Contacts of the helix formed by residues 67 - 78 (chain H) in PDB entry 1U3H
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 TYR 67 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96F ASP* 3.2 18.9 + - - -
104F TYR* 3.6 27.4 - + - -
47H TYR* 3.9 11.2 - - + -
60H TYR* 3.9 12.8 - + - -
61H TYR* 2.9 49.7 + + - +
63H LYS 5.0 0.2 - - - -
64H GLN* 1.3 99.7 - - + +
68H LEU* 1.3 65.8 + - - +
69H GLU 3.2 2.5 - - - -
70H ARG* 2.8 20.1 + - - -
71H THR* 3.0 11.8 + - - -
5I ARG* 3.6 39.9 - - + +
6I PRO* 3.2 34.9 + - + +
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Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 4.1 6.7 - - + -
45H GLY 3.6 9.0 - - - +
46H GLU* 4.0 15.0 - - + +
47H TYR* 4.4 6.0 - - + +
61H TYR 3.2 7.4 + - - -
62H ASN* 3.1 49.0 + - + +
63H LYS 4.6 1.1 + - - +
64H GLN 4.0 0.2 - - - -
67H TYR* 1.3 76.3 - - - +
69H GLU* 1.3 63.3 + - - +
71H THR* 3.6 0.5 + - - -
72H ARG* 3.0 73.8 + - + +
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Residues in contact with GLU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LEU* 4.0 21.9 - - + +
56E LYS* 5.2 8.9 + - - -
63H LYS 5.6 0.8 + - - -
67H TYR 2.9 2.8 + - - -
68H LEU* 1.3 77.4 - - - +
70H ARG* 1.3 65.8 + - + +
72H ARG* 3.9 9.8 + - - +
73H ALA* 3.5 18.9 + - - +
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E TYR* 3.7 28.9 + - - -
48E SER* 5.3 1.4 + - - -
50E LEU* 4.6 19.0 - - + +
100F GLY* 3.0 30.3 + - - -
104F TYR* 3.4 28.5 - - - +
105F GLU* 4.6 2.4 - - - +
64H GLN 3.8 16.6 + - - +
67H TYR* 2.8 14.9 + - - +
69H GLU* 1.3 73.1 - - + +
71H THR* 1.3 65.2 + - - +
73H ALA* 3.0 16.9 + - - +
74H GLU* 3.2 14.4 + - - +
5I ARG* 3.6 26.9 - - - +
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H TYR* 3.3 25.0 - - + +
28H THR* 4.7 4.3 - - - +
40H PHE* 3.5 37.9 - - + -
47H TYR* 2.6 35.1 + - - +
67H TYR 3.0 9.5 + - - -
68H LEU 4.2 2.7 - - - -
70H ARG* 1.3 76.0 - - - +
72H ARG* 1.3 64.1 + - - +
74H GLU* 3.2 22.5 + - - +
5I ARG* 3.6 12.9 + - - +
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Residues in contact with ARG 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 4.0 19.1 - - + -
45H GLY* 2.7 35.1 + - - -
46H GLU* 4.7 0.8 + - - +
68H LEU* 3.0 53.6 + - + +
69H GLU* 4.0 10.3 - - - +
71H THR* 1.3 78.0 - - - +
73H ALA* 1.3 63.6 + - - +
75H LEU* 3.2 23.2 + - - +
76H ASP* 5.2 1.4 - - - +
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Residues in contact with ALA 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ASP* 6.0 0.4 - - - +
50E LEU* 4.2 16.2 - - + -
52E VAL* 3.7 25.8 - - + -
69H GLU 3.5 11.1 + - - +
70H ARG* 3.0 11.7 + - - +
72H ARG* 1.3 76.5 - - - +
74H GLU* 1.3 54.3 + - + +
75H LEU 3.0 2.7 - - - -
76H ASP* 2.6 32.6 + - - +
77H THR* 3.0 17.5 + - + +
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Residues in contact with GLU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ASN 5.4 0.2 - - - +
26H TYR* 2.7 34.3 + - + +
70H ARG 3.2 10.1 + - - +
71H THR* 3.2 19.7 + - - +
73H ALA* 1.3 77.4 - - - +
75H LEU* 1.3 59.6 + - - +
76H ASP 2.8 0.2 - - - -
77H THR* 3.4 13.0 + - - +
78H VAL* 2.7 38.4 + - + +
79H CYS* 3.0 7.5 + - - -
1I ALA 3.6 2.6 - - - +
2I SER* 3.3 5.5 - - - -
3I GLN* 2.8 42.1 + - - +
5I ARG* 3.8 13.1 + - - +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ILE* 3.6 40.1 - - + +
26H TYR* 3.8 15.8 - - + -
42H SER* 3.5 31.4 - - - -
71H THR 3.9 2.0 + - - -
72H ARG 3.2 16.6 + - - +
73H ALA 2.9 1.0 + - - -
74H GLU* 1.3 77.7 - - - +
76H ASP* 1.3 73.2 + - - +
79H CYS* 3.2 14.3 - - - +
80H ARG* 3.1 28.4 + - - +
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Residues in contact with ASP 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 4.8 16.7 - - + +
72H ARG 5.2 1.4 - - - +
73H ALA* 2.6 9.8 + - - +
75H LEU* 1.3 89.6 - - - +
77H THR* 1.3 63.6 + - + +
78H VAL 3.2 1.3 - - - -
80H ARG* 2.6 44.4 + - + +
81H TYR* 3.1 28.8 + - - +
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Residues in contact with THR 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASP* 3.7 29.9 + - + +
50E LEU* 6.2 1.1 - - + -
51E SER* 3.8 22.2 - - - +
52E VAL* 4.1 16.6 - - + -
99E ASN* 3.3 28.1 + - - +
73H ALA* 3.0 15.3 + - + +
74H GLU* 3.4 17.2 + - - +
76H ASP* 1.3 75.7 - - + +
78H VAL* 1.3 63.5 + - - +
81H TYR* 3.3 11.0 - - - +
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Residues in contact with VAL 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ASN* 4.5 6.7 - - + +
9G TYR* 3.9 9.9 - - + -
15H CYS* 4.7 1.6 - - - -
74H GLU* 2.7 38.7 + - + +
76H ASP 3.2 0.2 - - - -
77H THR* 1.3 84.1 - - - +
79H CYS* 1.3 59.5 + - - +
80H ARG 3.7 0.2 - - - -
82H ASN* 2.7 58.4 + - - +
0I GLY* 4.0 4.5 - - - +
1I ALA 3.8 24.0 - - - +
2I SER* 3.9 25.4 - - - +
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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