Contacts of the helix formed by residues 44 - 52 (chain E) in PDB entry 1PQ3
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 HIS 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E GLY* 2.9 19.3 + - - +
43E GLU* 1.3 96.9 + - + +
45E GLY* 1.3 63.6 + - - +
46E PRO* 3.3 3.4 - - - -
47E ALA* 3.1 14.7 + - + +
48E ALA* 3.0 20.3 + - - +
299E PRO* 4.1 14.8 - - + +
300E GLN* 3.5 31.7 + - + -
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Residues in contact with GLY 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLY 3.8 0.8 + - - -
42E VAL 3.2 7.8 + - - -
44E HIS* 1.3 75.3 - - - +
46E PRO* 1.3 68.8 - - - +
48E ALA* 3.0 5.8 + - - +
49E ILE* 2.9 29.5 + - - +
117E GLY 3.9 7.0 - - - -
297E VAL* 3.3 27.8 + - - -
299E PRO* 4.0 4.7 - - - +
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Residues in contact with PRO 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLY* 4.2 11.0 - - - -
31E ALA 3.9 9.4 - - - +
32E PRO* 3.9 12.6 - - + -
43E GLU 3.6 10.5 - - - +
44E HIS 3.5 3.4 - - - -
45E GLY* 1.3 87.4 - - - +
47E ALA* 1.3 56.3 + - - +
49E ILE* 3.4 2.1 + - - +
50E ARG* 2.9 36.0 + - - +
70E ASP* 3.5 20.4 - - - +
116E LEU* 3.6 37.7 - - + +
117E GLY 3.5 13.2 - - - +
118E GLY 3.9 1.3 - - - +
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLU 5.3 0.2 + - - -
44E HIS* 3.1 17.7 + - + +
46E PRO* 1.3 78.7 - - - +
48E ALA* 1.3 58.5 + - - +
50E ARG* 3.3 9.4 + - - +
51E GLU* 2.8 52.3 + - - +
70E ASP* 4.4 5.0 + - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E HIS 3.0 5.5 + - - -
45E GLY* 3.0 9.4 + - - +
47E ALA* 1.3 76.5 - - - +
49E ILE* 1.3 61.8 + - - +
51E GLU* 3.2 9.9 + - - +
52E ALA* 3.1 21.8 + - - +
297E VAL* 4.6 5.2 - - + -
299E PRO* 3.5 31.6 - - + -
308E ALA 5.8 0.9 - - - +
312E ALA* 3.8 16.7 - - + +
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Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLY 2.9 20.6 + - - +
46E PRO 3.8 3.4 - - - +
48E ALA* 1.3 74.1 - - - +
50E ARG* 1.3 64.9 + - - +
52E ALA* 3.0 20.0 + - - +
54E LEU* 3.6 33.3 + - + -
116E LEU* 4.1 25.4 - - + -
117E GLY 5.2 2.0 - - - +
294E LEU* 4.1 19.3 - - + +
297E VAL* 4.3 15.3 - - + -
312E ALA* 4.5 4.0 - - - +
315E ALA* 3.9 24.2 - - + -
316E VAL* 3.6 16.0 - - + +
319E ILE* 4.3 7.9 - - + -
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Residues in contact with ARG 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 4.1 13.4 - - - +
30E GLY* 4.7 1.4 - - - +
46E PRO* 2.9 25.3 + - - +
47E ALA* 3.6 7.4 - - - +
49E ILE* 1.3 75.3 - - - +
51E GLU* 1.3 60.4 + - + +
53E GLY* 3.0 20.4 + - - -
54E LEU* 3.8 9.2 + - + +
55E MET* 3.5 28.1 + - + +
67E ASP* 2.6 43.2 + - - -
69E GLY* 3.7 12.1 + - - -
70E ASP* 2.6 33.9 + - - -
116E LEU* 4.7 10.2 - - + +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ALA* 2.8 38.4 + - - +
48E ALA* 3.2 7.8 + - - +
50E ARG* 1.3 73.8 - - + +
52E ALA* 1.3 57.4 + - - +
53E GLY 3.1 6.3 + - - -
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ALA 3.1 11.4 + - - +
49E ILE 3.0 13.9 + - - +
51E GLU* 1.3 76.8 - - - +
53E GLY* 1.3 58.9 + - - +
54E LEU 3.6 1.3 + - - -
57E ARG* 4.9 4.5 + - - -
309E LYS* 6.1 2.7 - - + -
312E ALA* 3.8 15.9 - - + +
313E ASN* 3.6 23.6 - - - +
316E VAL* 3.6 21.3 - - + +
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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