Contacts of the helix formed by residues 4 - 16 (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 THR 4 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2O PRO* 3.5 7.2 + - + +
3O ILE* 1.3 73.8 - - - +
5O LYS* 1.3 66.0 + - - +
6O GLU* 3.0 19.8 - - + +
7O GLU* 2.7 42.3 + - + +
8O LYS* 2.9 18.9 + - - +
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Residues in contact with LYS 5 (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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659A U 5.6 2.0 - - - +
660A G 3.3 36.8 + - - +
661A G 4.0 18.3 + - - -
3O ILE 3.6 1.4 + - - -
4O THR* 1.3 72.3 - - - +
6O GLU* 1.3 78.0 + - - +
8O LYS* 3.0 11.0 + - - +
9O GLN* 2.9 37.1 + - - +
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Residues in contact with GLU 6 (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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4O THR* 3.0 21.2 - - - +
5O LYS* 1.3 86.8 + - - +
7O GLU* 1.3 67.5 + - - +
8O LYS 2.7 2.3 + - - -
9O GLN* 4.7 5.6 - - - +
10O LYS* 2.7 28.3 + - + +
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Residues in contact with GLU 7 (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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2O PRO 4.6 0.3 - - - +
3O ILE* 3.3 15.7 - - + -
4O THR* 2.7 53.0 + - + +
6O GLU* 1.3 72.8 - - - +
8O LYS* 1.3 62.5 + - - +
10O LYS* 3.5 7.6 - - - +
11O VAL* 3.3 23.9 + - - +
34O LEU* 4.3 4.1 - - + +
38O ARG* 2.6 26.5 + - - -
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Residues in contact with LYS 8 (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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658A G 3.1 28.4 + - - -
659A U 2.6 38.2 + - - +
3O ILE* 3.9 14.3 - - + +
4O THR 2.9 10.7 + - - +
5O LYS* 3.1 12.1 - - - +
6O GLU 2.7 3.4 + - - -
7O GLU* 1.3 69.6 - - - +
9O GLN* 1.3 70.7 + - - +
10O LYS 3.0 0.7 - - - -
11O VAL* 2.7 19.3 + - - +
12O ILE* 2.9 11.0 + - + +
31O LEU* 3.7 21.3 - - + +
34O LEU* 4.8 4.9 - - + -
35O ARG* 6.4 1.6 - - - +
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Residues in contact with GLN 9 (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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659A U 3.9 32.1 + - - +
660A G 5.1 3.6 + - - -
5O LYS* 2.9 31.8 + - - +
6O GLU* 4.0 3.7 - - - +
8O LYS* 1.3 76.5 - - - +
10O LYS* 1.3 64.2 + - - +
12O ILE* 2.7 25.2 + - + +
13O GLN* 2.8 29.1 + - + +
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Residues in contact with LYS 10 (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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6O GLU* 2.7 23.7 + - + +
7O GLU* 3.5 10.3 - - - +
8O LYS 2.8 1.2 + - - -
9O GLN* 1.3 71.2 - - - +
11O VAL* 1.3 65.2 + - + +
13O GLN* 3.6 8.3 + - - +
14O GLU* 2.9 57.9 + - - +
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Residues in contact with VAL 11 (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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7O GLU 3.3 14.6 - - - +
8O LYS 2.7 12.2 + - - +
10O LYS* 1.3 81.8 - - + +
12O ILE* 1.3 63.3 + - - +
14O GLU* 3.0 18.7 - - + +
15O PHE* 3.1 19.2 - - + +
30O ALA* 3.7 29.3 - - + +
31O LEU* 4.3 15.0 - - + +
34O LEU* 3.9 21.3 - - + -
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Residues in contact with ILE 12 (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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658A G 3.4 37.2 - - - +
659A U 3.9 5.6 - - - +
8O LYS* 2.9 18.5 + - + +
9O GLN* 2.7 26.4 + - + +
11O VAL* 1.3 71.6 - - - +
13O GLN* 1.3 72.6 + - + +
14O GLU 2.9 0.2 - - - -
15O PHE* 2.8 14.0 + - - +
16O ALA* 2.8 13.4 + - + +
21O ASP 4.0 13.9 - - - +
22O THR* 4.7 7.4 - - + -
27O VAL* 3.9 20.3 - - + +
31O LEU* 4.0 20.9 - - + -
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Residues in contact with GLN 13 (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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9O GLN* 2.8 26.4 + - + +
10O LYS* 4.1 6.7 + - - +
12O ILE* 1.3 77.4 - - + +
14O GLU* 1.3 63.3 + - - +
15O PHE 3.0 2.4 + - - -
16O ALA* 3.6 17.5 + - - +
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Residues in contact with GLU 14 (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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10O LYS* 2.9 44.1 + - - +
11O VAL* 3.0 13.7 - - + +
12O ILE 2.8 0.8 + - - -
13O GLN* 1.3 76.2 - - - +
15O PHE* 1.3 74.7 + - + -
84O LYS* 3.7 27.7 + - - -
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Residues in contact with PHE 15 (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* 3.1 31.4 + - + +
12O ILE 2.8 10.5 + - - +
13O GLN 4.0 0.2 - - - -
14O GLU* 1.3 91.0 - - + +
16O ALA* 1.3 70.5 - - - +
17O ARG* 3.2 4.7 + - - +
26O GLU* 4.4 22.2 - - + +
27O VAL* 4.1 20.4 - - - +
30O ALA* 3.4 20.0 - - + -
81O LEU* 4.6 6.1 - - + -
84O LYS* 3.6 40.7 + - + +
85O LEU* 3.2 40.8 - - + -
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Residues in contact with ALA 16 (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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12O ILE* 2.8 15.2 + - + +
13O GLN* 3.6 15.3 + - - +
15O PHE* 1.3 83.3 - - - +
17O ARG* 1.3 60.4 + - - +
18O PHE* 3.1 12.8 + - - +
20O GLY 5.3 1.3 - - - +
21O ASP* 3.3 35.4 - - + +
27O VAL* 3.7 7.6 - - - +
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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