Contacts of the helix formed by residues 52 - 71 (chain E) in PDB entry 1HBS
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 SER 52 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E ASP* 3.0 40.1 + - - -
49E SER* 3.5 7.7 + - - -
51E GLY* 1.3 75.6 - - - +
53E ALA* 1.3 57.7 - - - +
54E GLN* 2.6 26.6 + - - +
55E VAL* 3.2 10.2 + - - +
56E LYS* 2.5 32.1 + - - +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLY 3.9 0.6 + - - -
52E SER* 1.3 76.3 - - - +
54E GLN* 1.4 55.9 - - - +
56E LYS* 3.8 13.0 - - + +
57E GLY* 2.4 34.5 + - - -
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E HIS 3.8 6.3 + - - -
46E PHE* 3.3 47.3 - - + +
47E ASP* 2.3 50.1 + - - +
52E SER* 2.6 20.3 - - - +
53E ALA* 1.4 76.0 - - - +
55E VAL* 1.2 59.1 + - - -
57E GLY* 3.7 0.5 - - - -
58E HIS 2.9 20.6 + - - -
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Residues in contact with VAL 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA* 3.3 25.9 - - + +
29E LEU* 3.8 33.0 - - + -
30E GLU* 4.7 10.5 - - + +
33E PHE* 4.9 5.4 - - + -
46E PHE* 4.3 6.5 - - + -
47E ASP 4.1 2.2 - - - +
48E LEU* 3.9 31.4 - - + -
49E SER 5.6 0.9 - - - +
52E SER* 3.2 17.2 + - - +
54E GLN* 1.2 71.4 - - - +
56E LYS* 1.3 73.0 + - - +
57E GLY 2.9 2.2 + - - -
58E HIS* 4.0 9.2 - - + +
59E GLY* 3.4 8.5 - - - -
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLY 4.4 4.1 - - - +
23E GLU* 6.1 8.1 - - + -
26E ALA* 4.0 13.9 - - + +
51E GLY* 5.1 11.0 + - - +
52E SER 2.5 19.5 + - - +
53E ALA* 2.9 12.7 + - + +
55E VAL* 1.3 84.0 - - - +
57E GLY* 1.4 51.4 + - - +
59E GLY* 3.4 2.8 - - - -
60E LYS* 3.0 23.2 + - - +
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Residues in contact with GLY 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ALA 2.4 19.7 + - - -
54E GLN 3.7 1.1 - - - -
55E VAL 2.9 0.4 - - - -
56E LYS* 1.4 67.9 - - - +
58E HIS* 1.3 64.4 - - - -
59E GLY 2.9 2.2 - - - -
60E LYS* 2.8 16.7 + - - +
61E LYS* 3.1 18.6 + - - +
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Residues in contact with HIS 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.1 33.7 - - + -
43E PHE* 4.5 10.5 - + - -
46E PHE* 3.8 26.2 - + + -
54E GLN 2.9 13.0 + - - +
55E VAL* 3.5 7.8 + - + -
57E GLY* 1.3 69.8 - - - +
59E GLY* 1.3 49.7 + - - +
61E LYS* 2.9 16.7 + - - +
62E VAL* 2.8 41.6 + - + +
142E HEM 3.2 75.3 + + + +
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Residues in contact with GLY 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLY* 3.7 8.1 - - - +
25E GLY* 4.0 11.2 - - - -
26E ALA* 3.9 12.6 - - - -
29E LEU* 5.6 2.9 - - - -
55E VAL 3.4 8.7 + - - -
56E LYS 3.4 11.0 - - - -
58E HIS* 1.3 71.9 - - - +
60E LYS* 1.3 61.7 + - - -
61E LYS 2.9 3.1 - - - -
62E VAL* 3.3 9.5 + - - +
63E ALA* 3.4 16.1 + - - +
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Residues in contact with LYS 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLY* 4.0 22.2 - - - +
56E LYS 3.0 10.3 + - - +
57E GLY* 2.8 14.5 + - - +
59E GLY* 1.3 73.5 - - - -
61E LYS* 1.4 63.9 + - + +
62E VAL 3.1 0.2 - - - -
63E ALA* 3.8 1.0 - - + +
64E ASP* 2.9 48.7 + - - +
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Residues in contact with LYS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLY 3.1 16.7 + - - +
58E HIS* 2.9 15.8 + - - +
59E GLY 2.9 1.0 - - - -
60E LYS* 1.4 84.2 - - + +
62E VAL* 1.3 60.3 - - - +
64E ASP* 3.4 9.0 - - + +
65E ALA* 3.0 21.1 + - - +
142E HEM 3.6 62.4 + - + +
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLY* 3.9 20.2 - - - +
