Contacts of the helix formed by residues 51 - 63 (chain I) in PDB entry 5BRR
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 51 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50I THR* 1.3 76.4 - - - +
52I GLY* 1.3 69.0 + - - -
53I GLU 3.1 0.5 + - - -
54I THR 2.9 16.8 + - - -
55I GLN* 3.2 7.2 + - - -
305I ASP* 2.9 38.0 + - - +
307I THR* 4.2 7.0 - - - -
308I SER* 4.5 2.0 - - - -
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Residues in contact with GLY 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I GLY* 1.3 66.9 - - - +
53I GLU* 1.3 60.4 + - - -
55I GLN* 3.5 8.5 + - - +
56I GLN* 3.0 33.7 + - - +
305I ASP* 3.5 7.0 + - - -
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Residues in contact with GLU 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I GLY 3.1 0.8 + - - -
52I GLY* 1.3 71.9 - - - -
54I THR* 1.3 61.2 + - - +
55I GLN 3.2 0.4 - - - -
56I GLN* 4.1 10.9 - - + +
57I GLN* 2.8 39.6 + - - +
297I ASP* 4.3 13.7 - - - +
305I ASP* 4.8 1.4 + - - +
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I THR* 3.8 16.2 - - + -
51I GLY 2.9 8.6 + - - -
53I GLU* 1.3 77.1 - - - +
55I GLN* 1.3 59.9 + - - +
57I GLN* 3.2 16.0 - - - +
58I ILE* 3.2 14.6 - - - +
297I ASP* 3.4 25.3 + - + +
298I MET* 3.9 24.7 - - + -
303I GLN 3.8 0.5 + - - -
305I ASP* 2.8 41.0 + - - +
306I PHE* 4.0 9.6 - - + -
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Residues in contact with GLN 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I GLN* 3.2 15.0 - - + +
48I LEU* 4.5 3.6 - - - +
50I THR* 2.9 40.7 + - - +
51I GLY* 3.2 8.2 + - - -
52I GLY* 3.5 16.0 + - - +
54I THR* 1.3 74.6 - - - +
56I GLN* 1.3 77.2 + - - +
57I GLN 2.7 3.3 + - - -
58I ILE* 2.7 16.9 + - - +
59I GLN* 3.0 41.3 + - - +
308I SER* 4.7 1.9 + - - -
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Residues in contact with GLN 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I GLY* 3.0 18.5 + - - +
53I GLU* 3.4 14.6 + - + +
55I GLN* 1.3 88.8 - - + +
57I GLN* 1.3 60.4 + - - +
59I GLN* 2.0 40.5 + - - +
60I ALA* 3.2 22.3 + - - +
65I LYS* 3.7 19.2 + - - +
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Residues in contact with GLN 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLU* 2.8 22.5 + - - +
54I THR 3.2 12.0 - - - +
55I GLN 2.7 0.6 + - - -
56I GLN* 1.3 77.2 - - - +
58I ILE* 1.3 59.2 + - + +
60I ALA* 3.1 21.9 - - - +
61I ALA* 3.3 8.3 + - - +
294I GLY 3.4 23.3 + - - +
295I MET* 3.6 9.3 - - + +
296I THR* 2.8 34.2 + - - +
297I ASP* 3.0 42.7 + - - +
298I MET* 4.3 3.6 + - - +
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU* 3.1 37.0 - - + +
46I LEU* 3.7 14.8 - - + -
47I GLN* 3.3 35.0 - - + +
50I THR* 4.6 1.6 - - - +
54I THR* 3.2 19.5 - - + +
55I GLN* 2.7 10.9 + - - +
57I GLN* 1.3 70.8 - - - +
59I GLN* 1.3 63.7 + - - +
60I ALA 3.2 0.2 - - - -
61I ALA* 3.6 1.2 + - - +
62I MET* 3.1 36.9 + - - +
295I MET* 3.9 18.8 - - + -
298I MET* 4.0 27.6 - - + -
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I GLN* 3.3 35.6 + - + +
55I GLN* 3.0 40.5 + - - +
56I GLN* 2.0 42.3 + - - +
58I ILE* 1.3 73.6 - - - +
60I ALA* 1.3 61.0 + - - +
62I MET* 4.6 0.2 - - - -
63I GLY* 2.8 29.8 + - - -
64I PHE 3.5 18.0 + - - +
65I LYS* 3.7 24.4 + - + +
67I ASP* 5.5 4.8 - - - +
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Residues in contact with ALA 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I GLN 3.2 16.1 + - - +
57I GLN* 3.1 14.1 - - - +
59I GLN* 1.3 79.9 - - - +
61I ALA* 1.3 64.7 + - - +
62I MET 3.1 0.3 + - - -
63I GLY* 3.3 8.0 + - - -
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Residues in contact with ALA 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PHE* 3.4 11.1 - - + -
18I ARG* 2.6 33.4 + - - -
57I GLN 3.3 4.6 + - - +
58I ILE 3.9 4.5 - - - +
59I GLN 3.4 0.4 - - - -
60I ALA* 1.3 81.2 - - - +
62I MET* 1.3 54.5 + - - +
293I LEU* 4.6 11.7 - - + +
295I MET* 2.8 39.9 - - + -
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Residues in contact with MET 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I LEU* 3.9 20.3 - - - +
12I ALA* 5.5 0.4 - - - -
15I PHE* 3.8 27.1 - - + +
18I ARG* 4.4 3.8 + - - -
40I ALA* 3.4 38.6 - - + +
43I LEU* 3.7 14.8 - - + +
44I ALA* 3.4 17.0 - - + +
47I GLN* 3.6 22.0 - - - +
58I ILE* 3.1 19.5 + - + +
59I GLN 4.1 1.6 - - - +
61I ALA* 1.3 77.7 - - - +
63I GLY* 1.3 61.7 + - - +
64I PHE* 3.5 42.0 - - + +
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Residues in contact with GLY 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I LEU* 3.5 15.5 - - - +
59I GLN 2.8 11.3 + - - -
60I ALA 3.3 7.8 + - - -
62I MET* 1.3 79.6 - - - +
64I PHE* 1.3 64.9 + - - +
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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