Contacts of the helix formed by residues 65 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.7 26.9 - - + -
61B PHE* 3.3 39.7 - - + +
62B LEU* 3.1 5.6 + - + +
64B ASN* 1.3 83.2 - - - +
66B ILE* 1.3 56.9 + - + +
67B ARG 3.3 1.3 - - - -
68B ASP* 2.9 9.4 + - - +
69B ALA* 2.6 43.1 + - + +
86B VAL* 4.7 3.6 - - + -
89B ALA* 4.2 3.8 - - + +
90B LEU* 3.7 34.3 - - + -
95B ARG* 4.7 1.1 - - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 4.5 23.8 - - + +
74A ILE* 4.4 16.6 - - + +
75A CYS* 4.2 29.8 - - + -
78A PHE* 4.6 7.6 - - + -
86A TRP* 4.9 13.7 - - + -
94A LEU* 4.8 12.6 - - + -
62B LEU* 2.8 43.6 + - + +
63B GLU* 5.2 0.4 - - - -
65B VAL* 1.3 73.4 - - + +
67B ARG* 1.3 59.4 + - - +
69B ALA* 3.8 7.0 - - + -
70B VAL* 2.5 42.0 + - + +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.5 39.3 - - + -
62B LEU 4.4 0.2 + - - -
63B GLU* 3.4 28.5 + - - +
64B ASN* 3.3 21.9 + - - +
65B VAL 3.3 0.4 - - - -
66B ILE* 1.3 77.8 - - - +
68B ASP* 1.3 66.7 + - - +
70B VAL* 4.5 2.7 - - + -
71B THR* 2.6 32.7 + - - +
95C LYS* 6.1 3.0 - - - +
99D ARG 5.0 11.1 + - - +
100D LEU* 4.4 1.4 - - - +
102D LEU 4.8 13.5 + - - -
103D PRO* 4.8 8.5 - - - +
104D GLY* 5.0 15.3 - - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 3.7 5.7 - - - +
65B VAL* 2.9 12.6 + - - +
67B ARG* 1.3 89.2 + - - +
69B ALA* 1.3 59.0 + - - +
71B THR* 4.3 2.3 - - - -
72B TYR* 4.1 19.1 + - - -
89B ALA* 3.3 30.5 - - + +
92B ARG* 3.6 27.2 + - - -
93B GLN* 3.6 23.4 + - - +
99D ARG 5.1 0.3 - - - +
100D LEU* 3.4 27.9 - - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 5.5 3.4 - - + -
65B VAL* 2.6 22.4 + - + +
66B ILE* 2.9 11.8 + - + +
68B ASP* 1.3 73.9 - - - +
70B VAL* 1.3 65.4 + - - +
71B THR 3.2 2.0 + - - -
72B TYR* 3.7 4.4 + - - +
73B THR* 3.2 22.6 + - - -
81B VAL* 4.4 6.6 - - + +
85B ASP* 4.2 7.8 - - - +
86B VAL* 4.3 22.2 - - + -
89B ALA* 3.8 13.0 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A CYS* 4.7 10.1 - - - +
78A PHE* 4.7 10.8 - - + -
79A THR* 3.7 34.1 - - + +
84A PHE* 4.1 26.9 - - + -
86A TRP* 6.6 0.2 - - + -
66B ILE* 2.5 32.8 + - + +
67B ARG* 4.3 5.4 - - + +
69B ALA* 1.3 72.8 - - - +
71B THR* 1.3 61.6 + - - +
73B THR* 3.2 8.9 + - - -
74B GLU* 2.7 34.8 + - + +
81B VAL* 5.0 5.8 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 2.6 27.9 + - - +
68B ASP 4.4 1.1 - - - -
69B ALA 3.2 0.4 - - - -
70B VAL* 1.3 80.8 - - - +
72B TYR* 1.3 63.2 + - + +
74B GLU* 3.8 6.7 - - + +
75B HIS* 3.0 29.1 + - - +
96D THR* 4.0 29.6 - - + +
99D ARG* 4.6 18.8 + - + +
100D LEU* 4.0 25.1 - - + +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP 4.1 9.3 + - - -
69B ALA 3.7 6.6 + - - +
70B VAL 3.4 0.4 - - - -
71B THR* 1.3 80.0 - - + +
73B THR* 1.3 62.6 + - - +
75B HIS* 3.6 13.4 + - - +
76B ALA* 3.9 5.7 + - - +
78B ARG* 4.4 8.5 + - - -
85B ASP* 4.0 25.5 - - + +
88B TYR* 3.6 45.4 + + + -
89B ALA* 4.0 4.9 - - - -
92B ARG* 4.5 10.2 - - + +
76D GLU* 3.1 21.1 + - - -
79D ARG* 5.0 4.7 + - - -
80D LEU* 3.8 31.9 - - + +
83D TYR* 4.7 12.5 - + - -
96D THR* 5.5 0.9 - - - -
100D LEU* 3.5 27.0 - - + +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 4.3 15.3 - - + -
69B ALA 3.2 13.2 + - - -
70B VAL* 3.2 10.0 + - - -
71B THR 3.2 0.8 - - - -
72B TYR* 1.3 78.8 - - - +
74B GLU* 1.3 59.3 + - - +
76B ALA 2.8 24.6 - - - +
78B ARG* 4.0 11.4 + - + +
79B LYS 4.6 0.2 - - - -
80B THR 3.4 35.4 - - - +
81B VAL* 3.4 22.9 - - + +
85B ASP* 3.1 19.7 + - - -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.5 28.0 - - + +
84A PHE* 5.1 10.8 - - + -
70B VAL* 2.7 19.5 + - - +
71B THR* 4.2 5.9 - - - +
73B THR* 1.3 73.6 - - - +
75B HIS* 1.3 64.1 + - - +
76B ALA 4.2 2.9 - - - -
77B LYS* 4.3 6.1 - - - +
78B ARG 5.1 6.1 - - - +
92D ARG* 3.6 9.8 + - - +
96D THR* 5.7 0.7 - - - -
99D ARG* 5.3 8.1 + - - -
7M GLU* 3.7 23.7 - - - +
10M LYS* 4.9 6.9 + - - -
11M ARG* 4.0 12.3 + - - +
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 3.0 17.2 + - - +
72B TYR* 3.8 9.8 + - - +
73B THR 3.1 0.6 - - - -
74B GLU* 1.3 74.3 - - - +
76B ALA* 1.3 70.4 + - - +
77B LYS* 3.3 6.2 + - - +
80D LEU* 3.6 20.7 - - + +
84D ASN* 3.1 31.6 + - - -
86D ARG* 5.5 3.6 - - - -
92D ARG* 3.0 52.3 + - - +
93D GLU* 3.3 39.2 - - + +
96D THR* 3.1 34.8 - - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR 3.9 4.5 + - - +
73B THR 2.8 15.6 - - - +
75B HIS* 1.3 79.8 + - - +
77B LYS* 1.3 53.2 + - - +
78B ARG* 2.7 45.6 + - + +
84D ASN* 3.8 29.2 - - - +
86D ARG* 6.2 2.7 - - - +
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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