Contacts of the helix formed by residues 18 - 32 (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 LYS 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A SER 4.3 0.4 + - - -
17A PHE* 1.3 73.8 - - - +
19A PRO* 1.3 74.8 - - + +
20A SER* 4.1 1.8 - - - +
21A ASP* 2.9 35.8 + - - +
22A VAL* 3.4 7.0 + - - +
49A PHE* 3.7 29.9 - - - -
53A ARG* 3.5 30.7 - - - +
501A CL 3.6 20.1 - - + +
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE 3.8 4.5 - - - +
18A LYS* 1.3 88.9 - - + +
20A SER* 1.3 60.6 + - - +
22A VAL* 3.2 13.3 + - + +
23A ARG* 3.1 28.2 + - - +
501A CL 3.7 12.6 - - + -
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Residues in contact with SER 20 (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* 3.1 1.9 - - - -
19A PRO* 1.3 75.6 - - - +
21A ASP* 1.3 60.9 + - - +
23A ARG* 3.3 15.4 + - - +
24A ILE* 2.9 35.5 + - - +
45A LEU* 4.3 15.8 - - - +
49A PHE* 3.4 31.2 - - - -
53A ARG* 4.7 3.8 - - - -
501A CL 2.9 24.3 - - - +
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Residues in contact with ASP 21 (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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16A SER 5.1 0.7 - - - +
17A PHE* 4.0 14.9 - - + +
18A LYS* 2.9 27.4 + - - +
20A SER* 1.3 77.1 - - - +
22A VAL* 1.3 57.9 + - - +
24A ILE* 3.5 2.1 + - - +
25A TYR* 2.9 32.6 + - - +
53A ARG* 2.8 55.1 + - - +
56A VAL* 4.9 2.1 - - - +
57A LEU* 4.1 31.5 - - + +
60A ARG* 5.5 1.4 + - - -
5B LEU* 3.9 2.8 - - - +
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Residues in contact with VAL 22 (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* 4.3 5.4 - - + -
18A LYS 3.8 11.2 - - - +
19A PRO* 3.2 12.7 + - + +
21A ASP* 1.3 77.6 - - - +
23A ARG* 1.3 57.1 + - + +
25A TYR* 3.9 0.5 - - - +
26A SER* 2.6 45.7 + - - +
3B ASN* 4.0 3.8 - - - +
5B LEU* 4.2 17.7 - - + -
6B GLY* 3.9 24.7 - - - +
9B VAL* 4.0 27.1 - - + -
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Residues in contact with ARG 23 (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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19A PRO* 3.1 18.1 + - - +
20A SER* 3.3 15.8 + - - +
22A VAL* 1.3 77.9 - - + +
24A ILE* 1.3 56.8 + - - +
26A SER* 3.9 4.3 - - - -
27A LEU* 3.0 31.4 + - - +
42A GLU 5.1 0.4 + - - -
43A LEU* 3.0 61.2 + - + +
45A LEU* 3.9 23.4 - - + +
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Residues in contact with ILE 24 (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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20A SER* 2.9 21.5 + - - +
21A ASP* 3.9 4.7 - - - +
23A ARG* 1.3 75.1 - - - +
25A TYR* 1.3 66.8 + - - +
27A LEU* 3.3 3.0 + - - +
28A LEU* 3.0 37.6 + - + +
39A ILE* 4.1 15.9 - - + -
43A LEU* 3.6 22.0 - - + -
45A LEU* 4.6 11.7 - - + -
50A VAL* 4.6 15.0 - - + +
53A ARG* 3.8 31.9 - - + -
54A LEU* 4.1 19.1 - - + +
57A LEU* 4.0 15.0 - - + -
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Residues in contact with TYR 25 (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 2.9 19.0 + - - +
22A VAL 4.0 1.1 - - - +
24A ILE* 1.3 80.5 - - - +
26A SER* 1.3 59.5 + - - +
28A LEU* 3.3 6.8 + - - +
29A LEU* 2.9 44.1 + - + +
57A LEU* 4.8 4.5 - - + +
62A PHE* 3.4 24.7 - - + -
