Contacts of the helix formed by residues 44 - 55 (chain A) in PDB entry 1ZIO
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 PRO 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY 4.5 1.3 - - - +
43A THR* 1.3 88.8 - - - +
45A LEU* 1.3 62.1 + - - +
47A LEU* 3.3 13.4 + - + +
48A GLN* 3.1 38.8 + - - +
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Residues in contact with LEU 45 (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 MET* 5.3 2.5 - - + +
35A PHE* 3.8 25.8 - - + -
38A ALA* 4.1 16.4 - - + -
43A THR* 3.2 5.9 + - - +
44A PRO* 1.3 78.6 - - - +
46A GLY* 1.3 58.8 + - - +
48A GLN* 3.2 9.7 + - + +
49A ALA* 2.9 31.0 + - + +
63A VAL* 3.2 35.7 - - + -
67A ILE* 3.5 30.3 - - + -
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Residues in contact with GLY 46 (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 PHE 4.5 1.3 - - - -
38A ALA* 3.4 35.4 - - - +
39A MET* 3.2 18.1 - - - +
43A THR* 3.0 11.4 + - - -
45A LEU* 1.3 76.7 - - - +
47A LEU* 1.3 65.0 + - - +
49A ALA* 4.1 1.7 - - - -
50A LYS* 3.1 20.4 + - - +
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Residues in contact with LEU 47 (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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39A MET* 4.9 5.4 - - - +
42A GLY* 3.8 27.8 - - - +
43A THR 3.0 22.5 + - - +
44A PRO* 3.6 11.9 - - + +
46A GLY* 1.3 80.0 - - - +
48A GLN* 1.3 62.5 + - + +
50A LYS* 3.6 21.7 - - + +
51A GLN* 3.9 13.5 - - - +
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Residues in contact with GLN 48 (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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44A PRO* 3.1 30.1 + - - +
45A LEU* 3.7 10.8 - - + +
47A LEU* 1.3 76.7 - - + +
49A ALA* 1.3 64.9 + - - +
50A LYS 3.4 0.3 + - - -
51A GLN* 3.5 11.8 + - - +
52A TYR* 3.3 26.1 - - + -
59A VAL* 5.9 1.6 - - + -
63A VAL* 4.4 20.4 - - + +
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Residues in contact with ALA 49 (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 PHE* 3.7 39.5 - - + +
45A LEU* 2.9 22.3 + - + +
46A GLY* 4.1 4.5 - - - +
48A GLN* 1.3 71.5 - - - +
50A LYS* 1.3 60.2 + - - +
52A TYR* 3.1 5.3 + - - +
53A MET* 2.9 35.4 + - - +
59A VAL* 3.9 20.6 - - + +
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Residues in contact with LYS 50 (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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39A MET* 3.7 35.9 - - + +
46A GLY 3.1 18.0 + - - +
47A LEU* 3.6 15.7 - - + +
49A ALA* 1.3 76.2 - - - +
51A GLN* 1.3 74.3 + - - +
53A MET* 4.5 1.1 - - - -
54A ASP* 2.8 58.0 + - - +
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Residues in contact with GLN 51 (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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47A LEU 3.9 15.1 - - - +
48A GLN* 3.9 8.3 - - - +
49A ALA 3.2 0.8 - - - -
50A LYS* 1.3 94.4 - - - +
52A TYR* 1.3 66.4 + - + +
54A ASP* 4.1 2.9 + - - +
55A ARG* 2.9 65.0 + - - +
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Residues in contact with TYR 52 (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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48A GLN* 3.3 31.4 - - + -
49A ALA* 3.1 7.6 + - - +
51A GLN* 1.3 76.7 - - + +
53A MET* 1.3 65.1 + - - +
55A ARG* 3.1 6.2 + - - +
56A GLY 3.0 4.3 + - - -
57A ASP* 2.9 51.8 + - + +
58A LEU 3.2 18.6 - - - +
59A VAL* 4.0 14.1 - - + -
60A PRO* 3.6 36.7 - - + +
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Residues in contact with MET 53 (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 GLY 3.7 13.5 - - - +
35A PHE* 3.6 22.2 - - + -
36A ARG* 3.3 34.8 - - + +
39A MET* 4.4 19.1 - - - +
49A ALA* 2.9 21.7 + - - +
50A LYS* 3.9 4.0 - - - +
52A TYR* 1.3 76.4 - - - +
54A ASP* 1.3 64.1 + - - +
56A GLY* 3.1 11.8 + - - +
59A VAL* 4.6 2.7 - - + -
162A ASP* 3.6 24.5 - - - +
218A AP5 3.2 47.6 + - - +
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Residues in contact with ASP 54 (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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39A MET* 5.1 5.5 - - - +
50A LYS* 2.8 54.0 + - - +
51A GLN* 4.1 7.2 + - - +
53A MET* 1.3 79.7 - - - +
55A ARG* 1.3 67.1 + - + +
56A GLY 3.7 0.2 + - - -
161A ALA* 4.5 19.2 - - - +
162A ASP* 5.0 5.4 - - - +
167A THR* 3.8 15.1 + - - +
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Residues in contact with ARG 55 (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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51A GLN* 2.9 57.6 + - - +
52A TYR* 3.1 6.5 + - - +
54A ASP* 1.3 84.0 - - + +
56A GLY* 1.3 58.7 + - - +
57A ASP* 4.0 18.6 - - - +
167A THR* 3.8 9.1 - - - +
170A ASN* 2.8 22.5 + - - +
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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