Contacts of the helix formed by residues 28 - 37 (chain D) in PDB entry 4A12
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 28 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PHE 4.5 3.8 - - - +
27D ILE* 1.3 77.0 - - - +
29D ASP* 1.4 64.6 + - - +
30D HIS* 3.9 9.5 + - - +
31D GLU* 3.1 39.5 + - - +
32D LEU* 3.2 25.9 + - - +
55D LEU* 3.8 25.1 - - + -
58D ARG* 4.8 0.4 - - - +
28G G 4.1 23.6 - - - +
29G T 3.8 9.0 - - - +
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 1.4 73.3 - - - +
30D HIS* 1.4 56.7 + - - +
32D LEU* 3.4 10.8 + - - +
33D SER* 3.0 28.3 + - - -
40D ILE* 4.6 2.6 - - + +
43D ILE* 3.8 18.9 - - + +
44D ARG* 3.3 33.5 + - - +
47D ARG* 2.8 50.0 + - - -
58D ARG* 4.6 2.9 + - - -
29G T 3.0 28.3 + - - +
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 3.2 8.9 - - - +
29D ASP* 1.4 77.9 - - - +
31D GLU* 1.4 67.4 + - + +
33D SER* 2.7 25.9 + - - -
34D ASP* 3.2 30.9 + - - +
40D ILE* 3.9 26.1 - - + +
28G G 6.1 1.3 - - - +
29G T 4.6 1.0 + - - -
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ASN* 5.0 2.9 + - - -
26D PHE 4.9 1.3 - - - +
27D ILE* 3.6 29.9 - - + +
28D THR* 3.1 35.0 + - - +
30D HIS* 1.4 83.0 - - + +
32D LEU* 1.4 56.0 + - - +
34D ASP* 3.5 6.9 + - - +
35D LEU* 3.0 29.6 + - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.8 8.7 - - + +
20D GLN* 3.9 23.6 - - + -
21D ILE* 3.9 26.5 - - + -
27D ILE* 4.0 21.3 - - + +
28D THR 3.2 19.5 + - - +
29D ASP* 3.6 12.8 - - - +
31D GLU* 1.4 72.5 - - - +
33D SER* 1.4 58.5 + - - +
35D LEU* 4.2 3.8 - - - -
36D PHE* 2.9 60.3 + - + +
43D ILE* 3.9 31.1 - - + +
58D ARG* 5.3 0.9 - - - +
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP 3.0 14.5 + - - -
30D HIS* 2.7 23.5 + - - -
32D LEU* 1.4 76.1 - - - +
34D ASP* 1.3 60.7 + - - +
37D GLN* 3.0 23.0 + - - -
38D VAL 3.1 30.4 + - - +
40D ILE* 3.8 20.7 - - - +
43D ILE* 3.5 15.0 - - - +
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D HIS* 3.2 37.2 + - - +
31D GLU* 3.8 8.9 - - - +
32D LEU 3.3 0.2 - - - -
33D SER* 1.3 84.0 + - - +
35D LEU* 1.4 61.5 + - - +
37D GLN* 2.8 31.8 + - - +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.8 32.8 - - + +
27D ILE* 4.7 6.1 - - + -
31D GLU 3.0 18.4 + - - +
32D LEU* 3.4 3.6 + - + +
34D ASP* 1.4 76.9 - - - +
36D PHE* 1.3 88.6 + - + +
37D GLN* 4.9 2.6 - - - +
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.2 16.6 - - + +
13D ARG* 3.7 32.1 - - + +
16D ALA* 3.5 45.5 - - + -
17D ILE* 3.7 19.3 - - + -
20D GLN* 4.3 4.3 - - + -
32D LEU* 2.9 37.7 + - + +
33D SER* 5.4 0.2 - - - -
35D LEU* 1.3 107.0 - - + +
37D GLN* 1.4 69.4 + - - +
38D VAL* 3.2 14.2 - - + +
43D ILE* 5.9 1.8 - - + -
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Residues in contact with GLN 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER 3.0 9.0 + - - -
34D ASP* 2.8 34.2 + - - +
35D LEU 3.5 3.3 - - - +
36D PHE* 1.4 77.7 - - - +
38D VAL* 1.3 63.4 + - - +
7F T 4.7 3.1 + - - -
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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