Contacts of the helix formed by residues 55 - 69 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLU* 3.6 17.2 - - - +
42H ALA* 3.4 11.7 - - - -
53H ASN 3.0 13.2 + - - +
54H MET* 1.3 77.6 - - - +
56H TYR* 1.3 57.4 + - - +
57H ASP* 2.6 43.2 + - - +
58H LYS* 2.8 39.2 + - - +
59H LEU 2.9 11.1 + - - -
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.9 23.1 - - + -
38H ALA* 4.2 14.1 - - + -
39H GLU* 4.1 21.7 + - - +
42H ALA* 3.3 14.3 - - + +
55H ASN* 1.3 69.5 - - - +
57H ASP* 1.3 52.9 + - - +
58H LYS 2.6 7.4 + - - -
59H LEU* 4.2 8.7 - - + +
60H SER* 2.3 58.7 + - - -
63H LEU* 4.8 2.0 - - + -
80H PHE* 4.3 15.7 - + - -
82H TYR* 2.4 33.3 + + - -
-14X A 4.1 29.4 - - + -
-13X C 3.2 21.7 + - - -
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Residues in contact with ASP 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-12F G 5.1 1.6 - - - +
-11F C 3.8 33.3 + - - -
-10F C 4.9 3.6 + - - -
55H ASN* 2.6 21.8 + - - +
56H TYR* 1.3 76.3 - - - +
58H LYS* 1.3 59.1 + - - +
60H SER* 2.9 13.5 + - - -
61H ARG* 3.9 7.1 + - - +
64H ARG* 3.6 14.0 + - - +
-13X C 5.8 2.8 + - - -
-12X C 4.5 4.0 + - - -
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Residues in contact with LYS 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10F C 4.9 8.2 + - + -
-9F T 2.5 88.7 + - + +
-8F T 4.2 5.2 - - + -
53H ASN* 3.8 22.4 + - - +
54H MET* 3.7 12.8 - - + -
55H ASN* 2.8 35.8 + - - +
56H TYR 2.6 5.1 + - - -
57H ASP* 1.3 81.6 - - - +
59H LEU* 1.3 66.1 + - - +
60H SER 3.0 1.1 - - - -
61H ARG* 3.0 5.0 + - - +
62H ALA* 2.8 22.9 + - - +
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Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 3.6 23.1 - - + -
10H PHE* 5.8 0.4 - - + -
11H LEU* 4.5 7.2 - - + -
35H LEU* 5.3 5.2 - - + -
41H VAL* 4.3 15.7 - - + +
42H ALA* 4.3 13.5 - - + +
45H TRP* 3.3 43.1 - - + +
54H MET* 3.6 7.0 - - - -
55H ASN 2.9 14.1 + - - +
56H TYR* 3.9 11.2 - - + +
58H LYS* 1.3 75.3 - - - +
60H SER* 1.3 53.0 + - - +
62H ALA* 3.0 8.4 - - - +
63H LEU* 2.7 50.4 + - + +
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TYR* 2.3 58.3 + - - +
57H ASP* 2.9 11.4 - - - -
59H LEU* 1.3 69.1 - - - +
61H ARG* 1.3 52.3 + - - -
63H LEU* 2.8 17.2 + - - +
64H ARG* 2.6 68.6 + - - +
82H TYR* 4.5 3.0 + - - -
-13X C 5.8 2.0 - - - -
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Residues in contact with ARG 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10F C 4.5 2.0 - - - +
-9F T 3.9 23.6 - - + +
-8F T 5.2 0.4 - - + +
57H ASP 4.0 7.4 - - - +
58H LYS* 3.0 10.0 + - - +
60H SER* 1.3 78.4 + - - +
62H ALA* 1.3 67.9 + - - +
64H ARG* 2.6 32.5 + - - +
65H TYR* 3.0 72.7 + - + +
-11X G 2.7 58.2 + - - +
-10X G 3.0 30.6 + - - +
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Residues in contact with ALA 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-8F T 4.2 34.0 - - + +
-7F C 4.6 9.6 - - + +
7H LEU* 3.9 15.0 - - + -
58H LYS 2.8 13.4 + - - +
59H LEU* 3.0 17.0 - - - +
61H ARG* 1.3 76.3 - - - +
63H LEU* 1.3 64.5 + - - +
