Contacts of the helix formed by residues 21 - 32 (chain B) in PDB entry 1JW9
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 PHE 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLN* 3.4 29.4 - - + -
18B LEU* 2.9 24.8 + - + +
19B ARG 3.2 0.2 - - - -
20B GLY* 1.3 79.6 - - - +
22B ASP* 1.3 71.2 + - - +
24B ASP* 4.0 2.4 + - - +
25B GLY* 2.9 37.1 + - - -
26B GLN* 3.4 31.6 - - + -
29B LEU* 3.7 20.6 - - + -
209B ILE* 4.1 15.5 - - + -
213B ALA* 3.5 26.9 - - + -
215B TYR* 3.9 30.3 - + + -
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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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16B ILE* 3.2 23.4 + - - +
18B LEU 3.2 6.4 + - - -
19B ARG 4.1 14.6 - - - +
20B GLY 4.8 0.7 - - - -
21B PHE* 1.3 89.2 - - - +
23B PHE* 1.3 93.6 + - - +
24B ASP* 4.2 7.4 - - + +
25B GLY 3.1 4.2 + - - -
26B GLN* 3.1 12.0 + - - +
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Residues in contact with PHE 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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4B LEU* 4.3 6.5 - - + +
9B MET* 3.5 34.5 - - + -
16B ILE* 3.4 40.8 - - + +
22B ASP* 1.3 92.4 + - - +
24B ASP* 1.3 59.9 + - - +
26B GLN* 3.2 2.2 + - - +
27B GLU* 2.8 45.2 + - - +
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Residues in contact with ASP 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 4.4 4.3 - - - +
22B ASP* 3.1 5.8 - - + +
23B PHE* 1.3 79.7 - - - +
25B GLY* 1.3 57.5 + - - +
27B GLU* 3.4 17.1 + - - +
28B ALA* 2.9 28.5 + - - +
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Residues in contact with GLY 25 (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* 2.9 42.8 + - - -
22B ASP 3.7 0.4 - - - -
24B ASP* 1.3 76.9 - - - +
26B GLN* 1.3 63.1 + - - +
28B ALA* 3.1 5.5 + - - +
29B LEU* 3.0 25.1 + - - +
213B ALA* 4.2 13.2 - - - +
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Residues in contact with GLN 26 (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 LEU* 3.9 16.6 - - + -
12B TYR* 3.5 44.8 - - + +
15B GLN* 2.9 33.3 + - - +
16B ILE* 3.9 17.7 - - + -
21B PHE* 3.4 6.3 - - + -
22B ASP 3.1 7.1 + - - +
23B PHE 3.8 5.4 - - - +
25B GLY* 1.3 76.4 - - - +
27B GLU* 1.3 61.6 + - - +
29B LEU* 3.1 11.0 + - - +
30B LYS* 3.0 21.0 + - - +
53B ALA 2.9 23.4 + - - -
54B GLY* 3.9 6.9 + - - -
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Residues in contact with GLU 27 (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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2B ALA* 3.5 36.9 + - + +
3B GLU* 4.8 1.2 - - - +
4B LEU* 3.9 25.6 + - + +
23B PHE* 2.8 32.0 + - - +
24B ASP* 3.7 16.2 - - - +
26B GLN* 1.3 73.4 - - - +
28B ALA* 1.3 66.1 + - - +
30B LYS* 3.2 5.0 + - - +
31B ASP* 3.0 29.5 + - - +
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Residues in contact with ALA 28 (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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24B ASP 2.9 15.0 + - - +
25B GLY* 3.1 10.5 + - - +
27B GLU* 1.3 75.4 - - - +
29B LEU* 1.3 58.9 + - - +
31B ASP* 3.3 7.9 + - - +
32B SER* 2.6 33.1 + - - -
212B LEU 4.0 19.7 - - - +
213B ALA* 4.2 9.6 - - - +
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Residues in contact with LEU 29 (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 GLN* 4.1 4.7 - - - +
21B PHE* 3.7 20.6 - - + -
25B GLY 3.0 17.7 + - - +
26B GLN* 3.1 10.9 + - - +
28B ALA* 1.3 76.9 - - - +
30B LYS* 1.3 62.9 + - - +
32B SER* 3.0 15.4 + - - -
53B ALA* 3.7 24.0 - - + +
54B GLY 3.5 13.5 - - - +
55B VAL* 3.5 7.6 - - + +
56B GLY 2.9 16.1 + - - -
209B ILE* 4.1 31.6 - - + +
212B LEU* 3.9 34.1 - - + -
213B ALA* 4.6 3.4 - - + -
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Residues in contact with LYS 30 (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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2B ALA* 4.0 16.8 - - + -
3B GLU 2.7 21.4 + - - +
4B LEU* 3.7 21.3 - - + -
5B SER 4.3 0.2 - - - +
8B GLU* 2.7 38.7 + - - +
12B TYR* 6.1 1.8 - - + -
26B GLN* 3.0 13.6 + - - +
27B GLU* 3.2 8.9 + - - +
29B LEU* 1.3 74.9 - - - +
31B ASP* 1.3 59.8 + - - +
54B GLY 3.5 10.9 + - - +
56B GLY* 3.3 21.6 - - - +
57B ASN* 3.8 5.9 + - - -
100B HIS 5.8 2.2 - - - -
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Residues in contact with ASP 31 (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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2B ALA* 2.8 46.4 + - - +
27B GLU* 3.0 14.8 + - - +
28B ALA* 3.8 6.5 - - - +
29B LEU 3.1 0.2 - - - -
30B LYS* 1.3 75.8 - - - +
32B SER* 1.3 62.4 + - - +
33B ARG* 3.9 7.1 + - - +
57B ASN* 4.2 5.9 + - - +
123B ASP* 4.2 4.0 - - - +
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Residues in contact with SER 32 (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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28B ALA 2.6 18.9 + - - -
29B LEU* 3.0 12.9 + - - -
31B ASP* 1.3 79.6 - - - +
33B ARG* 1.3 60.5 + - - +
34B VAL 4.2 0.2 - - - -
55B VAL* 4.3 4.9 - - - -
56B GLY 3.9 1.4 + - - -
57B ASN* 3.0 31.8 + - - +
123B ASP* 3.5 6.1 + - - -
212B LEU* 3.5 45.5 + - - +
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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