Contacts of the helix formed by residues 12 - 29 (chain B) in PDB entry 3UXO
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 ASN 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 4.0 0.2 + - - -
11B LEU* 1.3 86.2 - - - +
13B GLY* 1.3 61.3 + - - +
14B GLY 3.1 3.4 - - - +
15B ILE* 3.0 16.9 + - + +
16B THR* 2.9 30.4 + - + +
46B ILE* 3.6 25.1 + - + +
47B ALA* 5.7 2.8 - - - +
49B TYR* 3.7 12.3 + - - -
51B HIS 3.0 21.6 + - - -
52B LYS* 3.5 0.9 + - - +
53B ILE* 2.5 44.3 + - - +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.1 28.0 + - - -
11B LEU 3.7 1.4 - - - -
12B ASN* 1.3 76.3 - - - +
14B GLY* 1.3 56.8 + - - +
16B THR* 3.7 9.0 - - - -
17B ASP* 2.8 42.0 + - - +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 5.6 1.0 - - - +
11B LEU 5.4 0.2 + - - -
12B ASN 3.1 1.4 - - - -
13B GLY* 1.3 76.6 - - - +
15B ILE* 1.3 63.8 + - - +
17B ASP* 3.3 9.5 + - - +
18B MET* 3.2 21.8 + - - +
76B PHE* 3.6 28.5 - - - -
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.0 20.3 + - + +
14B GLY* 1.3 75.1 - - - +
16B THR* 1.3 64.4 + - - +
18B MET* 3.1 24.6 + - + +
19B LEU* 3.1 14.2 + - + +
46B ILE* 4.0 15.0 - - + -
53B ILE* 3.9 28.7 - - + +
73B ILE* 3.6 46.7 - - + -
76B PHE* 4.4 16.8 - - + -
77B LEU* 4.0 15.0 - - + -
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN 2.9 18.8 + - - +
13B GLY* 3.5 15.9 + - - -
15B ILE* 1.3 72.8 - - - +
17B ASP* 1.3 66.0 + - - +
19B LEU* 3.2 7.3 + - - +
20B VAL* 2.9 26.6 + - - +
43B ALA* 3.4 34.2 - - - +
46B ILE* 3.8 20.6 - - + -
47B ALA* 3.8 17.8 - - + +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 2.8 33.1 + - - +
14B GLY* 3.6 7.5 - - - +
15B ILE 3.2 0.2 - - - -
16B THR* 1.3 79.3 + - - +
18B MET* 1.3 59.7 + - - +
20B VAL* 2.9 24.9 - - - +
21B GLU* 3.1 14.8 + - - +
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Residues in contact with MET 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.2 9.0 + - - +
15B ILE* 3.1 28.3 + - + +
17B ASP* 1.3 79.2 - - - +
19B LEU* 1.3 74.9 + - + +
21B GLU* 3.4 2.1 + - - +
22B LEU* 3.0 30.4 + - + +
72B LYS* 3.9 26.0 - - + +
73B ILE 4.2 1.6 - - - +
76B PHE* 3.6 36.6 - - + -
82B LEU* 3.9 27.6 - - + -
85B LEU* 3.9 25.1 - - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.1 14.7 + - + +
16B THR* 3.2 8.0 + - - +
18B MET* 1.3 95.2 - - + +
20B VAL* 1.3 52.3 + - - +
22B LEU* 3.2 8.1 + - + +
23B ALA* 2.8 34.8 + - - +
39B TYR* 3.7 31.7 - - + +
42B ALA* 3.7 13.9 - - + -
43B ALA* 3.4 35.7 - - + +
46B ILE* 3.9 20.9 - - + -
69B ILE* 4.0 20.9 - - + -
72B LYS* 5.9 1.1 - - + -
73B ILE* 5.2 0.2 - - + -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR 2.9 13.8 + - - +
17B ASP* 2.9 29.4 - - - +
19B LEU* 1.3 75.6 - - - +
21B GLU* 1.3 55.0 + - - +
