Contacts of the helix formed by residues 22 - 36 (chain J) in PDB entry 1UW9
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 THR 22 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J PRO 4.6 4.7 - - - +
21J LEU* 1.3 75.7 - - - +
23J ASP* 1.3 60.0 + - - +
24J GLU* 3.5 10.0 + - - +
25J GLN* 2.9 45.5 + - - +
26J ILE* 2.9 27.7 + - - +
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Residues in contact with ASP 23 (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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21J LEU 5.3 0.5 - - - +
22J THR* 1.3 72.8 - - - +
24J GLU* 1.3 57.5 + - - +
26J ILE* 3.3 17.1 + - - +
27J ALA* 2.9 30.0 + - - +
90J LEU* 5.6 1.0 - - - +
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Residues in contact with GLU 24 (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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22J THR* 3.2 9.5 + - - +
23J ASP* 1.3 79.0 - - - +
25J GLN* 1.3 57.5 + - + +
27J ALA* 3.5 7.7 + - + +
28J ALA* 3.0 27.8 + - + +
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Residues in contact with GLN 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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429H GLN* 3.6 19.5 + - - +
433H GLU* 3.9 15.9 - - - +
19J PRO* 5.0 2.0 + - - +
20J PRO 3.9 4.0 + - - -
21J LEU* 3.3 24.4 - - + +
22J THR* 2.9 54.7 + - - +
24J GLU* 1.3 73.7 - - + +
26J ILE* 1.3 66.4 + - - +
28J ALA* 3.4 7.9 + - - +
29J GLN* 3.2 27.4 + - - +
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Residues in contact with ILE 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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21J LEU* 3.8 30.5 - - + +
22J THR 2.9 20.5 + - - +
23J ASP* 3.6 16.8 - - - +
25J GLN* 1.3 73.3 - - - +
27J ALA* 1.3 65.6 + - - +
29J GLN* 3.1 10.4 + - - +
30J VAL* 3.0 26.9 + - + +
90J LEU* 4.3 17.5 - - + -
93J ILE* 4.5 12.1 - - + -
121J PHE* 4.2 15.5 - - + -
122J LEU 5.9 0.4 - - - +
123J VAL* 4.8 19.5 - - + +
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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
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23J ASP 2.9 17.6 + - - +
24J GLU* 3.8 8.3 - - - +
26J ILE* 1.3 76.3 - - - +
28J ALA* 1.3 56.5 + - - +
30J VAL* 3.2 9.2 + - - +
31J ASP* 2.9 36.5 + - - +
86J PRO* 5.5 0.3 - - - +
90J LEU* 4.4 22.4 - - + +
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Residues in contact with ALA 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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432H ASN 4.2 5.6 - - - +
433H GLU* 4.0 27.7 - - + +
24J GLU* 3.0 17.5 + - + +
25J GLN* 3.6 8.3 - - - +
26J ILE 3.2 0.2 - - - -
27J ALA* 1.3 75.4 - - - +
29J GLN* 1.3 64.2 + - - +
31J ASP* 3.3 12.3 + - - +
32J TYR* 3.1 20.8 + - - +
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Residues in contact with GLN 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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429H GLN* 3.9 21.7 + - - +
432H ASN* 2.9 43.6 + - - +
433H GLU* 4.4 6.4 - - - +
15J PHE* 3.5 21.7 - - + -
21J LEU* 4.6 6.5 - - + -
25J GLN 3.2 14.6 + - - +
26J ILE 3.1 8.6 + - - +
28J ALA* 1.3 72.6 - - - +
30J VAL* 1.3 65.0 + - - +
32J TYR* 3.2 7.5 + - - +
33J ILE* 3.1 26.4 + - - +
119J MET* 4.1 11.9 - - + +
121J PHE* 3.6 29.4 - - + -
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Residues in contact with VAL 30 (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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26J ILE* 3.0 20.2 + - + +
27J ALA* 3.2 9.8 + - - +
29J GLN* 1.3 74.3 - - - +
31J ASP* 1.3 64.2 + - - +
33J ILE* 3.2 11.9 + - + +
34J VAL* 3.1 21.0 + - + +
86J PRO* 3.7 33.2 - - + +
89J VAL* 3.7 28.0 - - + -
90J LEU* 4.1 17.7 - - + -
93J ILE* 4.8 0.7 - - + -
107J LEU* 3.8 25.4 - - + -
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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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27J ALA* 2.9 20.2 + - - +
28J ALA* 3.5 14.8 - - - +
29J GLN 3.3 0.2 - - - -
30J VAL* 1.3 75.4 - - - +
32J TYR* 1.3 53.7 + - - +
34J VAL* 3.3 5.8 + - - +
35J ALA* 2.8 36.9 + - - +
86J PRO* 3.5 25.4 - - - +
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Residues in contact with TYR 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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431H ARG* 3.2 32.7 + - + -
432H ASN* 3.1 65.0 + - + +
28J ALA 3.1 9.2 + - - +
29J GLN* 3.2 13.9 + - - +
31J ASP* 1.3 73.2 - - - +
33J ILE* 1.3 65.5 + - - +
35J ALA* 3.6 5.8 + - + -
36J ASN* 2.9 50.3 + - - +
38J TRP* 3.7 27.4 - + - -
119J MET* 5.5 7.2 - - + -
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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 GLN 3.1 13.4 + - - +
30J VAL* 3.4 13.7 - - + +
32J TYR* 1.3 75.9 - - + +
34J VAL* 1.3 63.8 + - + +
36J ASN* 3.2 3.3 + - - +
37J GLY 3.1 16.3 + - - -
38J TRP* 3.1 39.5 + - + +
40J PRO* 4.0 19.3 - - + -
89J VAL* 5.5 0.4 - - + -
107J LEU* 3.9 27.4 - - + -
108J VAL 4.7 0.7 - - - +
109J ALA* 3.8 20.9 - - + -
119J MET* 3.5 40.8 - - + -
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Residues in contact with VAL 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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30J VAL* 3.1 16.1 + - + +
31J ASP* 3.8 6.5 - - - +
33J ILE* 1.3 77.8 - - + +
35J ALA* 1.3 66.9 + - - +
37J GLY* 3.0 15.4 + - - +
38J TRP 5.2 1.8 - - - +
40J PRO* 5.6 1.8 - - + -
83J CYS* 4.9 7.2 - - - +
84J ARG* 3.5 37.4 - - + +
85J ASP 4.4 3.8 - - - +
86J PRO* 4.0 33.4 - - + -
89J VAL* 5.1 5.6 - - + -
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Residues in contact with ALA 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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31J ASP 2.8 22.8 + - - +
32J TYR* 3.9 7.9 - - + +
34J VAL* 1.3 74.8 - - - +
36J ASN* 1.3 63.9 + - - +
37J GLY 3.7 0.2 + - - -
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Residues in contact with ASN 36 (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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32J TYR* 2.9 56.7 + - - +
34J VAL 3.1 0.8 - - - -
35J ALA* 1.3 81.2 - - - +
37J GLY* 1.3 62.7 + - - +
38J TRP* 3.3 44.3 + - + -
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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