Contacts of the helix formed by residues 24 - 35 (chain J) in PDB entry 2QJK
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 PRO 24 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214G TRP* 3.8 24.0 - - + +
218G SER* 3.9 17.7 - - - +
20J HIS* 3.8 33.8 - - + +
22J ARG 4.1 1.1 - - - -
23J LEU* 1.3 80.4 - - + +
25J ILE* 1.3 63.8 + - - +
26J VAL* 3.1 3.8 - - + +
27J ALA* 2.9 30.8 + - + +
28J LEU* 3.1 5.9 + - - +
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Residues in contact with ILE 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G ILE* 4.4 21.1 - - + -
214G TRP* 3.3 31.7 - - + -
19J LEU* 4.8 9.6 - - + -
23J LEU* 2.6 36.1 + - + +
24J PRO* 1.3 74.1 - - - +
26J VAL* 1.3 71.5 + - + +
28J LEU* 3.5 5.1 + - + +
29J ALA* 3.2 20.1 + - - +
505J ANJ 5.0 14.9 - - + +
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Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J TYR* 3.4 35.9 - - + +
16J GLU* 5.5 5.6 - - + -
19J LEU* 3.7 31.9 - - + -
24J PRO* 3.1 1.4 - - - +
25J ILE* 1.3 79.0 - - + +
27J ALA* 1.3 67.8 + - - +
29J ALA* 3.4 8.1 + - + +
30J TYR* 3.0 21.1 + - + +
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J TYR* 3.6 35.2 - - + -
20J HIS* 4.2 5.8 - - + +
24J PRO* 2.9 25.4 + - + +
26J VAL* 1.3 78.4 - - - +
28J LEU* 1.3 63.9 + - - +
30J TYR* 2.8 20.8 + - - +
31J ASP* 2.9 17.2 + - - +
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Residues in contact with LEU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G TRP* 3.8 31.6 - - + -
24J PRO 3.1 7.2 + - - +
25J ILE* 3.6 11.0 - - + +
27J ALA* 1.3 79.4 - - - +
29J ALA* 1.3 65.6 + - - +
30J TYR 3.0 0.3 + - - -
31J ASP* 3.1 11.5 + - + +
32J THR* 2.9 32.1 + - - +
505J ANJ 5.6 8.3 - - + -
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Residues in contact with ALA 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ILE 3.2 8.2 + - - +
26J VAL* 3.5 12.1 - - + +
28J LEU* 1.3 79.1 - - - +
30J TYR* 1.3 57.2 + - - +
32J THR* 3.3 8.3 + - - +
33J ILE* 2.9 32.7 + - - +
505J ANJ 3.6 34.4 - - + +
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Residues in contact with TYR 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J ASP* 3.0 30.6 + - - -
8J HIS 3.5 25.0 + - - -
9J TYR* 3.7 28.5 - + + -
26J VAL* 3.0 12.4 + - + +
27J ALA 2.8 10.8 + - - +
29J ALA* 1.3 76.6 - - - +
31J ASP* 1.3 77.3 + - - +
33J ILE* 2.8 13.1 + - + +
34J MET* 2.6 76.4 + - + +
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Residues in contact with ASP 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J HIS* 5.8 3.5 + - - -
7J ASP 5.0 0.5 - - - +
8J HIS* 4.2 10.0 - - - +
9J TYR 4.1 7.4 + - - -
27J ALA* 2.9 24.7 + - - +
28J LEU* 3.7 11.2 + - + +
30J TYR* 1.3 96.5 - - - +
32J THR* 1.3 60.1 + - - +
34J MET* 4.1 2.5 - - - +
35J ILE* 3.7 20.5 + - - +
217J HIS* 4.0 4.2 + - - -
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Residues in contact with THR 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J LEU* 2.9 21.4 + - - +
29J ALA* 3.4 11.7 - - - +
31J ASP* 1.3 78.3 - - - +
33J ILE* 1.3 64.7 + - + +
34J MET 3.5 0.2 - - - -
35J ILE* 4.1 5.2 - - - +
213J ILE* 5.7 2.2 - - + -
217J HIS* 3.3 33.9 + - + +
244J PHE* 4.6 3.6 - - - -
505J ANJ 3.7 43.2 - - + +
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Residues in contact with ILE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ALA 2.9 13.1 + - - +
30J TYR* 2.8 16.4 + - + +
32J THR* 1.3 85.5 - - + +
34J MET* 1.3 67.6 + - + +
35J ILE 3.6 0.7 - - - -
244J PHE* 3.4 17.0 - - + +
245J TRP* 3.2 37.8 + - + +
249J ILE* 3.3 34.1 - - + -
505J ANJ 5.0 11.9 - - + +
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Residues in contact with MET 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ASP* 5.8 0.9 - - - +
30J TYR* 2.6 65.9 + - + +
31J ASP* 4.5 2.0 - - - -
33J ILE* 1.3 80.3 - - + +
35J ILE* 1.3 66.4 + - - +
36J PRO* 3.4 4.9 - - - +
243J PRO* 3.7 34.4 - - + +
244J PHE* 4.0 6.0 + - - +
245J TRP* 3.8 39.5 - - + +
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Residues in contact with ILE 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J ILE* 6.1 4.0 - - + -
6J HIS* 6.5 0.4 - - + -
31J ASP 3.7 10.3 + - - +
32J THR 4.1 3.4 - - - +
33J ILE 3.6 0.2 - - - -
34J MET* 1.3 73.0 - - - +
36J PRO* 1.3 83.3 - - + +
37J THR* 3.2 11.8 + - - +
217J HIS* 3.6 57.4 - - + +
220J GLY* 4.8 9.0 - - - -
221J ASN* 4.1 21.5 - - - +
244J PHE* 3.0 33.4 + - + -
505J ANJ 6.1 2.0 - - + +
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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