Contacts of the helix formed by residues 65 - 76 (chain F) 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 VAL 65 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E LEU* 3.7 27.4 - - + -
61F PHE* 3.4 39.6 + - + +
62F LEU* 4.7 2.2 - - + +
63F GLU 3.4 0.2 - - - -
64F ASN* 1.3 82.1 - - - +
66F ILE* 1.3 59.7 + - + +
67F ARG 3.2 1.3 - - - -
68F ASP* 2.9 9.2 + - - +
69F ALA* 2.7 40.6 + - + +
86F VAL* 4.8 3.1 - - + -
89F ALA* 4.4 5.5 - - + +
90F LEU* 3.7 34.1 - - + -
93F GLN* 4.9 0.2 - - - +
95F ARG* 4.6 2.2 - - - +
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Residues in contact with ILE 66 (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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71E ALA* 4.2 24.9 - - + +
74E ILE* 4.3 11.9 - - + +
75E CYS* 4.1 31.0 - - + +
78E PHE* 4.6 6.1 - - + -
86E TRP* 4.3 17.5 - - + -
94E LEU* 4.5 19.5 - - + -
62F LEU* 3.3 39.5 + - + +
63F GLU* 5.3 0.2 - - - -
65F VAL* 1.3 75.2 - - + +
67F ARG* 1.3 59.9 + - - +
69F ALA* 4.1 7.0 - - + -
70F VAL* 2.9 33.6 + - + +
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Residues in contact with ARG 67 (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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78E PHE* 3.5 37.1 - - + -
63F GLU* 3.5 21.9 + - - +
64F ASN* 3.3 29.2 + - - +
65F VAL 3.2 0.6 - - - -
66F ILE* 1.3 80.8 - - - +
68F ASP* 1.3 71.5 + - - +
70F VAL* 4.0 3.0 - - + +
71F THR* 2.4 36.6 + - - +
92F ARG* 5.8 2.0 - - - +
95G LYS* 5.0 12.3 - - - +
99H ARG 4.9 10.8 + - - +
100H LEU 5.7 2.0 + - - -
102H LEU 4.9 10.6 + - - -
103H PRO* 5.2 3.4 - - - +
104H GLY* 5.5 14.0 - - - +
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Residues in contact with ASP 68 (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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64F ASN* 3.9 4.7 - - - +
65F VAL* 2.9 9.7 + - - +
67F ARG* 1.3 100.9 + - - +
69F ALA* 1.3 59.3 + - - +
71F THR* 3.9 6.0 - - - -
72F TYR* 3.2 27.2 - - + -
89F ALA* 3.3 22.7 - - + +
92F ARG* 3.5 23.3 + - - -
93F GLN* 3.7 20.8 + - - +
100H LEU* 3.3 28.0 - - + +
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E TRP* 5.4 4.3 - - + -
65F VAL* 2.7 23.3 + - + +
66F ILE* 4.1 9.0 - - + -
67F ARG 3.2 0.4 - - - -
68F ASP* 1.3 73.2 - - - +
70F VAL* 1.3 63.4 + - - +
71F THR 3.1 1.9 + - - -
72F TYR* 3.7 2.9 + - - +
73F THR* 3.4 20.6 + - - -
81F VAL* 4.5 7.4 - - + +
85F ASP* 3.4 27.6 - - - +
86F VAL* 4.4 15.0 - - + -
89F ALA* 3.8 5.2 - - + -
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Residues in contact with VAL 70 (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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75E CYS* 4.5 10.8 - - - -
78E PHE* 4.9 9.4 - - + -
79E THR* 3.9 21.3 - - + -
84E PHE* 3.9 36.6 - - + -
86E TRP* 6.1 0.9 - - + -
66F ILE* 2.9 27.2 + - + +
67F ARG* 4.0 7.4 - - - +
69F ALA* 1.3 76.4 - - - +
71F THR* 1.3 61.9 + - - +
73F THR* 3.7 5.4 - - - -
74F GLU* 2.9 30.3 + - - +
81F VAL* 4.5 13.4 - - + +
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Residues in contact with THR 71 (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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67F ARG* 2.4 27.4 + - - +
68F ASP 3.9 7.2 - - - -
69F ALA 3.1 0.8 - - - -
70F VAL* 1.3 78.4 - - - +
72F TYR* 1.3 60.8 + - - +
74F GLU* 3.4 4.4 + - - +
75F HIS* 3.0 28.6 + - - +
96H THR* 4.3 22.5 - - + +
99H ARG* 4.8 16.0 + - + +
100H LEU* 3.8 32.0 - - + +
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Residues in contact with TYR 72 (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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68F ASP* 3.2 24.5 - - + -
69F ALA 3.7 6.0 + - - +
71F THR* 1.3 77.4 - - + +
73F THR* 1.3 63.3 + - - +
75F HIS* 3.8 5.4 + - + +
76F ALA* 3.5 20.8 + - - +
78F ARG* 4.7 3.8 + - - -
85F ASP* 4.7 16.8 - - + +
88F TYR* 4.3 21.7 + + + +
89F ALA* 4.2 24.0 - - + -
92F ARG* 4.4 14.3 - - + +
76H GLU* 3.1 18.0 + - - +
79H ARG* 5.4 5.0 + - - -
80H LEU* 3.7 35.8 - - + +
83H TYR* 4.6 16.4 - + - -
84H ASN* 5.3 3.1 + - - -
100H LEU* 3.8 20.4 - - + +
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Residues in contact with THR 73 (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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84E PHE* 4.6 9.6 - - + -
69F ALA 3.4 8.6 + - - -
70F VAL* 3.4 8.0 + - - -
71F THR 3.2 0.8 - - - -
72F TYR* 1.3 78.3 - - - +
74F GLU* 1.3 57.2 - - - +
76F ALA 2.8 25.7 - - - +
78F ARG* 3.6 18.9 + - + +
79F LYS 4.3 4.9 - - - -
80F THR 3.4 35.2 - - - +
81F VAL* 3.4 23.0 - - + +
85F ASP* 3.3 19.6 + - - +
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Residues in contact with GLU 74 (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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79E THR* 4.1 25.5 - - - +
80E ARG* 5.7 3.1 + - - -
84E PHE* 5.1 13.2 - - + -
70F VAL* 2.9 19.3 + - - +
71F THR* 4.2 4.5 - - - +
73F THR* 1.3 77.6 - - - +
75F HIS* 1.3 64.1 + - - +
77F LYS* 4.4 6.9 - - - +
78F ARG 5.2 4.5 - - - +
92H ARG* 3.3 11.9 + - - +
99H ARG* 5.4 6.1 + - - -
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Residues in contact with HIS 75 (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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71F THR 3.0 18.0 + - - +
72F TYR* 3.8 8.6 + - - +
73F THR 3.2 0.4 - - - -
74F GLU* 1.3 75.8 - - - +
76F ALA* 1.3 75.1 + - + +
77F LYS* 3.2 7.6 + - - +
80H LEU* 3.6 18.5 - - + +
84H ASN* 3.1 27.5 + - + -
86H ARG* 6.0 2.5 - - - -
92H ARG* 2.8 51.2 + - - +
93H GLU* 3.3 39.6 - - + +
96H THR* 3.1 36.1 - - + +
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR 3.5 8.8 + - - +
73F THR 2.8 11.7 - - - +
75F HIS* 1.3 79.7 + - + +
77F LYS* 1.3 51.7 + - - +
78F ARG* 2.7 39.0 + - + +
84H ASN* 3.4 36.8 - - + +
86H ARG* 5.5 9.6 - - - +
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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