Contacts of the helix formed by residues 17 - 34 (chain A) in PDB entry 1UDY
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 THR 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 GLU 4.0 0.2 + - - -
16A LEU* 1.3 73.1 - - - +
18A GLU* 1.3 66.1 + - - +
19A GLN* 3.8 8.4 + - - +
20A GLN* 2.8 50.6 + - - +
21A LYS* 3.0 9.2 + - - +
11D GLY* 3.4 27.4 - - - +
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Residues in contact with GLU 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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16A LEU 4.1 0.3 - - - +
17A THR* 1.3 70.8 - - - +
19A GLN* 1.3 61.0 + - - +
21A LYS* 2.9 36.0 + - + +
22A GLU* 3.2 24.8 + - - +
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Residues in contact with GLN 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 THR* 2.9 9.2 + - - +
18A GLU* 1.3 75.8 - - - +
20A GLN* 1.3 62.7 + - - +
22A GLU* 2.8 34.7 + - - +
23A PHE* 3.1 47.6 + - + -
75A LEU* 4.5 6.8 - - - +
79A ASP* 5.0 2.4 - - - +
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Residues in contact with GLN 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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15A GLU 4.5 0.8 + - - -
16A LEU* 3.5 22.4 - - + +
17A THR* 2.8 52.2 + - - +
19A GLN* 1.3 75.6 - - + +
21A LYS* 1.3 62.1 + - - +
23A PHE* 3.4 10.8 + - + +
24A GLN* 3.1 26.3 + - - +
78A ILE* 3.7 15.9 - - - +
79A ASP* 3.2 27.6 - - - +
82A LEU* 3.4 24.2 - - + +
11D GLY* 4.5 5.9 - - - -
12D PHE* 4.7 4.6 - - - +
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Residues in contact with LYS 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 GLU* 3.6 20.3 + - - +
16A LEU* 2.8 45.9 + - + -
17A THR 3.0 12.5 + - - +
18A GLU* 2.9 38.6 + - + +
19A GLN 3.1 0.2 - - - -
20A GLN* 1.3 76.9 - - - +
22A GLU* 1.3 61.2 + - - +
24A GLN* 4.0 6.1 - - - +
25A ALA* 3.4 21.7 + - - +
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Residues in contact with GLU 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 GLU* 3.2 16.8 + - - +
19A GLN* 2.8 22.5 + - - +
21A LYS* 1.3 76.7 - - + +
23A PHE* 1.3 70.6 + - + +
25A ALA* 3.1 6.7 + - - +
26A THR* 3.1 25.6 + - - +
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Residues in contact with PHE 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 GLN* 3.1 48.4 + - + -
20A GLN* 3.4 11.4 + - - +
22A GLU* 1.3 80.9 - - + +
24A GLN* 1.3 63.0 + - - +
26A THR* 3.2 9.8 + - - -
27A ALA* 3.0 24.4 + - - +
61A LEU* 4.3 6.3 - - + +
73A LEU* 5.6 6.1 - - + -
75A LEU* 3.4 41.7 - - + -
79A ASP* 4.0 14.8 - - + -
82A LEU* 6.1 3.1 - - + -
83A ILE* 4.1 25.4 - - + -
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Residues in contact with GLN 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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16A LEU* 3.6 24.7 - - + +
20A GLN 3.1 15.5 + - - +
21A LYS* 4.0 6.2 - - - +
23A PHE* 1.3 79.9 - - - +
25A ALA* 1.3 57.7 + - - +
27A ALA* 3.4 4.8 + - - +
28A ARG* 2.8 51.8 + - - +
82A LEU* 4.5 22.5 + - + +
83A ILE* 5.2 0.4 - - - +
86A GLU* 3.9 25.8 + - + +
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Residues in contact with ALA 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 LYS 3.4 15.7 + - - +
22A GLU* 3.1 7.0 + - - +
24A GLN* 1.3 79.9 + - - +
26A THR* 1.3 62.6 + - - +
28A ARG* 3.8 7.4 - - - +
29A LYS* 3.1 25.1 + - - +
