Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 6H5H
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 4.2 14.4 - - - -
51A LYS* 4.7 6.5 - - - -
55A GLY 3.8 0.6 + - - -
56A VAL* 1.3 77.3 - - - +
58A THR* 1.3 66.2 + - - -
59A LYS* 3.2 3.6 - - - -
60A ILE* 3.1 16.1 + - - +
61A ALA* 3.0 21.7 + - - +
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Residues in contact with THR 58 (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 LYS* 3.7 27.9 - - + +
57A GLY* 1.3 71.0 - - - -
59A LYS* 1.3 79.1 + - - +
61A ALA* 3.1 9.4 + - - +
62A GLU* 3.0 31.4 + - - +
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Residues in contact with LYS 59 (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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26A ASP* 5.8 4.7 - - - +
30A TYR* 4.5 19.1 - - - +
57A GLY* 3.2 1.0 - - - -
58A THR* 1.3 89.6 + - - +
60A ILE* 1.3 65.3 + - + +
62A GLU* 3.1 18.4 + - - +
63A LYS* 3.1 29.6 + - + +
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Residues in contact with ILE 60 (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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11A LEU* 3.5 27.1 - - + -
29A GLN* 4.5 11.0 - - + +
30A TYR* 3.5 35.2 - - + -
33A ALA* 3.7 26.2 - - + -
37A LEU* 5.1 1.1 - - + -
55A GLY 3.7 6.1 - - - +
56A VAL* 4.1 11.4 - - + -
57A GLY* 3.1 29.0 + - - +
59A LYS* 1.3 78.6 - - + +
61A ALA* 1.3 62.7 + - - +
63A LYS* 3.1 10.7 + - - +
64A ILE* 3.0 31.4 + - + +
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Residues in contact with ALA 61 (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 GLY* 3.3 34.1 - - - +
48A ALA* 4.1 5.6 - - - +
51A LYS* 4.7 9.2 - - + +
56A VAL* 4.5 1.3 - - - +
57A GLY 3.0 12.0 + - - +
58A THR* 3.1 13.0 + - - +
60A ILE* 1.3 76.5 - - - +
62A GLU* 1.3 63.4 + - + +
64A ILE* 3.1 9.0 + - - +
65A ASP* 3.0 27.6 + - - +
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Residues in contact with GLU 62 (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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58A THR* 3.0 19.7 + - - +
59A LYS* 3.1 16.4 + - - +
61A ALA* 1.3 77.9 - - + +
63A LYS* 1.3 64.9 + - + +
65A ASP* 3.1 13.5 + - - +
66A GLU* 2.9 22.7 + - - +
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Residues in contact with LYS 63 (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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10A MET* 3.5 26.3 - - + +
11A LEU* 5.2 4.7 - - + -
14A GLU* 3.8 40.0 + - + +
17A LYS* 5.0 8.6 - - - +
30A TYR* 5.4 11.2 - - + -
59A LYS* 3.1 19.4 + - - +
60A ILE* 3.1 10.6 + - - +
62A GLU* 1.3 77.5 - - + +
64A ILE* 1.3 64.1 + - + +
66A GLU* 3.2 21.1 + - - +
67A PHE 3.0 18.4 + - - -
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Residues in contact with ILE 64 (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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7A LEU* 4.1 32.3 - - + -
10A MET* 4.7 1.3 - - + -
11A LEU* 5.4 3.8 - - + -
37A LEU* 4.6 14.1 - - + -
44A ILE* 5.1 5.2 - - + +
46A SER 4.0 4.9 - - - +
47A GLY* 3.5 20.9 - - - +
50A ALA* 3.1 34.8 - - + -
60A ILE* 3.0 26.2 + - + +
61A ALA* 3.1 8.0 + - - +
63A LYS* 1.3 77.1 - - + +
65A ASP* 1.3 62.6 + - - +
67A PHE* 3.2 7.8 + - - +
68A LEU* 3.0 33.7 + - + +
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Residues in contact with ASP 65 (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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46A SER* 3.9 6.9 - - - -
47A GLY* 2.9 26.2 + - - -
48A ALA* 4.1 5.4 + - - +
61A ALA* 3.0 19.0 + - - +
62A GLU* 3.1 15.5 + - - +
64A ILE* 1.3 75.0 - - - +
66A GLU* 1.3 62.7 - - - +
68A LEU* 3.3 9.6 + - - +
69A ALA* 2.9 21.9 + - - +
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Residues in contact with GLU 66 (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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10A MET* 6.2 0.6 - - - +
62A GLU 2.9 12.3 + - - +
63A LYS* 3.5 28.5 + - - +
65A ASP* 1.3 77.4 - - - +
67A PHE* 1.3 61.9 + - - +
69A ALA* 3.0 11.1 + - + +
70A THR* 2.9 31.3 + - - +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ALA* 4.1 30.1 - - + -
7A LEU* 3.1 36.8 - - + -
10A MET* 3.5 28.4 - - + -
63A LYS 3.0 12.6 + - - +
64A ILE 3.2 4.2 + - - +
66A GLU* 1.3 75.4 - - - +
68A LEU* 1.3 72.7 + - + +
70A THR* 3.2 12.4 + - + -
71A GLY 3.1 35.1 + - - +
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Residues in contact with LEU 68 (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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7A LEU* 5.3 6.5 - - + -
43A LYS* 4.3 21.5 - - - +
44A ILE 4.6 4.3 - - - +
45A LYS* 2.8 35.4 - - - +
46A SER* 3.7 11.4 - - - +
64A ILE* 3.0 23.1 + - + +
65A ASP* 3.5 10.3 - - - +
67A PHE* 1.3 85.9 - - + +
69A ALA* 1.3 63.7 + - - +
71A GLY* 3.0 21.2 + - - +
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Residues in contact with ALA 69 (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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65A ASP 2.9 13.0 + - - +
66A GLU* 3.0 14.8 + - + +
68A LEU* 1.3 76.8 - - - +
70A THR* 1.3 61.0 + - - +
71A GLY* 4.6 0.2 - - - -
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Residues in contact with THR 70 (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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66A GLU* 2.9 20.0 + - - +
67A PHE* 3.5 14.1 - - + -
68A LEU 3.2 0.2 - - - -
69A ALA* 1.3 77.1 - - - +
71A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 71 (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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67A PHE* 3.1 30.1 + - - +
68A LEU* 3.0 21.6 + - - -
69A ALA 3.3 0.6 - - - -
70A THR* 1.3 79.0 - - - +
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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