Contacts of the helix formed by residues 27 - 36 (chain A) in PDB entry 3D77
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 3.7 4.7 - - - -
25A GLY 4.2 6.3 - - - +
26A THR* 1.3 81.9 - - - +
28A GLN* 1.3 64.4 + - - +
29A ALA* 3.4 11.1 + - - +
30A GLN* 3.0 43.5 + - - +
31A ILE* 3.3 8.5 + - - +
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Residues in contact with GLN 28 (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 LYS* 2.9 32.7 + - - +
21A MET* 3.5 14.2 - - + +
27A THR* 1.3 72.6 - - - +
29A ALA* 1.3 56.2 + - - +
31A ILE* 3.1 23.2 + - - +
32A ASP* 2.9 56.5 + - - +
119A ILE* 5.0 0.2 + - - -
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Residues in contact with ALA 29 (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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27A THR* 3.2 10.8 - - - +
28A GLN* 1.3 79.2 - - - +
30A GLN* 1.3 56.2 + - + +
32A ASP* 3.3 12.8 + - - +
33A ASP* 3.0 27.2 + - - +
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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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25A GLY 3.8 3.3 - - - +
26A THR* 3.3 11.1 - - - -
27A THR* 3.0 47.0 + - - +
29A ALA* 1.3 76.3 - - + +
31A ILE* 1.3 62.0 + - - +
33A ASP* 3.3 8.7 + - - +
34A VAL* 3.1 26.2 + - - +
42A GLU* 4.6 7.1 - - - +
44A SER* 2.9 27.1 + - - -
45A ILE* 4.0 33.5 - - + +
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Residues in contact with ILE 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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17A LYS* 3.9 17.7 - - - -
21A MET* 4.2 14.6 - - + -
26A THR* 4.1 8.1 - - + -
27A THR 3.3 7.4 + - - +
28A GLN* 3.1 26.1 + - - +
30A GLN* 1.3 72.3 - - - +
32A ASP* 1.3 66.6 + - - +
34A VAL* 3.1 7.3 + - - +
35A ASN* 3.1 25.7 + - - +
45A ILE* 4.2 7.6 - - + -
48A TYR* 3.6 41.3 - - + +
118A VAL* 3.5 28.7 - - + +
119A ILE* 3.7 8.1 - - - +
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Residues in contact with ASP 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 GLN* 2.9 44.2 + - - +
29A ALA* 3.5 15.0 - - - +
31A ILE* 1.3 76.5 - - - +
33A ASP* 1.3 60.6 + - - +
35A ASN* 3.2 10.6 + - - +
36A LYS* 3.1 39.2 + - + +
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Residues in contact with ASP 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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29A ALA 3.0 14.3 + - - +
30A GLN* 3.4 12.8 - - - +
31A ILE 3.1 0.2 - - - -
32A ASP* 1.3 77.4 - - - +
34A VAL* 1.3 60.0 + - - +
36A LYS* 3.1 15.9 + - - +
37A GLY 3.3 0.2 + - - -
38A ASN* 2.9 63.5 + - - +
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Residues in contact with VAL 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 GLN 3.1 14.4 + - - +
31A ILE* 3.1 7.4 + - - +
33A ASP* 1.3 74.2 - - + +
35A ASN* 1.3 59.2 + - - +
37A GLY* 2.9 17.3 + - - -
38A ASN 3.5 9.4 - - - +
39A LEU* 3.7 22.2 - - + -
45A ILE* 3.6 26.5 - - + -
49A MET* 4.3 5.6 - - - -
109A GLN* 2.9 33.3 + - - +
116A TRP* 4.0 8.3 - - + +
118A VAL* 3.6 29.6 - - + -
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Residues in contact with ASN 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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28A GLN* 5.8 0.2 - - - +
31A ILE* 3.1 23.4 + - - +
32A ASP* 3.7 12.2 + - - +
34A VAL* 1.3 77.7 - - - +
36A LYS* 1.3 57.4 + - + +
37A GLY 3.3 1.1 + - - -
109A GLN* 5.0 1.7 + - - +
116A TRP 4.2 3.1 - - - +
117A PHE* 3.2 33.8 - - + -
118A VAL* 2.8 47.7 + - - +
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Residues in contact with LYS 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 ASP* 3.1 28.0 + - + +
33A ASP* 3.6 15.0 - - - +
34A VAL 3.1 0.8 - - - -
35A ASN* 1.3 77.6 - - + +
37A GLY* 1.3 58.9 + - - +
38A ASN* 3.5 15.2 + - - +
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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