Contacts of the helix formed by residues 74 - 86 (chain O) in PDB entry 1HNX
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 ASP 74 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70O LEU* 2.8 17.0 + - + +
73O GLU* 1.3 78.1 - - + +
75O PRO* 1.3 69.0 - - - +
76O GLU* 2.9 22.2 + - - +
77O ARG* 3.1 53.0 + - + +
78O TYR 3.3 8.1 + - - -
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Residues in contact with PRO 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O GLN* 3.3 28.1 - - - +
72O ARG 4.8 1.8 - - - +
73O GLU 3.7 6.7 - - - +
74O ASP* 1.3 86.4 - - - +
76O GLU* 1.3 65.8 + - + +
78O TYR* 3.1 19.6 - - + +
79O ARG* 3.3 40.5 + - - +
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Residues in contact with GLU 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ASP* 2.9 15.3 + - - +
75O PRO* 1.3 80.2 - - + +
77O ARG* 1.3 68.1 + - - +
78O TYR 3.0 1.0 + - - -
79O ARG* 3.1 37.5 + - - +
80O ALA* 3.2 13.4 + - + +
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Residues in contact with ARG 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A U 5.6 1.0 + - - -
752A G 4.3 14.1 + - - -
17O ARG* 2.6 53.3 - - - +
24O SER* 5.0 3.2 - - - -
25O THR* 5.1 3.8 + - - +
26O GLU* 2.7 43.1 + - - +
69O TYR* 5.9 3.6 - - - -
70O LEU* 3.8 21.9 - - + +
73O GLU* 5.5 4.9 - - - +
74O ASP* 3.1 36.0 + - - +
76O GLU* 1.3 78.5 - - + +
78O TYR* 1.3 67.5 + - - +
80O ALA* 3.1 11.1 + - - +
81O LEU* 2.8 20.5 + - - +
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Residues in contact with TYR 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O LEU* 3.9 26.8 - - + +
70O LEU* 3.0 28.0 - - + +
71O GLN* 3.3 49.3 - - + +
74O ASP 3.3 0.2 + - - -
75O PRO* 3.1 17.3 - - + +
76O GLU 3.0 0.4 + - - -
77O ARG* 1.3 78.1 - - - +
79O ARG* 1.3 86.1 + - + +
81O LEU* 2.7 12.3 + - - +
82O ILE* 3.1 44.6 + - + +
88O ARG* 3.8 24.3 + - - -
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Residues in contact with ARG 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O GLN* 5.8 1.8 - - - +
75O PRO* 3.3 41.8 + - - +
76O GLU* 3.1 33.8 + - - +
78O TYR* 1.3 91.4 - - + +
80O ALA* 1.3 65.5 + - - +
82O ILE* 3.2 4.1 + - - +
83O GLU* 2.9 29.4 + - + +
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Residues in contact with ALA 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O GLU* 3.2 11.1 + - + +
77O ARG* 3.1 14.5 + - - +
79O ARG* 1.3 77.8 - - - +
81O LEU* 1.3 58.7 + - - +
83O GLU* 4.1 6.7 - - - +
84O LYS* 3.0 32.3 + - - +
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PHE* 4.6 7.6 - - + -
25O THR 4.2 1.3 - - - +
26O GLU* 3.5 46.9 - - + +
29O VAL* 3.4 25.4 - - + -
67O LEU* 4.1 8.7 - - + -
70O LEU* 4.8 10.3 - - + -
77O ARG 2.8 10.7 + - - +
78O TYR* 2.7 15.7 + - - +
80O ALA* 1.3 70.4 - - - +
82O ILE* 1.3 56.7 + - + +
84O LYS* 3.2 7.6 - - - +
85O LEU* 2.7 69.2 + - + -
87O ILE* 4.9 0.2 - - + -
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Residues in contact with ILE 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O LEU* 4.6 13.7 - - + -
78O TYR* 3.1 55.8 + - + +
79O ARG* 3.8 6.3 - - - +
81O LEU* 1.3 73.1 - - - +
83O GLU* 1.3 73.3 + - - +
84O LYS 2.7 1.4 + - - -
85O LEU* 2.8 2.9 + - - -
86O GLY* 2.5 24.5 + - - +
87O ILE* 2.9 46.7 - - + +
88O ARG* 3.9 19.3 - - + +
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Residues in contact with GLU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O ARG 2.9 18.2 + - - +
80O ALA* 4.1 5.6 - - - +
82O ILE* 1.3 79.6 - - - +
84O LYS* 1.3 93.4 + - - +
86O GLY* 3.8 6.2 + - - -
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Residues in contact with LYS 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O GLU* 3.7 35.7 + - - -
15O PHE* 3.6 34.5 + - + +
80O ALA 3.0 20.9 + - - +
81O LEU* 3.2 5.2 - - - +
82O ILE 2.7 3.8 + - - -
83O GLU* 1.3 90.7 + - - +
85O LEU* 1.3 66.4 + - - +
86O GLY* 3.2 0.9 + - - -
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Residues in contact with LEU 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O VAL* 6.3 0.2 - - + -
15O PHE* 3.2 31.2 - - + -
29O VAL* 3.2 28.7 - - + +
30O ALA* 3.8 6.3 - - - +
33O THR* 3.3 29.4 - - + +
81O LEU* 2.7 45.1 + - + +
82O ILE 2.8 1.5 + - - +
84O LYS* 1.3 74.9 - - - +
86O GLY* 1.3 58.6 + - - +
87O ILE* 3.8 13.0 - - + -
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Residues in contact with GLY 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O THR* 6.4 0.4 - - - -
82O ILE 2.5 17.8 + - - -
83O GLU* 4.2 6.1 - - - -
84O LYS 3.2 3.0 + - - -
85O LEU* 1.3 74.9 - - - +
87O ILE* 1.3 62.0 + - - +
88O ARG 4.5 3.8 - - - +
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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