Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 1UZX
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 PRO 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER 3.9 6.3 - - - +
9A VAL* 1.3 87.6 - - + +
11A GLU* 1.3 59.7 + - - +
12A ALA* 4.3 7.9 - - + +
13A VAL* 2.8 38.7 + - + +
14A VAL* 3.1 9.0 + - - +
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Residues in contact with GLU 11 (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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9A VAL 3.3 10.5 + - - +
10A PRO* 1.3 71.8 - - - +
12A ALA* 1.3 57.1 + - - +
14A VAL* 3.6 24.2 - - - +
15A ASN* 3.0 48.2 + - - +
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Residues in contact with ALA 12 (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 PRO* 3.0 7.1 - - + +
11A GLU* 1.3 78.1 - - - +
13A VAL* 1.3 63.4 + - + +
15A ASN* 3.8 6.1 + - - +
16A TRP* 3.2 23.7 + - - +
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Residues in contact with VAL 13 (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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9A VAL* 4.0 17.0 - - + -
10A PRO* 2.8 29.4 + - + +
12A ALA* 1.3 78.5 - - + +
14A VAL* 1.3 59.8 + - - +
16A TRP* 3.2 8.5 + - + +
17A LEU* 2.8 31.3 + - + +
39A LEU* 4.5 8.5 - - + -
47A PRO* 4.1 29.4 - - + -
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Residues in contact with VAL 14 (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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9A VAL* 3.6 25.1 - - + +
10A PRO 3.1 13.8 + - - +
11A GLU* 3.3 28.7 + - - +
13A VAL* 1.3 77.7 - - - +
15A ASN* 1.3 60.1 + - - +
17A LEU* 3.3 7.0 + - - +
18A PHE* 3.0 25.7 + - + +
32A PHE* 3.7 24.8 - - + -
36A LEU* 4.2 19.5 - - + -
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Residues in contact with ASN 15 (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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11A GLU* 3.0 35.7 + - - +
12A ALA* 4.1 5.8 - - - +
14A VAL* 1.3 79.5 - - - +
16A TRP* 1.3 64.1 + - - +
18A PHE* 3.5 6.9 + - - +
19A LYS* 3.0 42.6 + - - +
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Residues in contact with TRP 16 (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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12A ALA 3.2 18.2 + - - +
13A VAL* 3.5 9.6 - - + +
15A ASN* 1.3 78.6 - - - +
17A LEU* 1.3 82.5 + - + +
19A LYS* 3.1 14.9 + - + +
20A VAL* 2.9 59.2 + - + +
47A PRO* 3.8 31.0 - - + -
48A ARG* 3.6 29.4 - - - -
49A THR* 3.9 16.8 - - + -
63A LEU* 4.3 5.6 - - + -
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Residues in contact with LEU 17 (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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13A VAL* 2.8 22.0 + - + +
14A VAL* 3.4 6.5 - - - +
16A TRP* 1.3 85.7 - - + +
18A PHE* 1.3 62.9 + - - +
20A VAL* 3.6 2.1 + - + +
21A ILE* 3.1 51.4 + - + +
32A PHE* 3.8 21.1 - - + -
35A SER* 3.2 24.2 - - - +
36A LEU* 4.0 22.0 - - + +
39A LEU* 4.4 15.9 - - + -
47A PRO* 5.0 2.7 - - + -
63A LEU* 3.8 26.5 - - + -
65A ILE* 5.9 0.2 - - + -
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Residues in contact with PHE 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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14A VAL* 3.0 13.0 + - + +
15A ASN* 3.8 7.2 - - - +
17A LEU* 1.3 77.4 - - - +
19A LYS* 1.3 68.4 + - + +
21A ILE* 3.5 0.6 + - - +
22A GLN* 2.8 66.6 + - + +
29A ARG* 6.5 1.3 - - + -
32A PHE* 3.6 39.9 - + + -
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Residues in contact with LYS 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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15A ASN* 3.0 37.6 + - - +
16A TRP* 3.1 15.2 + - + +
18A PHE* 1.3 85.5 - - + +
20A VAL* 1.3 66.1 + - + +
22A GLN* 3.6 5.2 + - - +
23A PRO* 3.3 18.2 - - - +
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Residues in contact with VAL 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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16A TRP* 2.9 63.3 + - + +
17A LEU* 3.7 7.9 - - + +
19A LYS* 1.3 75.3 - - + +
21A ILE* 1.3 71.3 + - + +
23A PRO* 3.5 11.4 - - - +
24A ILE* 3.4 22.2 - - + +
25A TYR* 5.6 0.2 - - - -
49A THR* 3.8 28.0 - - + +
61A LEU* 6.2 1.3 - - + -
63A LEU* 4.8 2.9 - - + -
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Residues in contact with ILE 21 (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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17A LEU* 3.1 41.4 + - + +
18A PHE* 3.8 3.6 - - - +
19A LYS 3.3 0.8 - - - -
20A VAL* 1.3 79.0 - - + +
22A GLN* 1.3 71.0 + - - +
24A ILE 3.1 1.6 + - - -
25A TYR* 3.1 44.3 + - + +
28A GLY* 3.7 32.7 - - - +
31A THR* 4.0 7.2 - - + -
32A PHE* 3.6 31.6 - - + +
35A SER* 3.8 4.9 - - - +
63A LEU* 4.1 9.0 - - + -
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Residues in contact with GLN 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 PHE* 2.8 70.5 + - + +
19A LYS* 4.0 4.9 - - - +
21A ILE* 1.3 89.7 - - - +
23A PRO* 1.3 70.2 - - + +
24A ILE 3.3 0.3 + - - -
25A TYR 4.2 10.1 - - - +
28A GLY* 4.8 13.8 + - - -
32A PHE* 5.3 0.4 - - - +
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Residues in contact with PRO 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 LYS 3.3 14.4 - - - +
20A VAL* 3.5 11.7 - - - +
22A GLN* 1.3 94.2 - - + +
24A ILE* 1.3 64.6 + - + +
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Residues in contact with ILE 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 VAL* 3.4 20.0 - - + +
21A ILE 3.1 2.1 + - - +
23A PRO* 1.3 85.5 - - + +
25A TYR* 1.3 96.3 + - + +
26A ASN* 4.0 2.9 + - - -
49A THR* 4.6 9.6 - - + -
60A GLN* 5.1 2.7 + - - +
61A LEU* 3.5 53.8 - - + +
62A LEU* 4.1 12.8 - - + -
63A LEU* 5.7 0.2 - - + -
89A SER* 3.6 16.1 - - - -
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Residues in contact with TYR 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 ILE* 3.1 31.3 + - + +
22A GLN 4.2 8.8 - - - +
24A ILE* 1.3 97.7 - - + +
26A ASN* 1.3 65.4 + - - +
27A ASP 3.3 1.5 + - - +
28A GLY* 3.7 17.7 + - - +
31A THR* 3.6 31.4 - - + +
62A LEU* 3.8 1.9 - - - -
63A LEU* 2.8 42.7 + - + +
87A VAL* 2.7 31.0 + - + +
88A PRO 3.2 30.3 - - - -
89A SER* 3.7 8.7 - - - +
91A TYR* 4.8 0.4 - - + -
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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