74A TYR* 1.3 60.9 + - - +
76A ILE* 3.2 15.6 + - + +
77A ASP* 3.0 31.3 + - - +
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Residues in contact with TYR 74 (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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65A ILE* 3.2 26.3 - - + +
66A PRO 4.3 4.8 + - - -
67A VAL* 4.5 9.0 - - + -
70A LYS* 3.3 56.8 - - + -
71A THR* 3.3 22.2 + - - +
72A HIS 3.2 0.2 - - - -
73A ARG* 1.3 78.6 - - - +
75A VAL* 1.3 60.7 + - - +
77A ASP* 3.3 7.7 + - - +
78A LEU* 3.2 46.3 + - + +
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Residues in contact with VAL 75 (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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24A PHE* 5.9 0.2 - - + -
26A ILE* 3.7 29.8 - - + -
36A ILE* 4.1 17.3 - - + -
59A LEU* 4.8 0.7 - - + -
62A VAL* 4.0 31.2 - - + -
67A VAL* 3.7 25.4 - - + -
71A THR 3.6 15.0 - - - +
72A HIS* 2.9 7.5 + - - +
74A TYR* 1.3 72.2 - - + +
76A ILE* 1.3 61.2 + - - +
77A ASP 3.1 0.2 - - - -
78A LEU* 2.9 8.4 + - - +
79A MET* 2.9 32.3 + - + +
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Residues in contact with ILE 76 (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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26A ILE* 3.6 26.2 - - + -
72A HIS* 3.1 47.8 + - + +
73A ARG* 3.5 16.8 - - + +
75A VAL* 1.3 74.4 - - - +
77A ASP* 1.3 62.8 + - - +
79A MET* 3.5 6.0 + - + +
80A HIS* 3.2 42.5 + - + +
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Residues in contact with ASP 77 (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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73A ARG* 3.0 20.4 + - - +
74A TYR* 3.4 11.2 - - - +
75A VAL 3.1 0.2 - - - -
76A ILE* 1.3 74.4 - - - +
78A LEU* 1.3 65.1 + - + +
80A HIS* 3.4 20.2 + - - +
81A HIS* 3.5 14.1 + - - +
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Residues in contact with LEU 78 (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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62A VAL* 3.9 29.4 - - + +
63A ASP* 5.2 4.3 - - + +
65A ILE* 3.6 37.0 - - + -
67A VAL* 4.7 4.7 - - + -
74A TYR* 3.2 59.6 + - + +
75A VAL* 2.9 10.8 + - - +
77A ASP* 1.3 73.7 - - + +
79A MET* 1.3 59.7 + - - +
81A HIS* 2.8 28.6 + - + +
82A ALA* 2.8 15.3 + - - +
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Residues in contact with MET 79 (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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22A PHE* 3.3 38.6 - - + -
24A PHE* 3.4 28.9 - - + -
26A ILE* 4.0 20.0 - - + -
62A VAL* 3.6 28.3 - - - -
75A VAL* 2.9 23.5 + - - +
76A ILE* 3.8 7.4 - - + +
78A LEU* 1.3 70.7 - - - +
80A HIS* 1.3 57.6 + - + +
82A ALA* 4.2 2.0 - - + -
83A ALA* 2.9 35.8 + - - +
88A VAL* 4.2 11.2 - - + -
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Residues in contact with HIS 80 (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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76A ILE* 3.2 34.7 + - + +
77A ASP* 3.5 15.5 - - - +
78A LEU 3.2 0.4 - - - -
79A MET* 1.3 77.4 - - + +
81A HIS* 1.3 55.8 + - - +
83A ALA* 4.6 3.4 - - - +
84A ARG* 3.2 46.3 + - - +
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Residues in contact with HIS 81 (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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63A ASP* 4.7 3.8 - - - +
77A ASP* 3.5 11.9 + - - +
78A LEU* 2.8 18.8 + - + +
80A HIS* 1.3 77.2 + - - +
82A ALA* 1.3 58.7 + - - +
83A ALA 3.2 1.8 - - - -
84A ARG* 2.8 36.4 + - - +
85A ASN* 3.1 16.4 + - - +
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Residues in contact with ALA 82 (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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22A PHE* 4.3 3.6 - - + -
62A VAL* 5.5 0.2 - - + -
63A ASP* 3.5 26.4 + - + +
78A LEU 2.8 17.3 + - - +
79A MET* 3.9 8.5 - - + +
81A HIS* 1.3 70.5 - - - +
83A ALA* 1.3 57.7 + - - +
85A ASN* 3.0 3.9 + - - +
86A GLY 2.9 17.7 + - - -
87A GLN 2.9 27.6 + - - +
88A VAL* 3.7 24.5 - - + -
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Residues in contact with ALA 83 (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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17A ARG* 3.1 44.3 + - - +
22A PHE* 4.0 11.5 - - + -
79A MET 2.9 17.5 + - - +
80A HIS* 5.1 4.3 - - - -
81A HIS 3.2 0.2 - - - -
82A ALA* 1.3 75.7 - - - +
84A ARG* 1.3 61.7 + - + +
86A GLY* 3.6 4.2 + - - -
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Residues in contact with ARG 84 (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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80A HIS* 3.2 42.3 + - - +
81A HIS* 2.8 21.9 + - - +
83A ALA* 1.3 74.0 - - + +
85A ASN* 1.3 64.4 + - - +
86A GLY* 3.0 5.9 + - - -
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Residues in contact with ASN 85 (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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63A ASP* 2.8 28.2 + - - +
81A HIS* 3.1 15.3 + - - +
82A ALA 3.0 10.3 + - - +
84A ARG* 1.3 75.1 - - - +
86A GLY* 1.3 56.3 + - - +
87A GLN* 2.9 34.4 + - + +
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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