Contacts of the helix formed by residues 55 - 69 (chain G) in PDB entry 1HBX
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 55 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLU* 3.7 20.6 - - - +
42G ALA* 3.6 13.7 - - - -
53G ASN 3.5 13.1 + - - -
54G MET* 1.3 80.8 + - - +
56G TYR* 1.3 53.4 + - - +
57G ASP* 3.2 13.1 + - - +
58G LYS* 2.8 51.5 + - - +
59G LEU 2.6 31.4 + - - -
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.8 25.6 - - + -
38G ALA* 3.3 28.9 - - + -
39G GLU* 3.3 22.8 + - - +
42G ALA* 3.8 5.6 - - + +
55G ASN* 1.3 68.6 - - - +
57G ASP* 1.3 52.5 + - - +
58G LYS 2.7 8.1 + - - -
59G LEU* 4.2 13.9 - - + +
60G SER* 2.6 54.9 + - - +
80G PHE* 4.5 10.3 - + - -
82G TYR* 2.5 30.8 + + - -
-14W A 3.9 25.4 - - - -
-13W C 2.9 31.1 + - - -
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-11C C 3.8 24.9 + - + +
-10C C 5.8 0.5 - - - -
-9C T 5.3 0.5 - - - +
39G GLU* 4.5 2.2 + - - -
55G ASN* 3.2 12.0 + - - +
56G TYR* 1.3 79.3 - - - +
58G LYS* 1.3 62.4 + - + +
60G SER* 4.4 3.6 - - - -
61G ARG* 4.3 4.0 + - - +
64G ARG* 4.1 13.5 + - - +
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Residues in contact with LYS 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10C C 3.8 17.6 + - + -
-9C T 3.2 84.9 - - + +
-8C T 4.5 3.4 - - + -
53G ASN* 3.6 15.9 + - - +
54G MET* 3.6 11.0 - - + -
55G ASN* 2.8 32.3 + - - +
56G TYR 2.7 1.0 + - - -
57G ASP* 1.3 80.7 - - + +
59G LEU* 1.3 66.2 + - - +
60G SER 2.7 5.4 + - - -
61G ARG* 2.7 21.7 + - - +
62G ALA* 3.5 3.2 + - - +
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-8C T 5.0 0.2 - - - -
7G LEU* 4.2 15.7 - - + -
10G PHE* 6.3 0.2 - - + -
11G LEU* 5.6 4.0 - - + -
35G LEU* 4.6 8.3 - - + -
41G VAL* 4.4 11.0 - - + -
42G ALA* 3.4 30.5 - - + +
45G TRP* 3.3 31.6 - - + +
54G MET* 3.4 13.9 - - - -
55G ASN 2.6 17.5 + - - +
56G TYR* 4.3 13.7 - - + -
58G LYS* 1.3 71.9 - - - +
60G SER* 1.3 66.6 + - - +
62G ALA* 3.3 20.8 + - - +
63G LEU* 3.3 25.5 + - + +
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 2.6 46.4 + - - +
57G ASP 4.4 0.4 - - - -
58G LYS 2.7 2.0 + - - -
59G LEU* 1.3 76.8 - - - +
61G ARG* 1.3 53.4 + - - -
63G LEU* 2.8 32.9 + - - +
64G ARG* 2.8 46.0 + - - +
82G TYR* 4.0 9.7 + - - -
-13W C 4.6 5.2 - - - -
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Residues in contact with ARG 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10C C 4.6 1.3 - - - +
-9C T 4.0 28.0 - - + +
-8C T 5.3 0.4 - - + -
57G ASP 4.3 4.7 + - - +
58G LYS 2.7 15.5 + - - +
60G SER* 1.3 71.0 + - - +
62G ALA* 1.3 69.5 + - - +
64G ARG* 2.9 52.7 + - - +
65G TYR* 3.0 61.3 + - + +
-11W G 2.4 46.0 + - - +
-10W G 2.7 34.1 + - - -
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-8C T 4.1 33.0 - - + +
-7C C 4.5 14.1 - - + -
7G LEU* 3.9 17.9 - - + -
58G LYS 3.5 2.2 + - - -
59G LEU* 3.3 14.1 + - - +
60G SER 3.2 0.4 + - - -
61G ARG* 1.3 79.7 - - - +
63G LEU* 1.3 66.0 + - - +
65G TYR* 3.1 13.2 + - - +
66G TYR* 3.4 16.9 + - + -
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 3.4 26.9 - - + -
11G LEU* 4.4 9.9 - - + -
