Contacts of the helix formed by residues 29 - 39 (chain A) in PDB entry 2I9W
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 CYS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A CYS* 3.5 8.0 - - - -
10A CYS* 3.8 5.2 - - - -
25A TYR* 3.4 9.8 + - + -
28A CYS* 1.4 79.5 - - - +
30A GLN* 1.3 65.1 + - - +
31A PRO 3.3 0.2 - - - -
32A TYR* 3.0 21.2 + - - +
33A HIS* 3.1 17.7 + - + +
57A ARG* 3.8 2.2 - - - -
58A THR* 3.7 28.7 - - + -
61A SER* 3.2 26.2 - - - -
200A ZN 2.4 32.8 - - - -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER* 3.0 27.6 + - - -
25A TYR* 3.1 49.8 + - + +
26A GLN* 3.1 23.7 + - - +
29A CYS* 1.3 76.7 - - - +
31A PRO* 1.4 67.4 - - + +
32A TYR 3.1 0.2 + - - -
33A HIS* 3.2 1.1 + - - +
34A ASP* 2.9 46.7 + - - +
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Residues in contact with PRO 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN 3.7 19.7 - - - +
27A ASP 5.2 1.3 - - - -
28A CYS 3.3 18.4 - - - +
29A CYS 3.4 0.2 - - - -
30A GLN* 1.4 94.3 - - + +
32A TYR* 1.3 60.1 + - + +
34A ASP* 3.9 4.9 - - + +
35A GLY* 2.9 25.6 + - - -
47A ILE* 3.3 30.2 - - + +
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A CYS 3.5 25.1 - - - -
29A CYS 3.0 6.9 + - - +
31A PRO* 1.3 78.0 - - + +
33A HIS* 1.3 68.6 + - - +
35A GLY* 3.8 0.2 - - - -
36A LEU* 3.2 17.2 + - - +
47A ILE* 3.6 34.6 - - + +
48A ARG* 3.6 21.4 + - - -
49A ALA* 3.6 22.9 - - - -
50A ASP* 5.5 1.4 + - - +
54A HIS* 5.9 4.8 - + + -
58A THR* 3.8 26.5 - - + -
70A TYR* 3.6 18.4 - - - +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 2.7 36.2 + + - +
29A CYS* 3.1 10.0 + - + -
30A GLN 3.7 4.7 - - - +
32A TYR* 1.3 79.2 - - - +
34A ASP* 1.3 67.5 + - - +
36A LEU* 3.4 1.6 + - - +
37A TYR* 3.1 23.2 + - - +
58A THR* 2.9 26.5 + - - -
61A SER* 3.7 17.9 - - - -
62A ALA* 3.7 23.5 + - + +
65A LEU* 4.5 0.4 - - + -
67A LYS* 3.8 19.1 - - + +
70A TYR* 3.8 36.5 - + + +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 5.0 1.4 + - - -
30A GLN* 2.9 47.3 + - - +
31A PRO* 4.1 4.8 - - + +
33A HIS* 1.3 82.5 - - - +
35A GLY* 1.3 57.4 + - - +
37A TYR* 3.3 6.9 + - - +
38A ASN* 3.0 42.0 + - - +
67A LYS* 5.1 6.1 + - - -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO 2.9 10.1 + - - -
32A TYR 3.4 0.6 + - - -
33A HIS 3.2 0.2 - - - -
34A ASP* 1.3 78.0 - - - +
36A LEU* 1.3 55.6 + - - +
38A ASN* 5.2 0.2 - - - -
39A GLN* 2.9 43.8 + - - +
47A ILE* 3.4 33.4 - - - -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR 3.2 14.8 + - - +
35A GLY* 1.3 74.8 - - - +
37A TYR* 1.3 62.8 - - - +
38A ASN 3.5 0.3 + - - -
39A GLN 3.6 19.6 + - - +
47A ILE 4.9 8.4 + - - +
48A ARG* 6.1 3.6 - - + -
70A TYR* 3.5 21.8 - - + -
73A LYS* 4.0 28.7 - - + +
74A THR* 3.4 32.8 - - + -
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS 3.1 17.5 + - - +
34A ASP* 3.6 7.9 - - - +
35A GLY 3.2 0.4 - - - -
36A LEU* 1.3 79.5 - - - +
38A ASN* 1.3 82.8 + - - +
69A GLU* 4.7 27.4 - - + +
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.0 27.1 + - - +
35A GLY* 5.2 0.2 - - - -
37A TYR* 1.3 102.0 - - - +
39A GLN* 1.3 68.8 + - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY* 2.9 29.1 + - - +
36A LEU* 3.6 20.7 - - - +
37A TYR 3.6 1.2 - - - -
38A ASN* 1.3 90.2 - - + +
46A ALA* 4.9 21.1 - - + -
47A ILE* 5.5 2.5 - - + -
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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