Contacts of the helix formed by residues 54 - 70 (chain H) in PDB entry 3H1J
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 CYS 54 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PRO* 3.8 6.2 - - + +
139D ALA* 3.0 28.6 + - - +
37H LEU* 3.8 12.1 - - + +
40H CYS* 2.0 47.1 - - + -
41H ASP* 3.3 13.5 - - + -
44H VAL* 3.4 15.3 - - - -
53H GLN* 1.3 72.0 - - - +
55H THR* 1.3 63.5 + - - +
57H GLU* 3.0 11.6 - - - +
58H LEU* 2.9 24.6 + - - +
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Residues in contact with THR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.6 12.3 - - + -
138D PRO* 3.9 10.4 - - - +
141D VAL* 3.8 22.0 - - - +
149D TYR* 5.0 4.0 + - - +
156D GLN* 5.2 6.1 - - - +
53H GLN* 3.3 11.7 + - - +
54H CYS* 1.3 75.2 - - - +
56H GLU* 1.3 55.7 + - - +
58H LEU* 2.9 6.5 + - - +
59H PHE* 2.7 72.0 + - + +
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Residues in contact with GLU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.0 23.5 - - + +
70G LYS 4.8 0.2 - - - +
71G ARG* 2.5 61.7 + - - +
72G LYS* 3.0 41.9 + - + +
36H ARG* 5.2 4.0 + - - -
53H GLN 4.7 1.2 + - - +
54H CYS 3.4 0.2 - - - -
55H THR* 1.3 80.9 - - - +
57H GLU* 1.3 69.9 + - + +
59H PHE* 3.1 5.0 + - - +
60H ASP* 2.8 33.8 + - - +
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G LYS* 2.8 36.3 + - - -
33H ALA 4.7 2.8 - - - +
36H ARG* 3.8 39.8 + - - +
37H LEU* 3.4 28.3 - - + +
40H CYS* 3.8 11.1 - - + +
43H ARG* 4.6 1.9 + - - -
54H CYS* 3.0 24.6 - - - -
56H GLU* 1.3 81.6 + - + +
58H LEU* 1.3 61.8 + - - +
60H ASP* 3.3 8.9 + - - +
61H PHE* 2.9 25.3 + - - +
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Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D CYS* 4.8 5.4 - - - -
136D ASP 4.5 6.1 - - - +
138D PRO* 3.6 37.0 - - + -
149D TYR* 3.9 16.8 - - + +
37H LEU* 3.5 25.5 - - + +
54H CYS 2.9 17.4 + - - +
55H THR* 2.9 5.5 + - - +
57H GLU* 1.3 75.9 - - - +
59H PHE* 1.3 55.3 + - + +
61H PHE* 3.3 5.6 + - + +
62H LEU* 2.7 62.8 + - + +
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Residues in contact with PHE 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.0 14.4 - - + -
4D GLU* 3.8 19.1 - - - -
5D LEU* 3.7 41.1 - - + +
149D TYR* 4.2 5.8 - - - -
151D PRO* 3.6 32.8 - - + -
156D GLN* 3.6 22.9 - - + -
55H THR* 2.7 44.3 + - + -
56H GLU* 3.4 8.5 - - - +
58H LEU* 1.3 72.9 - - + +
60H ASP* 1.3 61.5 + - - +
61H PHE 3.0 1.6 - - - -
62H LEU* 3.7 4.9 - - + +
63H HIS* 2.6 38.0 + - - +
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Residues in contact with ASP 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 2.6 46.4 + - - -
33H ALA* 4.3 10.7 - - + +
36H ARG* 3.9 15.3 + - - +
56H GLU* 2.8 27.1 + - - +
57H GLU* 3.8 4.0 - - - +
59H PHE* 1.3 74.1 - - - +
61H PHE* 1.3 62.1 + - - +
63H HIS* 3.8 5.6 - - - +
64H ALA* 3.2 23.7 + - - +
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Residues in contact with PHE 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLU* 3.2 33.9 - - + -
30H CYS* 3.8 28.3 - - + -
33H ALA* 3.7 13.9 - - + +
34H ARG* 3.5 55.2 - - + -
37H LEU* 4.4 14.6 - - + -
57H GLU 2.9 18.3 + - - +
58H LEU* 3.4 9.9 - - + +
60H ASP* 1.3 75.5 - - - +
62H LEU* 1.3 63.0 + - + +
64H ALA* 3.2 3.6 + - - +
65H ARG* 2.8 53.8 + - - +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.9 15.7 - - + -
135D CYS* 5.0 7.0 - - + -
151D PRO* 3.7 33.4 - - + -
152D TYR* 5.8 1.3 - - + -
58H LEU* 2.7 58.8 + - + +
59H PHE* 3.7 4.3 - - + +
