Contacts of the helix formed by residues 12 - 24 (chain B) in PDB entry 1NZ0
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 ARG 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.4 20.3 + - + +
11B LEU* 1.3 76.9 - - - +
13B LEU* 1.3 59.8 + - - +
14B ARG* 3.3 35.0 - - + +
15B ARG* 2.9 19.5 + - + +
16B ASP* 2.8 31.6 + - - +
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Residues in contact with LEU 13 (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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11B LEU* 3.6 15.9 + - + +
12B ARG* 1.3 73.1 - - - +
14B ARG* 1.3 80.3 + - - +
16B ASP* 4.1 1.6 - - - +
17B PHE* 3.0 45.5 + - + +
20B ILE* 5.0 2.5 - - + -
47B GLY* 3.9 6.7 - - - -
48B ILE 3.8 33.4 - - - +
49B VAL* 3.9 11.9 - - + -
85B VAL* 3.8 28.7 - - + -
14D ARG 5.0 1.7 - - - +
18D LEU* 3.9 19.7 - - + +
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Residues in contact with ARG 14 (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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11B LEU 4.2 6.2 + - - -
12B ARG* 3.5 33.6 - - + +
13B LEU* 1.3 113.2 - - - +
15B ARG* 1.3 67.8 + - + +
14D ARG* 3.1 23.8 - - - +
15D ARG* 4.6 3.9 - - - +
18D LEU* 4.4 7.7 - - - +
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Residues in contact with ARG 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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12B ARG* 2.9 20.7 + - + +
14B ARG* 1.3 91.0 + - + +
16B ASP* 1.3 70.7 + - - +
17B PHE 3.9 1.1 - - - -
18B LEU* 5.4 2.6 + - - +
19B LEU* 5.3 2.8 + - - +
14D ARG* 5.0 10.7 - - - +
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Residues in contact with ASP 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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11B LEU* 3.9 18.1 - - + +
12B ARG* 2.8 16.7 + - - +
13B LEU* 4.8 0.9 - - - -
15B ARG* 1.3 91.4 - - - +
17B PHE* 1.3 64.4 + - - +
18B LEU 3.4 2.5 - - - -
19B LEU* 3.2 23.7 + - + +
20B ILE* 3.0 38.6 + - + +
37B ARG* 4.9 4.1 + - - -
45B ARG* 4.3 8.8 + - - -
83B ASP* 4.5 3.1 - - - +
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Residues in contact with PHE 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 LEU* 3.0 32.4 + - + +
15B ARG 3.9 0.6 - - - -
16B ASP* 1.3 76.4 - - - +
18B LEU* 1.3 64.2 + - - +
20B ILE* 3.2 5.9 + - + +
21B PHE* 2.9 30.9 + + - +
35B LEU* 4.1 19.5 - - + -
49B VAL* 4.1 21.1 - - + -
85B VAL* 4.3 12.8 - - + -
87B ILE* 4.9 1.8 - - + -
14D ARG 5.9 0.9 + - - +
17D PHE* 3.6 33.4 - + + -
18D LEU* 3.7 40.4 - - + -
21D PHE* 4.0 34.5 - + - -
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Residues in contact with LEU 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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15B ARG 5.4 2.4 + - - +
16B ASP 3.4 0.4 - - - -
17B PHE* 1.3 80.8 - - - +
19B LEU* 1.3 64.4 + - - +
21B PHE* 3.3 1.1 + - - +
22B LYS* 3.0 53.9 + - + +
13D LEU* 3.8 30.3 - - + +
14D ARG* 3.8 21.6 + - + +
17D PHE* 3.6 30.1 - - + -
49D VAL* 3.9 18.4 - - + -
5016D SO4 3.9 11.4 - - - +
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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 ARG 5.3 2.0 + - - +
16B ASP* 3.2 28.7 + - + +
18B LEU* 1.3 79.0 - - - +
20B ILE* 1.3 64.0 + - - +
22B LYS* 4.8 4.0 - - + -
23B GLU* 3.0 70.6 + - + +
37B ARG* 3.7 34.3 - - - +
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Residues in contact with ILE 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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11B LEU* 4.4 8.5 - - + -
13B LEU* 5.0 1.8 - - + -
16B ASP* 3.0 31.4 + - + +
17B PHE* 3.7 5.6 - - + +
19B LEU* 1.3 77.1 - - + +
21B PHE* 1.3 57.5 + - - +
24B GLY* 2.9 28.2 + - - -
25B LYS 5.3 0.2 - - - +
35B LEU* 4.0 35.1 - - + +
36B PHE* 4.3 3.8 - - - +
37B ARG* 4.1 31.9 - - + +
83B ASP* 4.1 22.9 - - + +
85B VAL* 3.9 25.4 - - + -
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Residues in contact with PHE 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 PHE* 2.9 27.2 + + + +
18B LEU 3.6 4.0 - - - +
20B ILE* 1.3 76.3 - - - +
22B LYS* 1.3 62.8 + - - +
24B GLY 4.5 4.7 + - - +
35B LEU* 4.1 30.5 - - + +
17D PHE* 3.5 30.1 - + + -
21D PHE* 4.5 15.0 - + - -
49D VAL* 3.6 31.2 - - + -
51D LYS* 3.7 46.2 - - + +
87D ILE* 4.2 19.7 - - + -
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Residues in contact with LYS 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 LEU* 3.0 45.9 + - + +
19B LEU* 4.1 3.4 - - - +
21B PHE* 1.3 77.8 - - - +
23B GLU* 1.3 65.0 + - + +
24B GLY 3.7 1.7 - - - +
13D LEU* 6.3 0.8 - - - +
48D ILE 5.3 5.3 + - - -
49D VAL* 3.6 25.8 - - + -
50D VAL 3.7 24.7 - - - +
51D LYS* 3.6 9.3 - - - +
52D ARG* 2.9 28.7 + - - +
53D LYS 4.8 0.3 + - - -
64D LYS* 6.0 1.4 - - - +
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Residues in contact with GLU 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 40.5 + - + +
22B LYS* 1.3 81.2 - - + +
24B GLY* 1.3 66.9 + - - +
25B LYS* 5.4 0.7 - - - +
37B ARG* 4.2 21.1 + - + +
52D ARG* 2.9 57.4 + - + +
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Residues in contact with GLY 24 (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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20B ILE* 2.9 20.2 + - - +
21B PHE 4.7 5.0 - - - +
22B LYS 3.7 1.6 - - - +
23B GLU* 1.3 85.9 + - - +
25B LYS* 1.3 66.9 + - - +
36B PHE 3.2 13.9 - - - -
37B ARG* 4.1 10.3 - - - -
53D LYS* 5.7 4.7 - - - +
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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