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Residues in contact with THR 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 GLU* 3.1 15.7 + - - +
23A PHE* 3.3 10.0 - - - -
24A GLN 3.1 0.2 - - - -
25A ALA* 1.3 74.4 - - - +
27A ALA* 1.3 66.7 + - - +
29A LYS* 3.2 5.7 + - - +
30A PHE* 2.9 24.8 + - - +
59A LEU* 4.0 41.0 - - + +
61A LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 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 PHE 3.0 13.1 + - - +
24A GLN 3.8 1.8 - - - +
26A THR* 1.3 79.3 - - - +
28A ARG* 1.3 58.0 + - - +
30A PHE* 3.5 1.2 - - - +
31A ALA* 2.8 32.1 + - - +
61A LEU* 3.6 14.6 - - + +
83A ILE* 3.8 20.2 - - + +
86A GLU* 3.7 16.8 - - + -
87A LEU* 3.6 20.8 - - + +
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Residues in contact with ARG 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 GLN* 2.8 42.3 + - - +
25A ALA* 3.8 7.0 - - - +
27A ALA* 1.3 73.3 - - - +
29A LYS* 1.3 64.1 + - - +
31A ALA* 3.2 3.5 + - - +
32A ARG* 3.0 65.8 + - - +
86A GLU* 2.6 47.3 + - - +
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Residues in contact with LYS 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 ALA 3.1 16.5 + - - +
26A THR* 3.8 3.4 - - - +
28A ARG* 1.3 79.6 - - - +
30A PHE* 1.3 67.5 + - - +
32A ARG* 3.2 2.7 + - - -
33A GLU* 2.9 72.6 + - - +
34A GLU* 5.9 1.6 - - - +
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Residues in contact with PHE 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 THR 2.9 18.2 + - - +
27A ALA 3.5 2.7 - - - +
29A LYS* 1.3 77.9 - - - +
31A ALA* 1.3 57.8 + - - +
34A GLU* 2.9 76.8 + - + +
35A ILE* 3.2 28.7 + - + -
52A LEU* 3.5 30.1 - - + -
55A ARG* 4.0 14.6 - - + -
56A ALA* 4.1 19.5 - - + -
59A LEU* 3.9 20.6 - - + -
61A LEU* 3.9 17.5 - - + -
87A LEU* 4.3 7.6 - - + -
94A VAL* 5.6 0.4 - - + -
98A ILE* 5.1 5.2 - - + -
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Residues in contact with ALA 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 ALA 2.8 20.2 + - - +
28A ARG* 3.7 4.3 - - - +
30A PHE* 1.3 75.7 - - - +
32A ARG* 1.3 61.0 + - + +
35A ILE* 3.3 23.8 - - + +
36A ILE* 3.0 33.5 + - - +
86A GLU 3.3 28.7 - - - +
87A LEU* 4.2 3.1 - - + +
89A TYR* 5.4 0.7 - - + -
90A GLY* 4.2 4.9 - - - +
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Residues in contact with ARG 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 ARG* 3.0 55.6 + - - +
29A LYS* 4.2 2.7 - - - +
31A ALA* 1.3 80.2 - - + +
33A GLU* 1.3 64.2 + - + +
34A GLU 3.7 0.2 - - - -
36A ILE* 4.0 15.5 - - + +
37A PRO* 3.8 13.2 - - - +
86A GLU* 4.7 4.0 + - - -
89A TYR* 3.4 58.7 + - + -
268A GLN* 5.6 2.0 - - - +
272A ASP* 4.4 2.2 + - - -
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Residues in contact with GLU 33 (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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29A LYS* 2.9 61.7 + - - +
30A PHE* 5.3 0.2 - - - -
32A ARG* 1.3 80.2 - - + +
34A GLU* 1.3 71.1 + - + +
37A PRO* 3.1 18.7 - - - +
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Residues in contact with GLU 34 (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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29A LYS* 5.9 1.2 - - - +
30A PHE* 2.9 45.5 + - + +
33A GLU* 1.3 90.3 - - + +
35A ILE* 1.3 60.6 + - - +
37A PRO* 3.5 5.1 - - - +
38A VAL* 3.4 21.5 - - - +
52A LEU* 3.8 11.3 - - + +
55A ARG* 2.8 49.7 + - - +
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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