Contacts of the helix formed by residues 28 - 40 (chain P) in PDB entry 1ZQ3
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B G 4.3 9.9 - - - -
26P TYR* 3.9 3.1 + - + +
27P LEU* 1.3 79.4 - - - +
29P ALA* 1.3 65.7 + - - +
30P PRO* 3.4 22.4 - - - +
31P ARG* 3.0 18.6 + - - +
32P LEU* 3.0 26.0 + - - +
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Residues in contact with ALA 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B G 4.1 8.6 + - - +
28P THR* 1.3 73.6 - - - +
30P PRO* 1.3 57.8 - - + +
32P LEU* 3.4 14.7 - - + +
33P ALA* 2.7 37.7 + - - +
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Residues in contact with PRO 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P THR* 3.4 18.4 - - - +
29P ALA* 1.3 92.6 - - + +
31P ARG* 1.3 67.9 + - - +
33P ALA* 3.9 6.5 - - + +
34P ASP* 3.2 27.0 + - - +
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Residues in contact with ARG 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P HIS 6.1 0.2 - - - +
23P GLN* 3.4 29.3 + - - +
24P GLY* 4.0 19.3 - - - +
26P TYR 3.8 17.5 + - - +
27P LEU* 3.5 19.7 - - + -
28P THR* 3.0 21.7 + - - +
30P PRO* 1.3 80.6 - - - +
32P LEU* 1.3 60.4 + - - +
34P ASP* 3.7 6.5 - - - +
35P LEU* 3.1 33.4 + - - +
50P PHE* 5.6 1.3 - - + -
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Residues in contact with LEU 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B G 4.1 15.5 - - - +
27P LEU* 3.2 19.2 - - + +
28P THR 3.0 15.0 + - - +
29P ALA* 3.4 10.5 - - + +
31P ARG* 1.3 74.4 - - - +
33P ALA* 1.4 53.6 + - - +
36P SER* 3.0 30.5 + - - -
43P THR* 3.0 50.2 - - + +
46P VAL* 3.9 9.8 - - + +
47P LYS* 3.4 48.7 - - + +
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Residues in contact with ALA 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P ALA 2.7 22.5 + - - +
30P PRO* 3.9 6.5 - - + +
31P ARG 3.5 0.2 - - - -
32P LEU* 1.4 71.1 - - - +
34P ASP* 1.3 63.0 + - - +
36P SER* 3.3 3.2 + - - -
37P ALA* 3.1 24.3 + - - +
43P THR* 3.9 12.5 - - + +
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Residues in contact with ASP 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P HIS* 4.5 8.7 + - - +
30P PRO 3.2 16.3 + - - +
31P ARG* 3.7 6.9 - - - +
33P ALA* 1.3 80.0 - - - +
35P LEU* 1.3 62.3 + - - +
37P ALA* 3.5 4.6 + - - +
38P LYS* 2.8 61.6 + - - +
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Residues in contact with LEU 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 3.7 12.8 - - + +
17P LEU* 3.7 40.2 - - + +
20P HIS* 3.2 52.3 - - + -
21P PHE 4.2 2.2 - - - +
31P ARG* 3.1 19.3 + - + +
34P ASP* 1.3 73.4 + - - +
36P SER* 1.4 59.3 + - - +
38P LYS* 4.6 3.8 - - + -
39P LEU* 2.8 44.6 + - + +
46P VAL* 3.8 20.6 - - + -
50P PHE* 4.2 9.2 - - + -
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Residues in contact with SER 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P LEU 3.0 19.2 + - - -
33P ALA* 3.3 4.7 + - - -
35P LEU* 1.4 78.3 - - - +
37P ALA* 1.3 60.0 + - - +
39P LEU* 4.9 0.7 - - - -
40P ALA* 3.3 4.0 + - - -
41P LEU 2.7 45.4 + - - +
42P GLY* 3.8 2.9 - - - -
43P THR* 3.5 28.3 + - - +
46P VAL* 4.1 4.2 - - - +
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Residues in contact with ALA 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P ALA 3.1 16.0 + - - +
34P ASP* 3.9 6.3 - - - +
35P LEU 3.3 0.2 - - - -
36P SER* 1.3 78.9 + - - +
38P LYS* 1.3 64.9 + - + +
40P ALA* 3.6 12.0 + - - +
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Residues in contact with LYS 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 3.5 23.0 - - - +
20P HIS* 3.0 42.2 + - + +
34P ASP* 2.8 50.0 + - - +
35P LEU* 3.3 5.4 + - + +
37P ALA* 1.3 79.9 - - + +
39P LEU* 1.3 64.2 + - - +
40P ALA* 3.1 2.9 + - - +
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Residues in contact with LEU 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P GLN* 2.8 76.6 + - + +
16P GLU* 3.5 18.5 - - + +
17P LEU* 3.5 32.8 - - + -
35P LEU* 2.8 28.2 + - + +
38P LYS* 1.3 73.3 - - - +
40P ALA* 1.4 62.5 + - - +
41P LEU* 4.0 21.8 - - + +
46P VAL* 4.0 13.9 - - + -
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Residues in contact with ALA 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P GLN* 5.0 0.3 + - - -
36P SER 3.3 11.9 + - - -
37P ALA 3.6 7.8 + - - +
38P LYS 3.1 4.7 - - - +
39P LEU* 1.4 81.2 - - - +
41P LEU* 1.4 64.1 + - - +
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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