23B ALA* 3.3 9.2 + - + +
24B ASN* 2.9 43.4 + - - +
39B TYR 6.0 0.2 - - - -
40B ARG* 6.2 1.1 - - - +
43B ALA* 4.6 8.2 - - + +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP 3.1 19.9 + - - +
18B MET* 3.7 4.4 - - - +
19B LEU 3.3 0.2 - - - -
20B VAL* 1.3 73.7 - - + +
22B LEU* 1.3 69.3 + - - +
24B ASN* 3.0 18.4 + - + +
25B PHE* 3.1 12.1 + - + +
85B LEU* 3.8 30.7 - - + +
88B ILE* 3.7 24.9 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 3.0 22.1 + - + +
19B LEU* 3.3 13.0 - - + +
21B GLU* 1.3 75.3 - - - +
23B ALA* 1.3 64.9 + - - +
25B PHE* 2.9 19.7 + - + +
26B GLU* 3.1 15.2 + - + +
39B TYR* 3.7 41.1 - - + +
72B LYS* 3.7 13.2 - - + -
82B LEU* 3.6 25.4 - - + -
84B LYS* 3.8 32.1 - - + +
85B LEU* 4.0 15.9 - - + -
87B LYS* 5.3 1.6 - - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 2.8 16.7 + - - +
20B VAL* 3.4 14.4 - - + +
21B GLU 3.3 0.2 - - - -
22B LEU* 1.3 72.4 - - - +
24B ASN* 1.3 61.4 + - - +
26B GLU 3.6 0.9 + - - +
27B LYS* 3.5 11.8 + - - +
36B TYR* 3.0 47.7 - - + +
39B TYR* 3.5 24.1 - - + -
40B ARG* 4.3 8.1 - - + +
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 2.9 35.7 + - - +
21B GLU* 3.0 10.4 + - + +
23B ALA* 1.3 77.8 - - - +
25B PHE* 1.3 58.3 + - - +
27B LYS* 4.1 6.1 - - - -
28B ASN* 2.9 51.6 + - - +
36B TYR* 4.4 11.9 - - - -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU* 3.1 9.6 + - + +
22B LEU* 2.9 13.3 + - + +
24B ASN* 1.3 78.9 - - - +
26B GLU* 1.3 73.8 + - + +
29B VAL* 3.0 71.5 + - + +
30B SER* 3.3 17.6 + - - -
84B LYS* 4.3 12.3 - - + -
85B LEU* 5.7 0.9 - - + -
87B LYS* 3.5 45.3 - - + +
91B ASP* 5.5 6.5 - - - -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.1 15.7 + - + +
23B ALA 4.2 2.5 - - - +
24B ASN 3.4 0.2 - - - -
25B PHE* 1.3 90.9 - - + +
27B LYS* 1.3 55.9 + - - +
30B SER* 3.5 18.8 + - - -
31B GLN 3.1 5.1 + - - -
32B ALA* 2.6 50.7 + - + +
35B LYS* 3.6 26.2 + - + +
36B TYR* 4.1 11.0 - - - +
39B TYR* 3.7 29.1 + - + -
84B LYS* 4.3 13.4 + - - -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 3.5 13.2 + - - +
24B ASN* 4.1 7.6 - - - +
25B PHE 3.1 0.2 - - - -
26B GLU* 1.3 80.3 - - - +
28B ASN* 1.3 82.0 + - - +
29B VAL 3.3 2.0 - - - -
31B GLN* 3.2 29.9 + - - +
32B ALA 4.7 0.2 - - - +
33B ILE* 4.4 21.8 - - + +
36B TYR* 3.9 43.4 + - + -
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASN* 2.9 37.4 + - - +
27B LYS* 1.3 103.8 + - - +
29B VAL* 1.3 66.6 + - + +
31B GLN* 3.7 7.3 + - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE* 3.0 50.1 + - + +
27B LYS 3.3 0.4 - - - -
28B ASN* 1.3 89.0 - - + +
30B SER* 1.3 62.8 + - - +
31B GLN* 3.3 13.5 + - - +
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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