Contacts of the helix formed by residues 53 - 62 (chain F) 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 GLY 53 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F ARG 3.0 7.1 + - - -
51F GLU 3.3 3.4 + - - -
52F ALA* 1.3 79.3 - - - +
54F LEU* 1.3 64.1 + - - +
55F MET 3.2 2.8 + - - -
56F LYS* 3.5 17.3 + - - +
57F ARG* 3.1 26.3 + - - +
316F VAL* 4.6 0.4 - - - -
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 4.5 12.1 - - + -
49F ILE* 3.6 25.9 + - + +
50F ARG* 3.7 8.7 + - + -
52F ALA 3.5 3.8 + - - -
53F GLY* 1.3 75.4 - - - +
55F MET* 1.3 68.5 + - + +
57F ARG* 3.2 3.5 - - + +
58F LEU* 3.1 44.1 + - + +
114F VAL* 5.0 0.4 - - + -
116F LEU* 3.6 40.4 - - + -
316F VAL* 4.0 18.6 - - + +
319F ILE* 3.8 27.4 - - + -
320F ALA 5.2 0.4 - - - +
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Residues in contact with MET 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 3.2 48.5 - - + -
50F ARG* 3.6 19.3 + - + +
53F GLY 3.3 0.8 - - - -
54F LEU* 1.3 83.5 - - + +
56F LYS* 1.3 62.8 + - - +
58F LEU* 3.2 13.2 + - - -
59F SER* 3.2 10.4 + - - -
65F LEU* 3.3 30.7 - - + +
67F ASP* 3.1 37.2 - - + +
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F GLY* 3.5 16.4 + - - +
55F MET* 1.3 75.5 - - - +
57F ARG* 1.3 63.6 + - - +
59F SER* 3.7 9.7 - - - -
60F SER* 2.9 29.8 + - - -
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ALA 4.7 6.3 + - - -
53F GLY 3.1 21.3 + - - +
54F LEU* 3.2 8.3 - - + +
56F LYS* 1.3 81.7 - - - +
58F LEU* 1.3 60.9 + - + +
60F SER* 3.4 19.2 - - - -
61F LEU* 3.5 13.7 + - - +
313F ASN* 5.3 3.2 + - - +
316F VAL* 3.3 25.7 - - + +
317F ASP* 2.4 31.9 + - - +
320F ALA* 3.9 16.8 - - + -
325F GLN* 2.8 42.3 + - - +
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F VAL* 4.6 12.1 - - + -
28F VAL* 4.2 20.6 - - + -
54F LEU* 3.1 40.4 + - + +
55F MET* 3.2 11.6 + - - +
57F ARG* 1.3 76.8 - - + +
59F SER* 1.3 64.0 + - - +
61F LEU* 3.3 31.3 + - + +
63F CYS* 3.4 18.7 - - + +
65F LEU* 3.9 15.0 - - + -
114F VAL* 5.6 0.2 - - + -
319F ILE* 4.3 12.1 - - + -
320F ALA* 4.4 8.3 - - + -
323F PHE* 4.2 25.4 - - + -
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Residues in contact with SER 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET 3.2 8.0 + - - -
56F LYS* 3.7 11.9 - - - -
58F LEU* 1.3 72.0 - - - +
60F SER* 1.3 56.8 + - - +
61F LEU 2.9 4.5 - - - -
62F GLY* 2.5 30.1 + - - -
63F CYS 4.1 11.6 + - - -
65F LEU* 3.3 19.2 - - - +
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LYS 2.9 19.1 + - - -
57F ARG* 3.4 14.8 + - - -
59F SER* 1.3 77.6 - - - +
61F LEU* 1.3 62.9 + - - +
62F GLY* 4.6 0.5 - - - -
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ARG 3.5 15.2 + - - +
58F LEU* 3.3 17.0 + - + +
59F SER 2.8 1.0 + - - -
60F SER* 1.3 81.6 - - - +
62F GLY* 1.3 56.4 + - - +
63F CYS* 3.5 8.1 - - - -
320F ALA* 3.5 32.1 - - + +
323F PHE* 3.7 23.6 - - + +
324F GLY* 4.0 4.5 - - - +
325F GLN* 3.6 34.1 - - + +
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Residues in contact with GLY 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS 5.7 1.0 + - - -
59F SER 2.5 19.4 + - - -
60F SER 4.5 0.4 - - - -
61F LEU* 1.3 74.7 - - - +
63F CYS* 1.3 64.6 - - - +
64F HIS* 3.7 1.6 + - - +
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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