Contacts of the helix formed by residues 11 - 22 (chain A) in PDB entry 1DIZ
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 1.3 72.8 - - - +
12A TRP* 1.3 56.2 + - - +
13A SER* 3.2 14.2 + - - -
14A TRP* 3.0 31.1 + - + +
15A MET* 3.1 26.0 + - - +
102A ARG* 5.3 14.8 + - + +
104A GLY* 2.7 32.6 + - - +
105A LEU* 4.4 3.1 - - + +
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Residues in contact with TRP 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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6A TRP* 3.1 40.7 - + - -
10A TYR* 3.1 59.9 + + - -
11A ASP* 1.3 69.8 + - - +
13A SER* 1.3 60.1 + - - +
15A MET* 3.9 3.4 - - + -
16A LEU* 3.0 52.1 + - + +
52A PRO* 3.4 31.4 - - + -
54A ILE* 3.3 33.0 - - + -
59A LEU* 3.8 21.1 - - + -
82A PHE* 3.6 38.1 - + + -
84A LEU* 4.8 2.7 - - + -
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Residues in contact with SER 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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11A ASP* 3.2 10.5 + - - -
12A TRP* 1.3 77.2 - - - +
14A TRP* 1.3 61.8 + - - +
16A LEU* 4.5 4.2 - - - +
17A GLY* 3.1 22.5 + - - -
32A ASP 6.0 0.7 - - - -
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Residues in contact with TRP 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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11A ASP* 3.0 30.2 + - + +
13A SER* 1.3 78.9 + - - +
15A MET* 1.3 71.5 + - + +
17A GLY* 3.3 1.3 + - - -
18A PHE* 2.8 34.6 + + + +
102A ARG* 3.9 23.3 - - - +
104A GLY 5.6 0.2 - - - -
105A LEU* 3.3 39.6 - - + +
106A ARG 3.2 29.8 - - - -
108A PRO* 4.0 23.6 - - + -
269A LEU* 4.5 8.7 - - + -
273A TYR* 3.3 56.3 - + - -
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Residues in contact with MET 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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10A TYR* 3.5 32.5 - - + +
11A ASP 3.1 15.9 + - - +
12A TRP* 4.0 7.6 - - + +
14A TRP* 1.3 85.8 - - + +
16A LEU* 1.3 63.9 + - - +
18A PHE* 3.0 5.1 + - - +
19A LEU* 3.0 40.5 + - + +
81A LEU 4.4 6.5 - - - +
82A PHE* 4.0 18.8 - - + +
106A ARG* 3.6 25.4 - - + +
107A LEU 4.3 0.7 - - - -
108A PRO* 4.0 40.6 - - + -
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Residues in contact with LEU 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 TRP* 3.0 45.8 + - + +
13A SER* 4.5 4.3 - - - +
15A MET* 1.3 77.9 - - - +
17A GLY* 1.3 57.3 + - - +
19A LEU* 3.3 3.4 + - + +
20A ALA* 2.8 31.3 + - - +
30A VAL* 3.5 12.3 - - + +
31A ALA 3.7 13.5 - - - +
32A ASP* 3.2 29.4 - - - +
33A SER 4.8 1.8 - - - -
34A TYR* 4.2 14.1 - - - +
35A TYR* 4.1 27.8 - - + -
52A PRO* 5.0 4.9 - - + -
82A PHE* 4.9 8.5 - - + -
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Residues in contact with GLY 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 SER 3.1 20.6 + - - -
14A TRP 3.6 1.1 - - - -
16A LEU* 1.3 76.0 - - - +
18A PHE* 1.3 62.8 + - - +
20A ALA* 3.4 6.6 + - - +
21A ALA* 3.2 22.9 + - - +
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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 TRP* 2.8 37.4 + + + +
15A MET* 3.4 7.4 - - - +
17A GLY* 1.3 80.0 - - - +
19A LEU* 1.3 68.6 + - + +
21A ALA* 3.6 3.9 + - - -
22A ARG* 2.8 65.7 + - - +
108A PRO* 3.4 37.0 - - + -
222A TYR* 4.5 3.8 - + - -
226A ARG* 3.8 28.3 - - - -
269A LEU* 5.0 8.3 - - + -
272A TRP* 5.3 8.3 - + - -
273A TYR* 3.6 28.0 - + - +
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Residues in contact with LEU 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 MET* 3.0 32.4 + - + +
16A LEU* 3.9 7.9 - - + +
18A PHE* 1.3 89.0 - - + +
20A ALA* 1.3 64.9 + - - +
22A ARG* 3.4 6.2 + - + +
23A ALA* 3.0 23.0 + - - +
28A GLU* 4.7 6.7 - - - +
30A VAL* 4.0 3.7 - - + +
35A TYR* 4.1 29.8 - - + -
81A LEU* 4.3 23.6 - - + -
82A PHE* 3.9 27.8 - - + -
108A PRO* 4.6 7.2 - - + -
226A ARG* 4.6 7.9 - - - +
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Residues in contact with ALA 20 (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 LEU 2.8 19.0 + - - +
17A GLY* 3.7 9.2 - - - +
18A PHE 3.2 0.4 - - - -
19A LEU* 1.3 76.3 - - - +
21A ALA* 1.3 66.1 + - - +
22A ARG 3.1 1.0 + - - -
23A ALA* 3.1 14.8 + - - +
30A VAL* 3.9 23.5 - - + +
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Residues in contact with ALA 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 GLY 3.2 13.5 + - - +
18A PHE* 5.1 0.2 - - - -
19A LEU 3.4 0.2 - - - -
20A ALA* 1.3 79.4 - - - +
22A ARG* 1.3 75.7 + - - +
23A ALA 3.9 0.2 + - - -
128A VAL* 4.0 22.8 - - + +
129A ALA* 5.4 1.4 - - - -
132A ALA* 4.3 6.2 - - - +
273A TYR* 6.1 0.2 - - - +
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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 PHE* 2.8 81.5 + - - +
19A LEU* 3.4 7.7 + - + +
20A ALA 3.0 0.8 - - - -
21A ALA* 1.3 92.4 - - - +
23A ALA* 1.3 63.7 + - - +
24A VAL* 3.4 4.2 + - - +
28A GLU* 3.9 1.1 - - - +
119A ARG* 3.4 27.7 + - - +
128A VAL* 3.8 31.3 - - + +
132A ALA* 4.8 11.2 - - - +
222A TYR* 4.1 10.6 + - - -
226A ARG* 3.9 13.7 - - - +
272A TRP* 5.9 4.0 - - - -
273A TYR* 4.3 8.9 + - - -
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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