Contacts of the helix formed by residues 11 - 23 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B TYR* 1.3 72.1 - - - +
12B TRP* 1.3 63.9 + - - +
13B SER* 3.3 10.4 + - - -
14B TRP* 2.9 35.0 + - + +
15B MET* 3.1 20.3 + - - +
102B ARG* 4.2 18.2 - - - +
104B GLY* 2.8 32.1 + - - +
105B LEU* 4.8 1.8 - - + -
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Residues in contact with TRP 12 (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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6B TRP* 3.2 38.2 - + - -
10B TYR* 3.2 55.9 + + - -
11B ASP* 1.3 73.7 - - - +
13B SER* 1.3 57.4 + - - +
15B MET* 4.4 3.8 - - + -
16B LEU* 3.0 50.7 + - + +
32B ASP 5.9 0.2 - - - +
50B ALA* 6.1 0.2 - - + -
52B PRO* 3.5 32.1 - - + -
54B ILE* 3.2 34.8 - - + -
59B LEU* 3.8 20.0 - - + -
82B PHE* 3.6 39.3 - + + -
84B LEU* 4.7 2.2 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.2 8.1 + - - -
12B TRP* 1.3 78.8 - - - +
14B TRP* 1.3 61.9 + - - +
16B LEU* 4.2 4.7 - - - +
17B GLY* 3.2 18.7 + - - -
32B ASP 6.0 0.4 - - - -
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Residues in contact with TRP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 2.9 31.6 + - + +
13B SER* 1.3 77.1 - - - +
15B MET* 1.3 70.8 + - + +
17B GLY* 3.3 0.9 + - - -
18B PHE* 2.9 35.7 + + + +
102B ARG* 4.0 16.8 - - - -
105B LEU* 3.3 36.5 - - + +
106B ARG 3.2 30.3 - - - -
108B PRO* 4.1 21.1 - - + -
269B LEU* 4.3 11.4 - - + -
273B TYR* 3.0 60.8 - + - -
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Residues in contact with MET 15 (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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10B TYR* 3.6 33.2 - - + +
11B ASP 3.1 14.8 + - - +
12B TRP* 3.9 8.1 - - + +
14B TRP* 1.3 86.5 - - + +
16B LEU* 1.3 63.3 + - + +
18B PHE* 3.1 6.4 + - - +
19B LEU* 2.9 39.8 + - + +
81B LEU 4.6 5.2 - - - +
82B PHE* 3.9 19.7 - - + -
106B ARG* 3.6 27.4 - - + +
107B LEU 4.2 1.6 - - - +
108B PRO* 3.9 38.8 - - + -
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Residues in contact with LEU 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 TRP* 3.0 44.5 + - + +
13B SER* 4.5 3.1 - - - +
15B MET* 1.3 77.3 - - - +
17B GLY* 1.3 53.6 + - - +
19B LEU* 4.5 2.2 - - + +
20B ALA* 2.7 36.8 + - - +
30B VAL* 3.5 11.7 - - + +
31B ALA 3.5 14.4 - - - +
32B ASP* 3.2 30.5 - - - +
33B SER 4.6 2.2 - - - -
34B TYR* 4.2 13.2 - - - +
35B TYR* 4.2 27.8 - - + -
52B PRO* 5.0 4.9 - - + -
82B PHE* 4.8 8.1 - - + -
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Residues in contact with GLY 17 (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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13B SER 3.2 16.4 + - - -
14B TRP 3.7 3.6 - - - -
15B MET 3.2 0.8 - - - -
16B LEU* 1.3 74.0 - - - +
18B PHE* 1.3 64.8 + - - +
20B ALA* 3.8 5.4 - - - +
21B ALA* 3.2 24.1 + - - +
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Residues in contact with PHE 18 (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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14B TRP* 2.9 36.2 + + + +
15B MET* 3.1 10.1 + - - +
17B GLY* 1.3 76.0 - - - +
19B LEU* 1.3 69.1 + - + +
21B ALA* 3.8 0.6 + - - -
22B ARG* 3.0 78.1 + - - +
108B PRO* 3.5 39.0 - - + -
222B TYR* 4.4 5.2 - + - -
226B ARG* 3.7 23.3 - - - -
269B LEU* 5.2 8.1 - - + -
272B TRP* 5.3 7.0 - + - -
273B TYR* 3.6 24.5 - + - +
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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 MET* 2.9 40.4 + - + +
16B LEU* 3.9 7.0 - - + +
18B PHE* 1.3 89.1 - - + +
20B ALA* 1.3 63.7 + - - +
22B ARG* 3.4 4.8 + - + +
23B ALA* 3.0 23.7 + - - +
28B GLU* 4.8 5.4 - - - +
30B VAL* 4.0 2.9 - - + +
35B TYR* 4.3 29.4 - - + +
81B LEU* 4.3 22.0 - - + -
82B PHE* 3.8 24.5 - - + -
108B PRO* 4.7 2.9 - - + -
226B ARG* 4.5 13.5 - - - +
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Residues in contact with ALA 20 (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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16B LEU 2.7 22.8 + - - +
17B GLY* 3.3 6.9 + - - +
19B LEU* 1.3 76.0 - - - +
21B ALA* 1.3 64.0 + - - +
23B ALA* 3.1 16.5 + - - +
30B VAL* 3.8 25.6 - - + +
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Residues in contact with ALA 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 GLY 3.2 14.8 + - - +
18B PHE* 4.0 5.8 - - - +
20B ALA* 1.3 79.2 - - - +
22B ARG* 1.3 69.1 + - - +
23B ALA 3.9 0.7 + - - +
128B VAL* 4.1 17.5 - - + +
129B ALA* 5.3 1.9 - - - -
132B ALA* 4.3 11.1 - - - +
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Residues in contact with ARG 22 (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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18B PHE* 3.0 72.2 + - - +
19B LEU* 3.4 6.7 + - + +
20B ALA 3.1 0.4 - - - -
21B ALA* 1.3 89.2 - - - +
23B ALA* 1.3 64.6 + - - +
24B VAL* 3.5 2.6 + - - +
28B GLU* 5.0 0.2 - - - -
119B ARG* 3.2 27.9 + - - +
128B VAL* 3.7 32.5 - - + +
132B ALA* 4.5 10.5 - - - +
222B TYR* 4.1 10.3 + - - -
226B ARG* 3.9 14.1 - - - +
272B TRP* 5.7 5.3 - - - -
273B TYR* 4.3 9.1 + - - -
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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
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19B LEU 3.0 11.5 + - - +
20B ALA 3.1 16.1 + - - +
21B ALA 3.5 0.5 - - - +
22B ARG* 1.3 78.5 - - - +
24B VAL* 1.3 62.1 + - - +
25B SER 3.9 0.9 + - - -
28B GLU* 3.1 30.5 - - + +
30B VAL* 3.7 14.4 - - + -
132B ALA* 4.4 11.4 - - - +
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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