Contacts of the helix formed by residues 17 - 28 (chain A) in PDB entry 1UK0
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.1 20.5 - - - +
14A MET* 2.6 27.7 + - - +
15A ILE 3.5 2.6 - - - -
16A PHE* 1.4 76.3 - - - +
18A VAL* 1.4 63.7 + - - +
19A GLU* 3.5 8.1 + - - +
20A SER* 2.7 34.7 + - - -
21A MET* 3.7 12.9 + - - +
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Residues in contact with VAL 18 (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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16A PHE 3.8 0.4 + - - +
17A ASP* 1.4 71.0 - - - +
19A GLU* 1.3 67.5 + - - +
20A SER 3.2 0.3 + - - -
21A MET* 3.2 21.6 + - + +
22A LYS* 3.5 30.8 + - + +
37A LEU* 5.1 3.1 - - + -
114A TYR* 4.1 24.9 - - + -
117A LEU* 3.5 30.1 - - + -
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Residues in contact with GLU 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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17A ASP* 3.0 8.9 + - - +
18A VAL* 1.3 80.9 - - - +
20A SER* 1.4 59.6 - - - +
22A LYS* 2.9 27.2 + - - +
23A LYS* 3.2 36.2 + - - +
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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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14A MET 4.8 0.9 + - - -
17A ASP* 2.7 29.9 + - - -
19A GLU* 1.4 74.6 - - - +
21A MET* 1.4 65.3 - - - +
23A LYS* 2.9 30.2 + - - +
24A ALA* 3.1 9.7 + - - +
205A THR* 5.8 1.1 - - - -
206A THR* 4.4 15.1 - - - +
253A ASP* 5.3 8.3 - - - -
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Residues in contact with MET 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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15A ILE 5.5 0.7 - - - +
16A PHE* 4.0 10.3 - - - +
17A ASP 3.7 26.7 - - - +
18A VAL* 3.2 11.2 + - + +
20A SER* 1.4 79.0 - - - +
22A LYS* 1.4 64.5 + - - +
24A ALA* 3.3 6.1 + - - +
25A MET* 2.9 24.1 + - - +
37A LEU* 3.9 14.1 - - + -
110A ILE* 4.1 24.6 - - + +
113A ALA* 4.3 13.7 - - + -
114A TYR* 3.5 38.6 - - + +
117A LEU* 3.8 27.4 - - + -
206A THR* 4.9 9.6 - - + +
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Residues in contact with LYS 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 VAL* 3.5 36.3 - - - +
19A GLU* 2.9 13.1 + - - +
21A MET* 1.4 78.2 - - + +
23A LYS* 1.3 59.9 + - - +
25A MET* 3.2 6.4 + - - +
26A VAL* 2.8 31.8 + - - +
32A LEU* 3.5 34.0 - - + +
37A LEU* 4.0 23.3 - - + +
114A TYR* 6.0 0.4 + - - -
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Residues in contact with LYS 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 GLU* 3.2 28.2 + - - +
20A SER* 2.9 27.5 + - - +
22A LYS* 1.3 73.7 - - - +
24A ALA* 1.4 54.1 + - - +
26A VAL* 3.5 14.4 - - + +
27A GLU* 2.9 55.5 + - - +
252A GLY 4.3 16.2 + - - -
253A ASP* 4.9 14.2 + - - +
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Residues in contact with ALA 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 3.1 11.7 + - - +
21A MET 3.3 1.5 + - - +
23A LYS* 1.4 72.3 - - - +
25A MET* 1.4 52.6 + - - +
27A GLU* 3.0 10.2 + - - +
28A TYR* 2.7 43.7 + - + -
106A ASN* 5.9 0.4 - - + -
110A ILE* 3.8 24.5 - - + -
204A ARG* 3.7 31.6 + - - +
206A THR* 4.3 8.7 - - + -
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Residues in contact with MET 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 MET 2.9 17.9 - - - +
22A LYS* 3.3 4.9 - - - +
24A ALA* 1.4 69.3 - - - +
26A VAL* 1.4 54.5 - - - +
28A TYR* 3.0 16.3 + - - +
29A GLU 3.2 0.2 + - - -
30A ILE* 2.8 60.8 + - + +
32A LEU* 3.5 28.3 - - + -
35A MET* 4.5 4.9 - - - +
37A LEU* 3.7 38.1 - - + +
40A LEU* 4.0 10.8 - - + -
107A LEU* 4.0 10.1 - - + -
110A ILE* 3.9 26.5 - - + -
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Residues in contact with VAL 26 (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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22A LYS 2.8 16.6 + - - +
23A LYS* 3.5 16.2 - - + +
25A MET* 1.4 70.1 - - - +
27A GLU* 1.3 65.1 + - + +
29A GLU* 2.9 23.8 + - - -
30A ILE 4.2 9.9 + - - +
32A LEU* 3.6 28.0 - - + +
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Residues in contact with GLU 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 LYS* 2.9 40.6 + - - +
24A ALA* 3.0 6.1 + - - +
26A VAL* 1.3 78.3 - - + +
28A TYR* 1.4 68.7 + - + +
29A GLU* 3.3 5.1 - - - +
204A ARG* 3.6 24.0 + - - +
248A HIS* 5.2 6.8 - - - +
253A ASP* 5.6 1.7 - - - +
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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 ALA* 2.7 28.7 + - + -
25A MET* 3.0 9.9 + - - +
27A GLU* 1.4 80.9 - - + +
29A GLU* 1.4 67.2 + - - +
30A ILE* 3.7 3.1 - - + -
81A HIS* 4.0 1.7 + - - -
99A ALA 4.6 5.8 - - - -
100A LYS* 3.7 20.2 + - - -
102A GLU* 4.2 14.6 - - + +
103A MET* 3.1 52.4 - - + +
106A ASN* 3.4 38.3 + - + -
107A LEU* 5.8 1.3 - - + -
204A ARG* 3.0 34.9 + - - -
248A HIS* 4.5 5.5 - - - -
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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