63A VAL* 4.4 5.8 - - + -
79A ALA* 3.6 13.7 - - + -
80A GLU 2.7 29.2 + - - -
82A PRO 3.7 6.9 - - - -
85A VAL* 3.5 16.4 - - + +
3B ASN* 3.8 15.3 - - + -
4B PRO* 3.4 35.8 - - + +
5B LEU* 3.5 22.7 - - + -
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Residues in contact with SER 26 (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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22A VAL* 2.6 28.6 + - - +
23A ARG* 4.0 3.8 - - - -
25A TYR* 1.3 72.7 - - - +
27A LEU* 1.3 65.7 + - - +
29A LEU* 3.4 5.4 + - - +
30A GLU* 3.0 25.5 + - - +
3B ASN* 2.7 39.7 + - - -
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Residues in contact with LEU 27 (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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23A ARG 3.0 18.4 + - - +
24A ILE 3.6 3.8 - - - +
26A SER* 1.3 77.7 - - - +
28A LEU* 1.3 57.4 + - + +
30A GLU* 3.3 8.6 + - - +
31A ARG* 2.9 59.7 + - + +
34A MSE 3.7 25.8 - - + -
39A ILE* 4.3 11.9 - - + -
42A GLU* 3.6 36.6 - - + -
43A LEU* 3.9 24.0 - - + -
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Residues in contact with LEU 28 (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* 3.0 36.9 + - + +
25A TYR 3.7 3.4 - - - +
27A LEU* 1.3 73.7 - - + +
29A LEU* 1.3 67.6 + - - +
32A GLY* 2.9 32.5 + - - +
34A MSE 3.7 30.3 - - + -
39A ILE* 4.0 13.5 - - + -
54A LEU* 4.7 0.4 - - + -
63A VAL* 4.2 21.3 - - + -
77A TYR* 3.4 40.2 - - + +
78A SER 4.2 0.7 - - - +
79A ALA* 3.8 16.7 + - + +
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Residues in contact with LEU 29 (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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25A TYR* 2.9 44.7 + - + +
26A SER* 3.9 5.4 - - - +
27A LEU 3.4 0.2 - - - -
28A LEU* 1.3 76.5 - - - +
30A GLU* 1.3 63.4 + - - +
32A GLY* 4.4 1.4 + - - -
79A ALA* 3.5 19.8 - - + +
80A GLU 4.4 2.5 - - - +
81A LYS* 4.4 20.2 + - + +
82A PRO* 4.1 27.4 - - + -
2B SER 5.0 4.5 - - - +
3B ASN* 4.5 8.7 - - + -
4B PRO* 4.2 6.7 - - + -
104B PHE* 5.5 0.9 - - + -
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Residues in contact with GLU 30 (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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26A SER 3.0 17.7 + - - +
27A LEU* 3.7 7.6 - - - +
29A LEU* 1.3 80.0 - - - +
31A ARG* 1.3 84.1 + - + +
32A GLY 4.0 0.2 + - - -
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Residues in contact with ARG 31 (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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27A LEU* 2.9 36.3 + - + +
30A GLU* 1.3 93.3 + - - +
32A GLY* 1.3 59.6 + - - +
33A GLY 5.2 0.2 - - - +
34A MSE 4.2 28.7 - - + +
42A GLU* 3.0 41.6 + - - -
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Residues in contact with GLY 32 (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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28A LEU* 2.9 26.6 + - - +
29A LEU 4.4 1.4 + - - -
30A GLU 3.6 1.0 - - - -
31A ARG* 1.3 81.0 - - - +
33A GLY* 1.3 68.0 + - - +
34A MSE 3.4 10.9 + - - +
78A SER* 5.3 1.8 - - - -
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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