Contacts of the helix formed by residues 29 - 41 (chain A) in PDB entry 1Y0P
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 LEU 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.0 26.9 - - + -
26A ASN* 2.9 22.6 + - - +
28A SER* 1.3 78.3 - - - +
30A THR* 1.3 63.7 - - - +
32A GLU* 3.2 26.2 - - + +
33A ASN* 2.9 31.5 + - - +
69A THR* 3.7 26.0 - - + +
275A ASN* 5.5 0.7 - - - +
298A TYR* 3.6 50.0 - - + +
801A HEM 4.2 12.6 - - + +
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Residues in contact with THR 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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25A SER* 3.4 1.0 + - - -
26A ASN* 3.1 30.0 + - - +
28A SER* 3.1 14.1 - - - -
29A LEU* 1.3 75.0 - - - +
31A TYR* 1.3 65.4 + - - +
33A ASN* 3.5 4.1 + - - +
34A THR* 3.0 31.5 + - - +
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Residues in contact with TYR 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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15A ASP 4.8 3.6 + - - -
17A CYS 3.6 6.7 - - - -
18A HIS 3.5 29.1 + - - -
19A THR* 3.6 24.7 - - + -
20A PRO* 5.0 5.4 - - + +
25A SER* 3.1 25.6 + - - +
30A THR* 1.3 80.0 - - - +
32A GLU* 1.3 65.7 + - - +
34A THR* 3.2 7.5 + - + -
35A GLN* 3.1 61.6 + - + +
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Residues in contact with GLU 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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17A CYS* 3.6 26.2 - - + +
18A HIS* 4.7 6.8 + - + +
19A THR* 4.3 4.7 + - - +
23A GLU 4.0 3.8 - - - +
24A LEU* 3.4 20.2 - - + +
25A SER* 2.7 46.7 + - - -
29A LEU* 3.2 30.0 - - + +
31A TYR* 1.3 77.0 - - - +
33A ASN* 1.3 63.4 + - - +
35A GLN* 3.0 14.4 + - - +
36A CYS* 3.2 16.4 + - - -
69A THR* 5.5 0.9 - - + -
801A HEM 4.4 20.9 - - + -
802A HEM 4.3 2.7 - - + +
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Residues in contact with ASN 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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28A SER 3.6 7.3 + - - -
29A LEU* 2.9 34.3 + - - +
30A THR* 4.0 4.0 - - - +
32A GLU* 1.3 73.1 - - - +
34A THR* 1.3 66.0 + - - +
36A CYS* 3.1 9.0 + - - +
37A VAL* 3.0 28.2 + - + +
67A ALA* 3.9 14.1 - - + +
68A CYS* 2.9 34.4 + - - +
69A THR* 2.8 35.1 + - - +
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Residues in contact with THR 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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30A THR* 3.0 22.2 + - - +
31A TYR* 3.2 13.8 + - + -
33A ASN* 1.3 75.6 - - - +
35A GLN* 1.3 67.8 + - - +
37A VAL* 3.4 8.5 + - + +
38A SER* 2.9 27.7 + - - -
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Residues in contact with GLN 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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15A ASP 5.8 0.6 + - - -
16A SER 3.3 24.3 + - - +
17A CYS* 3.5 23.8 - - - +
31A TYR* 3.1 54.8 + - + +
32A GLU 3.0 7.5 + - - +
34A THR* 1.3 85.4 - - - +
36A CYS* 1.3 67.0 + - - +
38A SER* 2.8 31.5 + - - -
39A CYS 3.4 1.6 + - - -
802A HEM 3.3 12.7 - - + +
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Residues in contact with CYS 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 GLU 3.2 16.5 + - - -
33A ASN* 3.1 17.0 + - - +
35A GLN* 1.3 77.0 - - - +
37A VAL* 1.3 59.3 + - - +
39A CYS* 3.3 0.3 + - - -
40A HIS* 2.9 34.2 + - - +
68A CYS* 3.8 19.7 - - - -
802A HEM 1.8 74.9 - - + +
803A HEM 4.1 2.9 - - + -
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Residues in contact with VAL 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 ASN* 3.0 14.4 + - + +
34A THR* 3.7 10.8 - - + +
36A CYS* 1.3 74.5 - - - +
38A SER* 1.3 64.1 + - - +
41A GLY* 2.9 49.7 + - - +
42A THR* 3.8 17.9 - - + +
68A CYS* 4.3 3.4 - - - -
803A HEM 4.1 17.0 - - + -
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Residues in contact with SER 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 THR* 2.9 17.2 + - - -
35A GLN* 2.8 32.6 + - - +
37A VAL* 1.3 78.3 - - - +
39A CYS* 1.3 65.8 + - - +
802A HEM 4.6 0.7 - - - +
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Residues in contact with CYS 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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36A CYS 3.3 2.8 + - - +
37A VAL 3.1 0.2 - - - -
38A SER* 1.3 90.0 + - - +
40A HIS* 1.3 62.6 + - - +
41A GLY 3.5 0.8 + - - -
802A HEM 2.1 77.2 - - + -
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Residues in contact with HIS 40 (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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36A CYS 2.9 18.3 + - - +
39A CYS* 1.3 77.2 - - + +
41A GLY* 1.3 59.0 + - - +
45A GLU* 4.7 2.9 - - - +
46A VAL* 3.7 17.9 + - + +
802A HEM 2.0 104.3 + + + -
803A HEM 3.6 36.9 - - + +
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Residues in contact with GLY 41 (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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37A VAL* 2.9 35.9 + - - +
39A CYS 3.5 1.6 + - - -
40A HIS* 1.3 81.2 - - - +
42A THR* 1.3 68.2 + - - +
45A GLU* 3.2 16.6 - - - -
46A VAL* 3.8 5.4 - - - +
803A HEM 4.0 2.6 - - - +
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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