61H PHE* 1.3 77.6 - - + +
63H HIS* 1.3 58.5 + - - +
65H ARG* 3.1 26.8 + - - +
66H ASP* 2.8 51.9 + - - +
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Residues in contact with HIS 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 3.9 20.1 - - + +
6D HIS* 4.5 16.3 + - + +
8D PRO* 5.8 0.3 - - - +
152D TYR* 5.5 0.7 - - - -
59H PHE 2.6 23.3 + - - +
60H ASP* 3.8 7.0 - - - +
62H LEU* 1.3 73.5 - - - +
64H ALA* 1.3 59.0 + - - +
66H ASP* 4.6 1.5 - - - +
67H HIS* 3.0 48.2 + + + +
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR* 6.1 0.5 - - - +
29H LYS* 4.2 32.3 - - + +
30H CYS* 4.1 13.2 - - - +
33H ALA* 5.1 1.3 - - + -
60H ASP 3.2 13.8 + - - +
61H PHE* 3.2 5.0 + - - +
63H HIS* 1.3 80.0 + - - +
65H ARG* 1.3 68.2 + - - +
67H HIS* 3.7 4.9 + - - +
68H CYS* 3.3 17.5 + - - +
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Residues in contact with ARG 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLY* 6.0 2.0 - - - -
21H ARG* 3.2 52.9 - - - +
24H CYS* 4.4 3.1 - - + -
25H GLU* 3.6 42.1 + - + -
30H CYS* 3.7 14.6 - - - -
34H ARG* 5.7 0.2 - - - +
61H PHE* 2.8 32.6 + - + +
62H LEU* 3.1 26.8 + - - +
64H ALA* 1.3 75.0 - - - +
66H ASP* 1.3 83.1 + - - +
68H CYS* 2.8 28.3 + - - +
69H VAL* 2.8 17.1 + - + +
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Residues in contact with ASP 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.0 12.5 - - + +
10D PHE* 5.2 1.5 - - + -
152D TYR* 2.8 33.6 + - - +
17H LEU* 5.8 0.2 - - - +
21H ARG* 4.3 5.7 + - - -
62H LEU* 2.8 32.9 + - - +
63H HIS* 4.6 1.1 - - - +
65H ARG* 1.3 103.6 + - - +
67H HIS* 1.3 66.9 + - - +
69H VAL* 3.3 13.7 - - + +
70H ALA* 2.7 27.0 + - - +
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Residues in contact with HIS 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.0 17.5 - - + +
63H HIS* 3.0 38.2 + + + +
64H ALA* 3.7 7.2 - - - +
66H ASP* 1.3 78.3 - - - +
68H CYS* 1.3 68.6 + - - +
70H ALA* 3.5 4.0 + - - +
71H HIS* 3.4 34.8 + + - +
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Residues in contact with CYS 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H HIS* 4.8 1.1 - - - -
24H CYS* 2.0 47.6 - - + +
27H THR* 4.4 12.8 - - + +
30H CYS* 5.5 1.8 - - - -
64H ALA 3.3 9.1 + - - +
65H ARG* 2.8 13.8 + - - +
67H HIS* 1.3 82.4 + - - +
69H VAL* 1.3 64.0 + - - +
71H HIS* 2.8 22.2 + - - +
72H LYS* 3.3 28.7 - - - +
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Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PHE* 5.2 3.8 - - + -
17H LEU* 3.8 28.5 - - + +
20H ILE* 4.3 8.6 - - + +
21H ARG* 4.0 21.3 - - + -
24H CYS* 3.4 13.2 - - - -
65H ARG* 2.8 27.3 + - + +
66H ASP* 3.3 24.5 - - + +
68H CYS* 1.3 76.6 - - - +
70H ALA* 1.3 53.7 - - - +
71H HIS 2.7 11.3 + - - -
72H LYS* 3.2 1.6 + - - +
73H LEU* 2.9 40.7 + - + +
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Residues in contact with ALA 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.8 16.6 - - + -
9D ALA 4.1 6.2 - - - +
10D PHE* 3.4 46.2 - - + +
11D PRO* 3.5 25.3 - - - +
66H ASP 2.7 19.1 + - - +
67H HIS 3.8 3.6 - - - +
69H VAL* 1.3 70.6 - - - +
71H HIS* 1.3 59.7 - - - +
72H LYS 3.4 1.2 + - - -
73H LEU* 4.6 2.5 - - - -
74H PHE 5.8 0.2 - - - -
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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
------------------------------------------------------------
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