29E LEU* 5.3 3.1 - - + -
58E HIS* 2.8 42.5 + - + +
59E GLY* 3.9 4.9 - - - +
60E LYS 3.1 0.2 - - - -
61E LYS* 1.3 75.9 - - - +
63E ALA* 1.2 64.0 + - - +
64E ASP 3.0 2.9 + - - -
65E ALA 3.1 2.6 + - - -
66E LEU* 2.4 44.4 - - + +
101E LEU* 4.6 18.2 - - + -
105E LEU* 6.2 1.3 - - + -
142E HEM 3.7 32.1 - - + +
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E TRP* 3.1 34.7 - - - -
21E ALA* 2.7 43.7 - - + +
22E GLY* 3.6 2.7 - - - +
25E GLY* 4.3 2.5 - - - -
59E GLY 3.4 15.2 + - - +
60E LYS* 3.8 4.3 - - + +
62E VAL* 1.2 81.9 - - - +
64E ASP* 1.3 59.0 - - - +
66E LEU* 3.5 1.9 - - - +
67E THR* 3.3 11.8 + - - -
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Residues in contact with ASP 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ALA* 5.9 1.9 - - - +
60E LYS* 2.9 44.0 - - - +
61E LYS* 3.4 9.6 - - + +
63E ALA* 1.3 78.2 - - - +
65E ALA* 1.4 71.5 + - - +
66E LEU 3.2 0.9 - - - -
67E THR* 3.2 12.2 - - + +
68E ASN* 3.0 18.4 + - - +
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E LYS 3.0 12.5 + - - +
62E VAL 3.1 3.8 + - - -
64E ASP* 1.4 77.1 - - - +
66E LEU* 1.4 51.0 - - - +
68E ASN* 3.0 10.6 + - + +
69E ALA* 3.0 27.4 + - - +
80E LEU* 4.5 8.5 - - + +
83E LEU* 3.4 34.5 - - + -
142E HEM 3.6 20.9 - - + -
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E TRP* 4.0 13.5 - - + -
62E VAL* 2.4 45.1 - - + +
63E ALA* 3.5 7.9 - - - +
65E ALA* 1.4 66.4 - - - +
67E THR* 1.3 52.6 + - - +
68E ASN 3.2 1.1 - - - -
69E ALA* 3.3 8.0 + - - +
70E VAL* 2.8 39.7 + - - +
101E LEU* 6.3 0.4 - - + -
105E LEU* 4.0 28.7 - - + -
128E PHE* 4.0 13.8 - - + -
129E LEU* 5.6 3.1 - - + -
132E VAL* 5.2 8.5 - - + -
142E HEM 2.4 59.2 - - + +
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Residues in contact with THR 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E TRP* 2.6 38.0 + - - +
18E GLY 5.6 0.7 + - - -
21E ALA* 4.7 5.7 - - - +
63E ALA 3.3 13.6 + - - -
64E ASP* 3.2 17.9 - - + +
66E LEU* 1.3 70.3 - - - +
68E ASN* 1.3 73.1 + - + +
70E VAL* 3.8 2.3 - - - +
71E ALA* 3.1 18.9 + - - +
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Residues in contact with ASN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ASP 4.0 4.0 - - - +
65E ALA* 3.0 17.0 + - - +
67E THR* 1.3 87.7 - - + +
69E ALA* 1.3 59.4 + - + +
71E ALA* 2.7 13.9 + - - +
72E HIS* 2.2 69.4 + - - -
79E ALA* 3.7 27.7 + - - +
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ALA 3.0 7.3 + - - +
66E LEU 3.3 7.3 + - - +
67E THR 3.2 0.4 - - - -
68E ASN* 1.3 77.6 - - + +
70E VAL* 1.3 57.3 + - - +
71E ALA 2.6 5.6 - - - -
72E HIS* 2.8 16.2 + - - +
73E VAL* 3.1 19.2 + - - +
76E MET* 4.4 10.1 - - + +
79E ALA* 5.7 2.9 - - + -
80E LEU* 3.4 42.6 - - + -
128E PHE* 5.0 4.9 - - + -
132E VAL* 4.7 5.8 - - + -
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Residues in contact with VAL 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 4.3 9.2 - - + +
11E LYS* 3.9 45.9 - - + +
14E TRP* 4.1 32.5 - - + -
66E LEU 2.8 24.3 + - - +
67E THR 3.7 2.2 + - - +
68E ASN 3.3 0.2 - - - -
69E ALA* 1.3 77.6 - - - +
71E ALA* 1.3 73.1 - - - +
72E HIS 3.5 0.2 + - - -
73E VAL* 3.6 20.0 - - + +
128E PHE* 3.2 32.3 - - + -
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 5.5 3.6 - - - -
67E THR 3.1 17.1 + - - +
68E ASN* 2.7 15.3 + - - +
69E ALA 2.6 1.6 - - - -
70E VAL* 1.3 87.0 - - - +
72E HIS* 1.3 74.1 + - + +
73E VAL* 5.6 0.4 - - - -
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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