Contacts of the helix formed by residues 16 - 24 (chain B) in PDB entry 2NXJ
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 ILE 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.7 26.7 - - + -
13B LEU* 2.8 47.5 + - + +
14B ASP 2.8 0.4 + - - -
15B PRO* 1.3 78.4 - - + +
17B LEU* 1.3 63.5 + - - +
18B PRO* 3.2 4.7 - - - -
19B GLY* 2.9 15.9 + - - -
20B LEU* 3.7 7.2 + - + +
47B TYR* 3.3 57.1 + - + -
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Residues in contact with LEU 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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14A ASP* 5.2 1.6 - - - +
17A LEU* 4.5 3.6 - - + -
21A PHE* 3.8 25.8 - - + -
10B LEU* 4.7 8.5 - - + +
13B LEU* 3.5 18.5 + - + +
14B ASP* 3.0 38.4 + - - +
16B ILE* 1.3 76.5 - - - +
18B PRO* 1.4 61.7 - - + +
20B LEU* 3.0 30.0 + - + +
21B PHE* 2.9 52.6 + - + -
28B LEU* 4.2 17.7 - - + -
35B VAL* 5.6 1.3 - - + -
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Residues in contact with PRO 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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14A ASP* 4.7 15.7 - - - +
14B ASP 3.9 7.2 - - - +
15B PRO 4.1 5.8 - - - +
16B ILE* 3.2 8.7 - - - +
17B LEU* 1.4 89.1 - - + +
19B GLY* 1.3 55.3 + - - +
20B LEU 3.3 0.2 - - - -
21B PHE* 3.9 14.5 - - + +
22B ASP* 2.7 42.2 + - - +
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Residues in contact with GLY 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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16B ILE 2.9 6.4 + - - -
18B PRO* 1.3 79.1 - - - +
20B LEU* 1.3 60.4 + - - +
22B ASP* 3.7 7.3 - - - +
23B GLY 3.2 15.6 + - - -
45B LEU* 3.8 11.8 - - - +
47B TYR* 3.0 31.5 + - - -
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Residues in contact with LEU 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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4B TYR* 3.8 28.7 - - + -
6B LEU* 4.0 16.6 - - + -
13B LEU* 6.1 0.4 - - + -
16B ILE* 4.2 9.4 - - + +
17B LEU* 3.0 35.2 + - + +
19B GLY* 1.3 74.0 - - - +
21B PHE* 1.3 65.4 + - + +
23B GLY 3.2 8.5 + - - -
25B ALA* 3.2 29.6 + - + +
28B LEU* 3.9 15.5 - - + -
35B VAL* 5.6 2.9 - - + -
37B ALA* 4.5 7.6 - - + -
39B PHE* 3.3 12.9 - - + -
45B LEU* 4.1 7.9 - - + -
47B TYR* 3.9 19.7 - - + -
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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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10A LEU* 3.8 37.9 - - + -
11A GLU* 4.9 14.4 - - + +
14A ASP* 3.9 25.8 - - - -
17A LEU* 4.0 17.7 - - + -
17B LEU* 2.9 42.1 + - + +
18B PRO* 3.9 9.9 - - + +
20B LEU* 1.3 72.6 - - + +
22B ASP* 1.3 57.6 + - - +
24B GLY* 3.0 18.9 + - - -
25B ALA* 3.7 19.5 + - + +
28B LEU* 3.7 31.0 - - + -
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Residues in contact with ASP 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 PRO* 2.7 26.6 + - - +
19B GLY* 3.7 9.1 - - - +
21B PHE* 1.3 69.8 - - - +
23B GLY* 1.3 60.3 + - - +
24B GLY* 3.1 5.6 + - - -
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Residues in contact with GLY 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 GLY 3.2 8.1 + - - -
20B LEU 3.2 8.8 + - - -
22B ASP* 1.3 78.2 - - - +
24B GLY* 1.3 55.3 + - - +
39B PHE* 3.4 21.1 - - - -
40B PRO* 5.9 0.3 - - - +
41B ALA 4.9 1.6 - - - +
43B VAL* 4.0 27.6 - - - +
45B LEU* 4.5 3.6 - - - -
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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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21B PHE 3.0 11.9 + - - -
22B ASP 3.1 1.5 - - - -
23B GLY* 1.3 79.3 - - - +
25B ALA* 1.3 64.2 + - - +
26B ARG* 3.6 9.2 + - - -
39B PHE* 3.5 11.8 - - - -
40B PRO* 3.6 20.3 - - - +
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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