33G PHE* 5.9 0.2 - - + -
35G LEU* 4.4 4.7 - - + -
56G TYR* 5.2 0.2 - - + -
59G LEU* 3.5 29.4 - - + +
60G SER* 2.8 8.7 + - - +
62G ALA* 1.3 75.0 - - - +
64G ARG* 1.3 64.2 + - - +
66G TYR* 2.8 33.6 + - + +
67G TYR* 3.0 21.2 - - + -
72G ILE* 4.2 20.8 - - + +
82G TYR* 3.4 40.6 - - + +
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Residues in contact with ARG 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-11C C 4.3 1.0 - - - +
57G ASP* 4.1 13.1 + - - +
60G SER* 2.8 46.6 + - - +
61G ARG* 2.9 28.6 - - - +
63G LEU* 1.3 71.7 - - - +
65G TYR* 1.3 57.1 + - - +
67G TYR* 2.8 43.7 - - + +
68G VAL* 4.1 0.7 + - - +
82G TYR* 5.8 0.4 - - - +
-13W C 4.0 15.4 - - - +
-12W C 2.9 54.1 - - - +
-11W G 2.4 58.3 + - + +
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Residues in contact with TYR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.2 30.3 - - + -
-8C T 3.3 35.2 + - + -
-7C C 4.8 9.6 - + - -
61G ARG* 3.0 52.8 + - + -
62G ALA* 3.4 7.6 - - - +
63G LEU 3.1 0.2 - - - -
64G ARG* 1.3 71.3 - - - +
66G TYR* 1.3 57.9 + - - +
67G TYR 2.5 17.9 + - - -
68G VAL* 2.6 25.1 + - + +
69G LYS* 3.1 19.4 + - + -
-11W G 5.8 0.2 - - + -
-10W G 4.2 3.7 + + - -
-9W A 3.0 28.4 + - - -
-8W A 3.8 5.0 + - - -
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Residues in contact with TYR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-7C C 3.0 39.3 + - - -
7G LEU* 3.3 11.4 - - + +
8G TRP* 2.9 45.7 + + + -
62G ALA* 3.4 9.1 + - + -
63G LEU* 2.8 44.8 + - + +
65G TYR* 1.3 78.6 - - - +
67G TYR* 1.3 53.0 + - - +
69G LYS* 3.4 16.8 - - + +
70G ASN 2.6 31.4 + - - -
71G ILE* 3.0 36.1 + - + -
72G ILE* 3.8 21.8 - - + +
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Residues in contact with TYR 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 3.0 26.0 - - + -
64G ARG* 2.8 35.6 - - + +
65G TYR 2.5 4.6 + - - -
66G TYR* 1.3 74.9 - - - +
68G VAL* 1.3 59.0 + - - +
70G ASN* 3.2 12.5 + - - +
72G ILE* 3.1 20.4 - - + -
73G LYS* 3.6 43.3 + - + +
74G LYS* 3.2 14.1 - - + +
82G TYR* 3.0 29.4 + + - -
-12W C 2.5 45.9 + - - -
-11W G 5.8 3.6 - - - -
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Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 6.0 3.8 - - - +
154A LYS* 6.5 1.1 - - + -
155A LEU* 4.5 19.7 - - + -
64G ARG 5.2 0.4 - - - +
65G TYR* 2.6 24.7 + - + +
67G TYR* 1.3 73.3 - - - +
69G LYS* 1.3 69.8 + - + +
70G ASN* 2.8 15.1 + - - +
73G LYS* 5.5 0.2 - - - +
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Residues in contact with LYS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 6.0 1.3 - - - +
155A LEU* 3.7 32.5 - - + -
-7C C 4.1 15.1 + - - +
-6C A 3.5 29.7 + - - +
-5C G 5.9 1.0 - - - +
65G TYR* 3.1 10.3 + - + +
66G TYR* 3.0 26.5 + - + +
68G VAL* 1.3 81.3 - - + +
70G ASN* 1.3 67.3 + - - +
71G ILE* 3.4 18.2 + - + +
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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
------------------------------------------------------------
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