Contacts of the helix formed by residues 46 - 60 (chain A) in PDB entry 1SFX
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.3 0.2 - - - -
45A LEU* 1.3 76.0 - - - +
47A ALA* 1.3 65.7 + - - +
48A ARG* 3.8 7.0 + - - +
49A PHE* 3.1 25.5 + - - +
50A VAL* 3.0 21.8 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.8 17.9 - - + +
37A SER* 5.7 2.5 - - - -
40A ALA* 4.1 13.0 - - + +
45A LEU 3.7 1.8 + - - -
46A SER* 1.3 72.8 - - - +
48A ARG* 1.3 58.0 + - - +
50A VAL* 3.3 3.0 + - - +
51A ARG* 2.9 49.9 + - - +
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A SER* 3.2 7.4 + - - +
47A ALA* 1.3 78.4 - - - +
49A PHE* 1.3 57.7 + - - +
51A ARG* 3.0 68.0 + - - +
52A ASP* 2.9 57.3 + - - +
55A LYS* 4.2 12.7 - - - +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.7 36.6 - - - -
20A SER* 3.4 31.6 - - - -
24A ILE* 5.5 0.2 - - + -
45A LEU* 4.0 27.6 - - + -
46A SER* 3.1 23.8 + - - +
48A ARG* 1.3 77.0 - - - +
50A VAL* 1.3 65.5 + - - +
52A ASP* 3.2 12.1 + - + +
53A ARG* 3.0 41.2 + - + +
501A CL 4.3 2.7 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.6 9.4 - - + +
36A VAL* 4.1 13.7 - - + -
39A ILE* 3.8 31.4 - - + -
40A ALA* 4.0 17.9 - - - -
45A LEU* 3.9 25.6 - - + -
46A SER 3.0 17.2 + - - +
47A ALA 3.6 7.2 - - - +
49A PHE* 1.3 77.2 - - - +
51A ARG* 1.3 57.6 + - - +
53A ARG* 3.3 1.9 + - - +
54A LEU* 2.8 49.2 + - + +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.0 21.9 - - + +
47A ALA* 2.9 39.3 + - - +
48A ARG* 3.0 70.6 - - - +
50A VAL* 1.3 74.8 - - - +
52A ASP* 1.3 63.7 + - - +
54A LEU* 3.3 10.5 + - - +
55A LYS* 3.1 29.3 + - + +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 2.9 54.3 + - - +
49A PHE* 3.2 16.2 + - + +
51A ARG* 1.3 78.7 - - - +
53A ARG* 1.3 69.6 + - - +
55A LYS* 3.4 26.8 + - - +
56A VAL* 3.5 15.8 + - - +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.5 26.9 - - - +
20A SER* 4.7 1.8 - - - -
21A ASP* 2.8 44.2 + - - +
24A ILE* 3.8 20.4 - - + -
49A PHE* 3.0 56.3 + - + +
50A VAL 4.0 0.2 - - - +
52A ASP* 1.3 78.5 + - - +
54A LEU* 1.3 66.2 + - - +
56A VAL* 3.1 40.9 + - - +
57A LEU* 2.9 27.4 + - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.1 24.2 - - + -
28A LEU* 4.7 0.7 - - + -
36A VAL* 3.8 23.1 - - + -
39A ILE* 4.3 5.8 - - + -
50A VAL* 2.8 41.5 + - + +
51A ARG* 3.6 7.0 - - - +
53A ARG* 1.3 78.1 - - - +
55A LYS* 1.3 56.2 + - - +
57A LEU* 3.7 4.1 - - + +
58A LEU* 2.8 43.8 + - + +
63A VAL* 4.1 16.6 - - + -
77A TYR* 3.9 38.8 - - + -
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 4.2 10.7 - - - +
51A ARG* 3.1 15.3 + - + +
52A ASP* 3.6 35.2 + - - +
53A ARG 3.2 0.4 - - - -
54A LEU* 1.3 75.8 - - - +
56A VAL* 1.3 62.7 + - + +
58A LEU* 3.5 11.0 + - + +
59A LYS* 3.1 45.1 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 4.9 3.6 - - - +
52A ASP 3.5 12.8 + - - +
53A ARG* 3.1 41.8 + - - +
55A LYS* 1.3 78.1 - - + +
57A LEU* 1.3 59.0 + - + +
59A LYS* 3.3 13.1 + - - +
60A ARG* 3.0 49.9 + - + +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 5.3 2.5 - - + -
21A ASP* 4.1 40.4 - - + +
24A ILE* 4.0 29.6 - - + -
25A TYR* 4.8 2.2 - - + +
53A ARG 2.9 23.0 + - - +
54A LEU* 3.2 6.0 + - - +
56A VAL* 1.3 80.4 - - + +
58A LEU* 1.3 59.9 + - - +
60A ARG* 3.6 3.7 + - - -
61A GLY 3.2 3.5 + - - -
62A PHE* 2.9 54.1 + - + +
63A VAL* 3.3 25.7 + - + +
5B LEU* 4.5 8.5 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 2.8 30.4 + - + +
55A LYS* 3.7 10.3 - - + +
57A LEU* 1.3 74.8 - - - +
59A LYS* 1.3 65.9 + - + +
61A GLY* 3.1 14.4 + - - -
63A VAL* 3.4 30.4 - - + +
64A ARG* 3.8 22.4 - - - -
65A ARG* 3.8 15.7 - - + +
77A TYR* 4.1 20.4 - - + -
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 3.1 39.1 + - - +
56A VAL* 3.9 10.8 - - - +
58A LEU* 1.3 79.4 - - + +
60A ARG* 1.3 61.8 + - + +
61A GLY* 3.4 0.9 + - - -
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS 4.9 2.7 + - - -
15A LEU* 2.9 42.5 + - - +
16A SER 3.1 26.3 + - - -
17A PHE* 3.5 23.4 - - - +
21A ASP* 5.5 1.4 + - - -
56A VAL* 3.0 37.6 + - + +
57A LEU* 4.0 4.5 - - - +
58A LEU 3.2 0.2 - - - -
59A LYS* 1.3 78.0 - - + +
61A GLY* 1.3 61.3 + - - +
62A PHE* 3.4 42.0 - - + -
88A GLU* 3.9 12.6 - - - +
89A PHE* 3.9 10.5 - - - -
92A SER* 5.6 3.9 + - - -
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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