Contacts of the helix formed by residues 53 - 66 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F ARG* 2.5 41.8 + - - -
52F VAL* 1.3 81.4 - - + +
54F TRP* 1.3 64.6 + - - +
55F ALA* 3.0 5.2 - - - +
56F ALA* 4.1 18.8 - - + +
57F ALA* 3.0 18.3 + - - +
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Residues in contact with TRP 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ASP 5.0 1.6 - - - -
80E MSE 3.2 29.8 - - + -
81E ARG* 3.5 48.0 - - + -
84E VAL* 3.7 32.5 - - + +
85E GLU* 5.4 4.9 - - + -
43F LEU* 4.0 5.2 - - + +
47F ALA* 3.4 30.3 - - + -
51F ARG* 2.9 17.0 + - - +
52F VAL 4.4 9.4 + - - -
53F ASP* 1.3 72.5 - - - +
55F ALA* 1.3 90.9 + - + +
57F ALA* 3.7 5.2 - - - +
58F SER* 2.7 39.4 + - - -
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Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASP* 3.0 1.8 - - - -
54F TRP* 1.3 107.6 - - + +
56F ALA* 1.3 67.6 + - - +
58F SER* 2.7 20.5 + - - -
59F ARG* 3.0 28.3 + - - +
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Residues in contact with ALA 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASP* 3.6 17.9 + - + +
55F ALA* 1.3 77.5 - - - +
57F ALA* 1.3 58.6 + - - +
59F ARG* 3.0 25.5 + - - +
60F HIS* 2.9 49.2 + - + +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 4.0 14.7 - - + +
51F ARG* 4.0 27.8 - - - +
53F ASP* 3.0 22.9 + - - +
54F TRP* 3.7 3.8 - - - +
56F ALA* 1.3 77.7 - - - +
58F SER* 1.3 63.3 + - - +
60F HIS* 3.1 11.3 + - - +
61F LEU* 2.9 23.7 + - - +
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Residues in contact with SER 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 3.3 18.1 - - - +
77E ASP* 4.1 14.4 + - - -
80E MSE 3.4 36.3 - - - +
43F LEU* 3.4 11.6 - - - +
54F TRP* 2.7 20.6 + - - -
55F ALA* 2.7 20.1 + - - -
57F ALA* 1.3 73.5 - - - +
59F ARG* 1.3 56.6 + - - +
61F LEU* 3.5 0.6 + - - -
62F LYS* 3.1 23.0 + - - +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ASP* 3.5 26.7 + - - +
55F ALA* 3.0 20.6 + - - +
56F ALA* 3.0 49.3 + - - +
58F SER* 1.3 77.2 + - - +
60F HIS* 1.3 69.4 + - + +
62F LYS* 3.2 10.4 + - + +
63F LYS* 3.2 36.6 + - - +
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Residues in contact with HIS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.7 47.1 + + - +
2C ALA* 5.5 2.8 - - - -
56F ALA* 2.9 40.5 + - + +
57F ALA* 3.1 9.7 + - - +
59F ARG* 1.3 80.0 + - + +
61F LEU* 1.3 61.0 + - - +
63F LYS* 3.3 7.7 + - - +
64F VAL* 2.9 34.7 + - + +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 3.5 24.7 - - + -
12F LEU* 4.2 13.9 - - + -
13F TYR* 4.5 10.8 - - + +
16F ALA* 5.7 4.5 - - + -
39F ALA* 3.7 26.9 - - + +
43F LEU* 4.2 18.6 - - + -
57F ALA 2.9 16.8 + - - +
58F SER* 3.7 6.7 - - - +
60F HIS* 1.3 77.0 - - - +
62F LYS* 1.3 63.7 + - - +
64F VAL* 4.3 6.5 - - + -
65F MSE 3.1 42.4 + - + +
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PRO* 4.2 18.7 - - - +
76E LEU* 4.7 12.5 - - + +
77E ASP* 3.5 46.2 + - + +
58F SER 3.1 14.2 + - - +
59F ARG* 3.3 13.5 - - + +
60F HIS 3.1 0.2 - - - -
61F LEU* 1.3 78.8 - - - +
63F LYS* 1.3 65.6 + - + +
65F MSE 3.3 3.7 + - - +
66F SER* 3.2 20.5 + - - -
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 4.2 31.4 - - + +
2C ALA* 5.3 1.3 - - - +
3C VAL 3.3 28.1 + - - +
4C GLU* 3.8 21.4 - - - +
101C SER 4.8 0.3 - - - +
102C SER* 4.1 14.2 - - - +
103C GLY* 4.5 18.9 + - - +
104C LEU* 5.3 1.3 - - + -
19F TYR* 5.5 1.9 + - - -
59F ARG* 3.2 25.6 + - - +
60F HIS* 3.8 12.3 - - - +
62F LYS* 1.3 78.1 - - + +
64F VAL* 1.3 69.7 + - - +
66F SER* 2.6 27.7 + - - -
67F SER* 3.9 2.3 + - - -
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.7 24.8 - - - -
12F LEU* 4.1 23.6 - - + -
16F ALA* 4.3 25.4 - - + +
19F TYR* 4.1 18.2 - - + -
22F TRP* 4.3 18.9 - - + -
60F HIS* 2.9 21.2 + - + +
61F LEU* 3.8 8.1 - - + +
63F LYS* 1.3 76.2 - - - +
65F MSE 1.3 58.7 + - - +
67F SER* 2.9 25.8 + - - -
68F PHE* 3.5 3.9 - - + -
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Residues in contact with MSE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 4.0 19.5 - - - -
12F LEU* 3.9 16.6 - - + -
31F ILE* 3.5 28.7 - - + +
35F THR* 3.7 14.1 - - + +
36F ILE* 3.5 41.3 - - + +
39F ALA* 4.2 9.2 - - + -
61F LEU* 3.1 40.7 + - + +
62F LYS* 3.9 4.3 - - - +
63F LYS 3.1 0.2 - - - -
64F VAL* 1.3 71.2 - - - +
66F SER* 1.3 58.3 + - - +
67F SER 3.0 10.6 + - - -
68F PHE* 3.1 26.6 + - + +
70F VAL* 5.8 0.3 - - - +
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU 4.0 3.1 - - - +
101C SER* 3.0 14.1 - - - +
102C SER 3.2 1.2 - - - -
103C GLY* 3.0 36.2 + - - -
62F LYS* 3.2 11.4 + - - -
63F LYS* 2.6 22.9 + - - -
65F MSE 1.3 76.2 - - - +
67F SER* 1.3 58.8 + - - +
68F PHE 3.3 4.0 - - - +
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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