Contacts of the helix formed by residues 17 - 28 (chain A) in PDB entry 1CXZ
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 GLY 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA 3.1 6.7 + - - -
16A CYS* 1.3 77.9 - - - +
18A LYS* 1.3 61.7 + - - +
20A CYS* 4.3 0.7 - - - +
21A LEU* 3.3 20.1 + - - +
117A ASN* 3.3 16.8 + - - -
118A LYS* 4.3 0.4 - - - -
161A ALA* 5.2 0.5 - - - +
500A GSP 3.1 41.8 + - - -
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Residues in contact with LYS 18 (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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10A ILE* 3.5 25.4 - - + +
11A VAL* 3.3 37.9 - - - +
12A GLY* 2.9 12.9 + - - +
13A ASP 2.9 18.8 + - - -
16A CYS* 3.8 12.3 - - - -
17A GLY* 1.3 74.4 - - - +
19A THR* 1.3 64.1 + - - +
21A LEU* 3.3 5.7 + - - +
22A LEU* 3.2 26.5 + - - +
59A ASP* 4.2 6.1 - - - +
60A THR 3.5 20.6 - - - -
61A ALA 4.6 0.7 - - - -
62A GLY* 3.8 2.9 - - - +
83A CYS* 4.3 3.1 - - + -
117A ASN* 4.4 1.1 - - - +
500A GSP 2.6 52.1 + - - +
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Residues in contact with THR 19 (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* 1.3 69.5 - - - +
20A CYS* 1.3 68.1 + - - +
22A LEU* 3.1 3.6 + - - +
23A ILE* 2.9 43.2 + - + +
31A PRO* 4.5 9.4 - - + -
35A VAL 5.6 3.4 - - - +
37A THR* 3.0 4.5 + - - +
42A TYR* 4.2 7.0 - - - +
59A ASP* 2.5 24.8 + - - +
500A GSP 2.8 21.0 + - - +
501A MG 2.3 29.5 - - - -
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Residues in contact with CYS 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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17A GLY 4.3 0.4 - - - +
19A THR* 1.3 72.0 - - - +
21A LEU* 1.3 57.7 + - - +
24A VAL* 2.8 36.2 + - - +
30A PHE* 3.8 20.4 - - + -
31A PRO* 3.8 31.0 - - + -
161A ALA* 3.8 7.6 - - + -
500A GSP 2.9 67.7 + - + +
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Residues in contact with LEU 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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10A ILE* 4.0 19.7 - - + -
17A GLY 3.3 17.1 + - - +
18A LYS 3.4 4.0 - - - +
19A THR 3.1 0.4 - - - -
20A CYS* 1.3 79.1 - - - +
22A LEU* 1.3 61.6 + - - +
24A VAL* 4.2 0.7 - - - +
25A PHE* 3.2 24.4 + - - +
81A LEU* 4.6 7.0 - - + -
83A CYS* 4.3 3.8 - - - -
115A VAL* 4.3 13.0 - - + -
117A ASN* 3.7 17.9 - - - +
159A CYS* 3.6 24.0 - - - -
161A ALA* 3.9 10.0 - - + +
167A VAL* 4.3 17.7 - - + +
170A VAL* 4.7 4.5 - - + -
171A PHE* 3.8 24.6 - - + -
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Residues in contact with LEU 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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8A LEU* 4.3 12.6 - - + -
10A ILE* 3.6 38.6 - - + -
18A LYS 3.2 11.5 + - - +
19A THR 3.1 6.7 + - - +
21A LEU* 1.3 77.1 - - - +
23A ILE* 1.3 52.6 + - - +
25A PHE* 3.5 1.9 + - - +
26A SER* 2.8 38.4 + - - -
42A TYR* 3.9 22.4 - - + -
57A LEU* 4.0 16.6 - - + +
58A TRP 4.5 0.4 - - - -
59A ASP* 3.7 30.7 - - + +
81A LEU* 4.9 0.2 - - + -
171A PHE* 3.9 26.7 - - + -
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Residues in contact with ILE 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 THR* 2.9 32.7 + - + +
22A LEU* 1.3 72.7 - - - +
24A VAL* 1.3 61.9 + - - +
25A PHE 3.1 1.3 - - - -
26A SER* 3.9 2.2 - - - -
27A LYS* 2.7 49.8 + - + +
28A ASP 3.2 3.8 + - - -
29A GLN* 3.5 19.8 - - + +
31A PRO* 3.8 21.3 - - + -
42A TYR* 3.6 44.4 - - + +
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Residues in contact with VAL 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 CYS 2.8 26.2 + - - +
21A LEU 4.2 1.8 - - - +
23A ILE* 1.3 73.2 - - - +
25A PHE* 1.3 60.0 + - - +
28A ASP* 3.0 28.5 + - - +
29A GLN 3.3 20.6 - - - +
30A PHE* 3.7 21.3 - - + -
161A ALA* 3.2 31.0 - - + +
164A LYS* 4.1 28.4 - - + +
167A VAL* 4.2 15.5 - - + -
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Residues in contact with PHE 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 LEU 3.2 16.9 + - - +
22A LEU 3.8 1.1 - - - +
23A ILE 3.1 0.6 - - - -
24A VAL* 1.3 82.8 - - - +
26A SER* 1.3 62.2 + - - +
27A LYS 3.8 0.2 + - - -
28A ASP* 4.0 4.3 - - - +
44A ALA* 3.5 28.5 - - + -
45A ASP 4.5 5.4 - - - -
46A ILE* 3.9 26.7 - - + -
55A LEU* 4.6 5.6 - - + -
57A LEU* 4.4 4.7 - - + -
167A VAL* 3.8 15.7 - - + -
168A ARG* 5.0 11.9 - - + -
171A PHE* 3.5 61.9 - + + -
53B LYS* 3.5 18.5 + - - -
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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 LEU 2.8 25.1 + - - -
23A ILE* 3.9 0.3 - - - -
25A PHE* 1.3 79.0 - - - +
27A LYS* 1.3 93.3 + - - +
42A TYR* 4.3 5.1 - - - +
43A VAL 4.0 4.5 - - - +
44A ALA* 3.9 16.3 - - - +
57A LEU* 3.8 21.5 - - - +
53B LYS* 3.9 6.7 + - - +
81B SER* 3.2 17.1 + - - +
84B LEU* 6.1 0.2 - - - +
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Residues in contact with LYS 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 ILE* 2.7 37.8 + - + +
26A SER* 1.3 106.1 + - - +
28A ASP* 1.3 71.8 + - - +
29A GLN* 3.3 22.8 + - + +
42A TYR* 4.3 19.9 - - - +
43A VAL* 3.7 21.0 + - - +
78B ARG* 3.8 7.4 - - - +
81B SER* 3.7 18.8 + - - -
85B ASP* 3.1 29.7 + - - +
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Residues in contact with ASP 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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23A ILE 3.2 0.4 + - - -
24A VAL* 3.0 22.2 + - - +
25A PHE 4.4 3.2 - - - +
27A LYS* 1.3 78.2 - - - +
29A GLN* 1.3 55.8 + - - +
164A LYS* 3.1 37.8 + - - +
53B LYS* 3.4 19.9 + - - -
57B GLU* 4.9 1.6 - - - +
74B GLU* 4.9 3.2 - - - +
77B LEU* 3.7 37.3 - - + +
78B ARG* 3.2 17.8 - - + +
81B SER* 3.0 20.8 + - - -
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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