Contacts of the helix formed by residues 57 - 65 (chain D) in PDB entry 6MUO
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 LYS 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C PRO* 4.2 18.2 - - + -
103C ALA* 5.9 4.5 - - + +
104C GLN* 4.2 28.3 - - + +
55D SER* 3.1 4.0 + - - +
56D SER* 1.3 81.4 + - - +
58D ALA* 1.3 59.4 + - - +
59D MET 3.2 2.2 - - - -
60D GLY* 2.9 18.8 + - - -
61D ILE* 3.4 14.5 + - + +
99F GLY 5.7 4.2 - - - +
100F PHE* 6.0 6.1 - - - -
-55I G 4.9 0.8 + - - -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE* 3.6 18.2 - - + +
79C ILE 4.6 0.2 - - - -
80C PRO* 3.9 16.3 - - + +
83C LEU* 4.3 11.9 - - + +
54D ILE* 3.7 12.3 - - + -
55D SER* 3.1 23.6 + - - +
57D LYS* 1.3 75.1 - - - +
59D MET* 1.3 63.9 + - - +
61D ILE* 3.4 9.4 + - - +
62D MET* 3.2 25.5 + - - +
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Residues in contact with MET 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D TYR 5.2 0.2 - - - -
38D SER* 3.7 49.4 - - - +
41D VAL* 4.1 20.0 - - + -
42D TYR* 4.3 15.0 - - + +
54D ILE* 3.8 34.7 - - + +
55D SER 3.3 12.3 + - - +
56D SER* 4.4 9.0 - - - +
57D LYS 3.2 0.6 - - - -
58D ALA* 1.3 75.2 - - - +
60D GLY* 1.3 63.9 + - - +
62D MET* 3.2 7.1 + - - +
63D ASN* 3.1 28.2 + - - +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER 4.3 3.2 + - - -
57D LYS* 2.9 13.5 + - - -
59D MET* 1.3 77.0 - - - +
61D ILE* 1.3 62.3 + - - +
63D ASN* 3.3 23.6 + - - +
64D SER* 3.4 7.4 + - - -
98F TYR 4.1 5.6 - - - +
99F GLY 4.6 10.8 - - - +
101F GLY* 5.8 0.5 - - - +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ILE* 6.5 0.4 - - + -
80C PRO* 3.7 33.4 - - + -
83C LEU* 3.8 24.5 - - + -
102C ILE* 3.8 40.6 - - + -
103C ALA* 4.2 6.7 - - + +
57D LYS* 3.4 9.9 + - + +
58D ALA* 3.4 6.3 + - - +
59D MET 3.3 0.4 - - - -
60D GLY* 1.3 75.0 - - - +
62D MET* 1.3 59.4 + - + +
63D ASN 3.1 1.7 + - - -
64D SER* 3.2 1.9 + - - -
65D PHE* 2.8 30.2 + - + +
98F TYR* 3.5 27.5 - - + +
99F GLY* 5.1 4.3 - - - +
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C THR* 3.9 31.2 - - + +
62C ILE* 3.7 27.8 - - + -
63C LEU* 4.3 20.9 - - + -
83C LEU* 4.8 9.6 - - + -
37D TYR* 5.3 0.3 - - - +
41D VAL* 3.8 41.1 - - + +
54D ILE* 4.6 9.2 - - + -
58D ALA 3.2 14.4 + - - +
59D MET* 3.2 15.1 + - - +
61D ILE* 1.3 76.2 - - - +
63D ASN* 1.3 60.8 + - - +
65D PHE* 4.3 12.1 - - + -
66D VAL* 3.3 21.8 - - - +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 2.4 37.8 + - - +
37D TYR* 3.5 14.3 - - - +
38D SER 4.9 0.4 - - - +
59D MET* 3.1 25.0 + - - +
60D GLY* 3.4 14.4 - - - +
61D ILE 3.1 0.4 - - - -
62D MET* 1.3 77.1 + - - +
64D SER* 1.3 60.8 + - - +
65D PHE 3.1 4.0 - - - -
66D VAL* 3.0 22.2 + - - +
67D ASN* 3.0 25.8 + - - +
101F GLY* 5.0 7.4 - - - +
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Residues in contact with SER 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLY 3.4 4.8 + - - -
61D ILE 3.2 3.0 + - - -
63D ASN* 1.3 74.5 - - - +
65D PHE* 1.3 59.7 + - - +
67D ASN* 4.6 5.8 - - - +
68D ASP* 3.3 14.7 + - - +
97F LEU 4.7 2.7 - - - -
98F TYR* 3.1 52.2 + - - -
100F PHE 4.7 0.3 + - - -
101F GLY* 2.3 42.8 + - - -
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 4.2 23.1 - - + -
59C THR* 4.0 27.4 - - + -
62C ILE* 4.5 24.9 - - + -
87C ILE* 6.0 1.1 - - + -
93C LEU* 5.8 0.4 - - + -
96C LEU* 4.4 8.5 - - + -
97C LEU* 3.7 33.2 - - + -
61D ILE* 2.8 18.8 + - + +
62D MET* 4.5 13.5 - - - -
64D SER* 1.3 80.0 - - - +
66D VAL* 1.3 62.3 + - + +
67D ASN 3.4 0.2 - - - -
68D ASP* 3.4 1.7 + - - +
69D ILE* 3.1 49.7 + - + +
98F TYR* 3.7 24.9 - + + -
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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