Contacts of the helix formed by residues 53 - 67 (chain H) in PDB entry 1V8O
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 ASP 53 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ARG* 2.5 43.6 + - - +
52H VAL* 1.3 77.2 - - - +
54H TRP* 1.3 66.4 + - - +
55H ALA* 3.1 3.8 - - - -
56H ALA* 2.9 16.2 + - + +
57H ALA* 2.5 47.5 + - - +
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Residues in contact with TRP 54 (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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77G ASP 4.8 2.5 - - - -
80G MSE 3.4 22.7 - - + -
81G ARG* 3.5 49.1 - - + -
84G VAL* 3.7 32.9 - - + +
85G GLU* 5.6 3.4 - - + -
43H LEU* 4.0 6.0 - - + +
47H ALA* 3.7 28.3 - - + -
51H ARG 3.8 3.1 + - - +
52H VAL* 5.7 2.0 - - - -
53H ASP* 1.3 86.3 + - - +
55H ALA* 1.3 89.1 + - + +
57H ALA* 3.7 5.3 - - - +
58H SER* 2.7 39.9 + - - -
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ASP* 4.8 2.1 - - - +
53H ASP* 3.1 1.5 - - - -
54H TRP* 1.3 113.2 - - + +
56H ALA* 1.3 61.5 + - - +
58H SER* 2.8 18.0 + - - -
59H ARG* 3.0 24.1 + - - +
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Residues in contact with ALA 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H ASP* 2.9 18.1 + - + +
55H ALA* 1.3 77.9 - - - +
57H ALA* 1.3 59.5 + - - +
59H ARG* 2.8 46.2 + - - +
60H HIS* 3.0 12.5 + - - +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.7 23.4 - - + +
53H ASP* 2.5 36.6 + - - +
54H TRP* 3.7 4.0 - - - +
56H ALA* 1.3 73.3 - - - +
58H SER* 1.3 56.4 + - - +
60H HIS* 3.2 10.8 + - - +
61H LEU* 2.9 27.5 + - - +
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Residues in contact with SER 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G LEU* 3.3 27.5 - - - +
77G ASP* 4.0 12.7 + - - -
80G MSE 3.9 15.6 - - - +
43H LEU* 3.8 14.1 - - - +
54H TRP* 2.7 20.1 + - - -
55H ALA* 2.8 22.9 + - - -
57H ALA* 1.3 71.1 - - - +
59H ARG* 1.3 60.4 + - - +
61H LEU* 4.3 2.0 - - - -
62H LYS* 2.8 31.4 + - - +
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Residues in contact with ARG 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ASP* 4.5 15.9 + - - +
55H ALA* 3.0 18.9 + - - +
56H ALA* 2.8 46.9 + - - +
58H SER* 1.3 78.6 + - - +
60H HIS* 1.3 59.4 + - - +
62H LYS* 3.1 10.7 - - + +
63H LYS* 3.0 20.3 + - - +
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Residues in contact with HIS 60 (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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16H ALA* 3.4 28.6 + - + -
19H TYR* 5.1 5.2 - - + -
56H ALA 3.0 10.3 + - - +
57H ALA* 3.5 11.7 - - - +
59H ARG* 1.3 73.8 - - - +
61H LEU* 1.3 68.5 + - + +
63H LYS* 3.1 41.9 + - - +
64H VAL* 3.0 39.0 + - + +
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Residues in contact with LEU 61 (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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76G LEU* 3.3 22.4 - - + -
12H LEU* 4.0 21.8 - - + -
13H TYR* 4.7 11.2 - - + -
16H ALA* 5.5 5.6 - - + -
39H ALA* 3.7 29.2 - - + +
40H GLY 4.3 0.2 - - - +
43H LEU* 3.9 22.2 - - + -
57H ALA 2.9 16.2 + - - +
58H SER* 3.7 5.6 - - - +
60H HIS* 1.3 80.0 - - + +
62H LYS* 1.3 57.7 + - - +
64H VAL* 3.3 7.1 + - + +
65H MSE 2.8 51.6 + - + +
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Residues in contact with LYS 62 (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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75G PRO* 3.8 19.8 - - - +
76G LEU* 4.3 13.4 - - + +
77G ASP* 2.9 50.0 + - + +
78G GLU* 5.9 0.2 - - - +
58H SER 2.8 13.9 + - - +
59H ARG* 3.1 13.7 - - + +
61H LEU* 1.3 78.1 - - - +
63H LYS* 1.3 64.9 + - - +
65H MSE 3.5 8.0 - - - +
66H SER* 3.1 22.0 + - - -
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Residues in contact with LYS 63 (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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19H TYR* 3.6 46.2 + - + +
59H ARG 3.0 12.2 + - - +
60H HIS* 3.1 44.5 + - - +
62H LYS* 1.3 75.4 - - - +
64H VAL* 1.3 64.4 + - - +
66H SER* 2.6 26.1 + - - +
67H SER* 3.6 5.9 + - - -
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Residues in contact with VAL 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 4.2 11.0 - - + +
16H ALA* 4.1 21.1 - - + -
19H TYR* 4.1 19.3 - - + -
22H TRP* 3.5 30.5 - - + -
60H HIS* 3.0 44.5 + - + +
61H LEU* 3.7 6.5 - - - +
63H LYS* 1.3 74.7 - - - +
65H MSE 1.3 62.8 + - - +
67H SER* 3.1 13.3 + - - -
68H PHE* 3.1 23.6 - - + -
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Residues in contact with MSE 65 (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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76G LEU* 4.2 10.3 - - + -
12H LEU* 3.0 48.5 - - + -
31H ILE* 4.3 17.0 - - + +
35H THR* 4.4 2.9 - - + +
36H ILE* 3.9 40.2 - - + +
39H ALA* 4.0 14.4 - - - -
61H LEU* 2.8 37.9 + - + +
62H LYS* 3.5 7.4 - - - +
63H LYS 3.2 0.2 - - - -
64H VAL* 1.3 72.1 - - - +
66H SER* 1.3 55.6 + - - +
67H SER 2.7 12.0 + - - -
68H PHE* 2.9 21.4 + - + +
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Residues in contact with SER 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H LYS* 3.1 10.1 + - - -
63H LYS* 2.6 25.5 + - - +
65H MSE 1.3 77.3 - - - +
67H SER* 1.3 62.4 + - - +
68H PHE 3.2 7.9 + - - +
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Residues in contact with SER 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H TYR* 3.4 26.7 + - - -
22H TRP* 4.1 16.2 - - - -
23H ILE* 4.2 5.5 - - - +
26H ARG* 3.6 40.6 + - - +
63H LYS 4.0 3.3 + - - -
64H VAL 3.1 16.2 + - - -
65H MSE 2.7 5.9 + - - -
66H SER* 1.3 76.4 + - - +
68H PHE* 1.3 62.2 + - - -
69H LYS 4.0 0.9 + - - -
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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