Contacts of the helix formed by residues 12 - 24 (chain A) in PDB entry 1X57
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 LEU 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 5.0 9.6 - - + -
11A THR* 1.3 77.1 - - - +
13A GLU* 1.3 71.0 + - - +
14A VAL* 3.2 11.2 - - + +
15A GLY 3.0 5.9 + - - +
16A LYS* 2.9 24.9 + - - +
46A TYR 5.3 0.2 - - - +
47A GLU 4.2 0.8 + - - -
48A SER 3.4 16.4 + - - +
49A GLY* 4.1 26.5 - - - +
53A PRO* 5.9 7.0 - - + -
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Residues in contact with GLU 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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12A LEU* 1.3 82.9 - - - +
14A VAL* 1.3 60.1 + - + +
16A LYS* 3.7 7.7 - - - +
17A VAL* 2.8 35.7 + - + +
71A GLY 5.6 2.2 - - - +
72A LYS* 6.1 1.2 - - - +
74A ILE* 3.7 30.5 - - + -
89A SER* 4.2 24.6 + - - -
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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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12A LEU* 3.2 9.8 - - + +
13A GLU* 1.3 82.0 - - + +
15A GLY* 1.3 57.7 + - - +
17A VAL* 3.2 1.0 + - - +
18A ILE* 2.8 54.5 + - + +
46A TYR* 3.6 23.8 - - + +
53A PRO* 4.9 7.4 - - + -
58A LEU* 3.9 13.2 - - + -
69A LEU* 3.4 28.9 - - + +
74A ILE* 3.7 10.1 - - + -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 4.9 0.9 - - - -
12A LEU* 3.0 7.9 + - - +
14A VAL* 1.3 78.7 - - - +
16A LYS* 1.3 61.0 + - - +
18A ILE* 3.4 4.9 + - - +
19A GLN* 3.0 25.1 + - - +
46A TYR 3.3 23.5 + - - -
47A GLU* 3.4 25.0 - - - +
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Residues in contact with LYS 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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11A THR* 3.9 23.4 + - - +
12A LEU 2.9 12.5 + - - +
13A GLU* 3.7 11.7 - - - +
15A GLY* 1.3 74.5 - - - +
17A VAL* 1.3 52.5 + - + +
19A GLN* 3.1 19.0 + - - +
20A GLN* 2.8 66.5 + - + +
47A GLU 4.5 0.4 + - - -
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Residues in contact with VAL 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 GLU* 2.8 23.7 + - + +
14A VAL 3.9 2.7 - - - +
16A LYS* 1.3 72.2 - - + +
18A ILE* 1.3 56.4 + - - +
20A GLN* 4.1 13.7 - - - +
21A GLY 2.8 25.6 + - - -
65A ILE* 3.4 21.1 - - + +
67A LEU* 4.5 3.8 - - + -
68A LYS 3.8 20.6 - - - +
69A LEU* 4.2 4.9 - - + -
74A ILE* 3.8 30.1 - - + -
75A GLY* 3.8 18.4 - - - +
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Residues in contact with ILE 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* 2.8 48.2 + - + +
15A GLY* 3.4 7.0 - - - +
16A LYS 3.2 0.2 - - - -
17A VAL* 1.3 72.2 - - - +
19A GLN* 1.3 57.4 + - - +
21A GLY 3.8 0.2 - - - -
22A ARG* 2.9 41.7 + - + +
32A LEU* 5.2 4.9 - - + -
43A ILE* 4.4 20.9 - - + +
46A TYR* 3.5 27.1 - - + -
47A GLU* 4.3 14.6 - - + -
61A ILE* 3.7 30.1 - - + -
65A ILE* 4.3 7.6 - - + +
69A LEU* 3.8 5.2 - - + -
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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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11A THR* 5.7 7.7 + - - +
15A GLY 3.0 13.3 + - - +
16A LYS* 3.4 22.9 + - - +
18A ILE* 1.3 76.2 - - - +
20A GLN* 1.3 58.1 + - + +
22A ARG* 3.3 26.0 - - - +
23A GLN* 2.8 38.3 + - + +
47A GLU* 3.9 20.7 + - - -
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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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16A LYS* 2.8 50.2 + - + +
17A VAL* 3.8 13.3 - - - +
19A GLN* 1.3 74.5 - - + +
21A GLY* 1.3 57.1 + - - +
23A GLN* 3.2 14.0 + - + +
24A SER* 2.9 33.4 + - - -
67A LEU* 5.7 2.2 - - + -
85A LYS 5.6 2.1 - - - +
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Residues in contact with GLY 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 VAL 2.8 19.5 + - - -
20A GLN* 1.3 69.1 - - - +
22A ARG* 1.3 68.5 + - - +
24A SER* 3.5 11.6 + - - -
25A LYS* 3.6 22.3 + - - +
65A ILE* 3.5 24.7 - - - -
67A LEU* 4.5 11.6 - - - +
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Residues in contact with ARG 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 ILE* 2.9 26.8 + - + +
19A GLN* 3.3 22.9 - - - +
21A GLY* 1.3 74.5 - - - +
23A GLN* 1.3 62.6 + - - +
25A LYS* 2.9 19.8 + - - +
27A LEU* 2.8 62.0 + - - +
28A THR* 3.6 16.2 - - - +
29A GLN* 3.3 27.1 - - - +
32A LEU* 3.5 34.1 - - + -
43A ILE* 4.6 0.7 - - - -
47A GLU* 2.7 31.9 + - - -
65A ILE* 3.6 4.1 - - - +
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Residues in contact with GLN 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* 2.8 24.3 + - + +
20A GLN* 3.2 18.8 + - + +
22A ARG* 1.3 76.4 - - + +
24A SER* 1.3 92.0 + - - +
25A LYS 3.1 1.2 + - - -
26A GLY* 3.2 14.9 + - - +
27A LEU 5.2 0.4 - - - -
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Residues in contact with SER 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 GLN 2.9 16.5 + - - -
21A GLY* 3.7 10.1 - - - -
22A ARG 3.2 0.4 - - - -
23A GLN* 1.3 93.8 + - - +
25A LYS* 1.3 61.5 + - - +
26A GLY 3.7 0.2 - - - -
67A LEU* 6.4 0.7 - - - -
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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