65H TYR* 3.1 19.1 + - - +
66H TYR* 3.7 11.5 + - - -
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 4.2 2.2 - - + -
11H LEU* 3.8 21.5 - - + -
33H PHE* 5.5 0.7 - - + -
35H LEU* 5.1 2.5 - - + -
56H TYR* 4.8 3.8 - - + -
59H LEU* 2.7 35.6 + - + +
60H SER* 2.8 11.8 + - - +
62H ALA* 1.3 71.3 - - - +
64H ARG* 1.3 53.6 + - - +
66H TYR* 2.6 48.3 + - + +
67H TYR* 3.4 6.7 - - + -
72H ILE* 3.4 36.3 - - + +
82H TYR* 3.5 47.8 - - + +
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Residues in contact with ARG 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TYR* 6.0 0.2 - - - -
57H ASP* 3.6 15.0 + - - +
60H SER* 2.6 43.2 + - - +
61H ARG* 2.6 35.6 + - - +
63H LEU* 1.3 71.3 - - + +
65H TYR* 1.3 60.3 + - - +
67H TYR* 3.0 36.5 - - + +
68H VAL* 5.5 0.2 - - - +
82H TYR* 6.0 0.9 - - + +
-13X C 4.6 13.1 - - - +
-12X C 2.7 59.3 - - + +
-11X G 2.6 50.8 + - + +
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Residues in contact with TYR 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.6 26.5 - - + -
-8F T 3.4 35.6 + - + -
-7F C 4.3 17.0 - + - -
61H ARG* 3.0 50.0 + - + -
62H ALA 3.3 9.6 - - - +
63H LEU 2.7 5.3 + - - -
64H ARG* 1.3 72.0 - - - +
66H TYR* 1.3 53.4 + - + +
68H VAL* 2.6 46.5 + - + +
69H LYS* 4.5 10.8 - - + -
-9X A 2.9 30.8 + - - -
-8X A 3.6 7.3 + - - -
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Residues in contact with TYR 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-7F C 2.8 42.0 + - - -
7H LEU* 2.9 33.8 - - + +
8H TRP* 3.0 13.1 + + + -
62H ALA 3.7 6.1 - - - -
63H LEU* 2.6 45.6 + - + +
65H TYR* 1.3 72.3 - - + +
67H TYR* 1.3 52.0 + - - +
68H VAL 2.5 13.3 + - - -
69H LYS* 2.5 26.9 + - + +
70H ASN* 2.8 10.6 + - - -
71H ILE* 3.2 34.7 + - + -
72H ILE* 3.5 39.3 - - + +
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Residues in contact with TYR 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU 3.4 5.6 - - - -
64H ARG* 3.0 44.3 - - + +
65H TYR 2.7 3.6 + - - -
66H TYR* 1.3 72.6 - - - +
68H VAL* 1.3 55.7 + - + +
70H ASN* 4.1 10.7 + - - +
72H ILE* 3.2 17.9 - - + -
73H LYS* 4.7 5.2 - - - +
74H LYS* 3.5 24.3 - - + +
82H TYR* 3.5 24.5 + + - -
-13X C 4.2 0.7 - - - -
-12X C 2.2 53.7 + - - -
-11X G 5.1 10.1 - - - -
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Residues in contact with VAL 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASN* 5.7 5.4 + - - +
154D LYS* 6.5 0.9 - - + -
155D LEU* 4.3 26.2 - - + -
65H TYR* 2.6 30.5 + - + +
66H TYR 2.5 6.9 + - - -
67H TYR* 1.3 73.8 - - + +
69H LYS* 1.3 66.9 + - + +
70H ASN* 3.2 11.1 + - - -
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Residues in contact with LYS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.4 17.3 - - + -
-7F C 4.0 18.0 + - - +
-6F A 3.1 34.4 + - - +
65H TYR* 4.2 9.2 - - + +
66H TYR* 2.5 23.2 + - + +
68H VAL* 1.3 87.1 - - + +
70H ASN* 1.3 72.4 + - - +
71H ILE* 3.1 26.4 - - + +
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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