Contacts of the helix formed by residues 19 - 30 (chain A) in PDB entry 5UAK
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 TRP 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 4.2 20.9 - - + +
8A LYS 4.8 2.5 - - - +
9A ALA* 4.0 19.5 - - + -
13A SER* 3.6 23.6 - - - -
14A LYS* 4.0 19.7 - - + -
17A PHE* 3.7 31.9 - + - -
18A SER* 1.3 84.2 + - - +
20A THR* 1.3 70.5 + - + +
21A ARG 3.2 0.4 - - - -
22A PRO* 3.5 23.9 - - + +
23A ILE* 3.9 11.0 + - + +
38A TYR* 3.3 29.4 + - + +
143A PHE* 5.8 3.8 - + - -
1090A PHE* 5.9 8.0 - + - -
1091A LEU* 4.9 3.6 - - + -
1094A SER* 3.8 24.4 + - - -
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Residues in contact with THR 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 PHE* 2.7 28.4 + - + +
18A SER 3.1 0.4 + - - -
19A TRP* 1.3 82.2 - - + +
21A ARG* 1.3 58.4 + - - +
23A ILE* 3.1 11.3 - - + +
24A LEU* 2.8 39.1 + - - +
1094A SER* 3.4 36.8 - - - +
1095A THR* 3.9 14.6 - - + +
1098A TRP* 3.6 28.2 + - + -
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Residues in contact with ARG 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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17A PHE 5.4 0.4 - - - +
18A SER* 2.8 25.1 + - - +
20A THR* 1.3 74.5 + - - +
22A PRO* 1.4 64.4 - - + +
24A LEU* 4.1 5.7 - - - +
25A ARG* 3.0 32.7 + - - +
1032A TYR* 4.4 13.2 + - - +
1098A TRP* 3.6 38.8 - - + +
1102A ARG* 4.1 17.8 - - - +
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Residues in contact with PRO 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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18A SER 3.5 6.7 - - - +
19A TRP* 3.5 18.2 - - + +
21A ARG* 1.4 95.5 - - + +
23A ILE* 1.3 56.0 + - + +
25A ARG* 3.4 8.4 + - + +
26A LYS* 2.8 35.1 + - - +
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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 TRP* 3.9 7.9 - - + +
20A THR* 3.1 25.1 - - + +
22A PRO* 1.3 76.5 - - + +
24A LEU* 1.3 63.0 + - + +
26A LYS* 3.7 6.9 - - + +
27A GLY* 2.8 25.6 + - - -
32A LEU* 4.6 5.9 - - + +
36A ASP* 6.2 0.2 - - - +
38A TYR* 4.6 20.2 - - + -
1036A THR* 3.7 6.9 - - + +
1091A LEU* 3.7 35.7 - - + -
1095A THR* 3.6 28.3 - - + -
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Residues in contact with LEU 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 THR* 2.8 28.3 + - - +
21A ARG* 4.1 4.5 - - + +
23A ILE* 1.3 74.0 - - + +
25A ARG* 1.3 56.1 + - - +
28A TYR* 2.8 37.6 + - - +
1029A LEU* 6.1 0.9 - - + -
1032A TYR* 3.7 43.6 - - + +
1033A PHE* 4.9 12.3 - - + -
1036A THR* 3.8 28.0 - - + +
1095A THR* 4.0 26.7 - - + -
1098A TRP* 4.0 26.9 - - + +
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Residues in contact with ARG 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 ARG 3.0 21.0 + - - +
22A PRO* 3.5 8.1 - - - +
24A LEU* 1.3 75.6 - - - +
26A LYS* 1.3 60.9 + - - +
28A TYR* 4.3 3.2 - - - +
29A ARG* 3.2 30.0 + - + +
1032A TYR* 3.7 9.5 + - - +
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Residues in contact with LYS 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 PRO 2.8 21.1 + - - +
23A ILE* 3.7 9.4 - - + +
25A ARG* 1.3 74.4 - - - +
27A GLY* 1.3 54.7 + - - +
29A ARG* 3.8 6.0 - - + +
30A GLN* 2.8 60.0 + - + +
31A ARG 6.1 1.3 - - - -
32A LEU* 4.2 14.1 - - + -
36A ASP* 2.9 35.8 + - - +
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Residues in contact with GLY 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 2.8 21.9 + - - -
24A LEU 3.9 0.4 - - - -
26A LYS* 1.3 72.0 - - - +
28A TYR* 1.3 63.2 + - - +
30A GLN 3.2 16.7 - - - +
32A LEU* 3.7 17.0 - - - +
1035A GLN* 4.9 6.1 - - - +
1036A THR* 4.0 13.0 - - - -
1039A GLN* 3.9 11.2 + - - -
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Residues in contact with TYR 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 LEU 2.8 22.4 + - - +
25A ARG* 4.3 3.4 - - - +
27A GLY* 1.3 73.2 - - - +
29A ARG* 1.3 65.2 + - - +
1031A ALA 4.8 1.8 - - - -
1032A TYR* 3.9 43.1 - + + +
1035A GLN* 3.9 35.3 - - + +
1036A THR* 4.6 2.4 - - + +
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Residues in contact with ARG 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 ARG* 3.2 22.3 + - + +
26A LYS* 3.8 6.5 - - - +
27A GLY 4.3 0.2 - - - -
28A TYR* 1.3 85.3 - - + +
30A GLN* 1.3 73.7 + - + +
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Residues in contact with GLN 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 LYS* 2.8 45.4 + - + +
27A GLY* 3.2 15.2 - - - +
29A ARG* 1.3 90.0 + - + +
31A ARG* 1.3 81.7 + - + +
32A LEU* 3.5 2.8 + - - +
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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