Contacts of the helix formed by residues 42 - 50 (chain l) in PDB entry 4PJO
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 MET 42 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8k ASN* 5.7 3.6 - - - +
9k LEU* 4.3 18.4 - - + -
12k LEU* 4.4 11.7 - - + -
38l TYR 3.4 13.2 - - - +
39l GLN* 2.7 31.5 + - + +
41l TRP* 1.3 102.9 - - + +
43l GLU* 1.3 53.8 + - - -
44l GLU* 5.5 0.9 - - - +
45l GLN* 2.8 42.8 + - + +
46l ALA* 3.7 1.7 + - - +
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Residues in contact with GLU 43 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39l GLN 3.9 0.6 + - - +
40l LYS* 2.8 32.8 + - + +
42l MET* 1.3 72.4 - - - +
44l GLU* 1.3 63.5 + - - +
46l ALA* 3.1 28.7 + - - +
47l GLN* 3.4 19.1 + - - +
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Residues in contact with GLU 44 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40l LYS 4.2 0.2 + - - -
41l TRP* 2.9 60.2 + - + +
42l MET* 5.5 0.5 - - - +
43l GLU* 1.3 77.2 - - - +
45l GLN* 1.3 67.8 + - - +
47l GLN* 3.2 40.5 + - - +
48l SER* 3.5 3.6 + - - -
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Residues in contact with GLN 45 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42l MET* 2.8 36.2 + - + +
44l GLU* 1.3 81.4 + - - +
46l ALA* 1.3 62.8 + - - +
48l SER* 3.0 30.1 + - - +
49l LEU* 3.7 4.8 + - + +
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Residues in contact with ALA 46 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42l MET 3.7 2.2 + - - +
43l GLU* 3.1 25.5 + - - +
45l GLN* 1.3 75.6 + - - +
47l GLN* 1.3 61.6 + - + +
48l SER 3.1 0.3 + - - -
49l LEU* 3.1 40.2 + - + +
50l ILE* 3.4 10.1 + - + +
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Residues in contact with GLN 47 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43l GLU* 3.6 18.8 + - - +
44l GLU* 3.2 32.4 + - + +
46l ALA* 1.3 75.8 - - + +
48l SER* 1.3 56.0 + - - +
50l ILE* 3.2 31.3 - - + +
51l ASP* 3.4 15.2 + - - +
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Residues in contact with SER 48 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44l GLU 3.5 4.2 + - - -
45l GLN* 3.0 23.2 + - - +
47l GLN* 1.3 74.2 - - - +
49l LEU* 1.3 63.8 + - - +
50l ILE 3.2 2.0 - - - -
51l ASP* 3.1 25.6 + - - +
52l LYS* 3.6 10.9 + - - +
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Residues in contact with LEU 49 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45l GLN* 3.7 2.4 + - + +
46l ALA* 3.1 32.8 - - + +
48l SER* 1.3 81.4 + - - +
50l ILE* 1.3 73.2 + - + +
52l LYS* 3.7 23.2 - - - +
53l THR* 4.8 0.5 + - - -
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Residues in contact with ILE 50 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46l ALA* 3.4 13.2 + - + +
47l GLN* 3.2 34.3 - - + +
48l SER 3.2 0.8 - - - -
49l LEU* 1.3 88.7 - - + +
51l ASP* 1.3 68.5 + - + +
52l LYS 3.4 1.3 - - - -
53l THR* 3.3 24.2 - - - +
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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