Contacts of the helix formed by residues 78 - 95 (chain C) in PDB entry 1MBU
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 ALA 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 4.0 23.7 + - + +
144A GOL 3.7 20.0 - - - +
25C PRO* 5.0 3.2 - - + +
26C SER 3.6 11.8 + - - +
28C TYR* 3.5 37.7 - - + -
77C THR* 1.3 72.6 - - - +
79C GLU* 1.3 57.4 + - - +
81C ALA* 3.7 0.3 - - - +
82C GLU* 3.0 32.1 + - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.4 9.1 - - + +
27A VAL* 2.9 25.8 + - - +
28A GLU* 2.6 32.4 - - - +
61A PHE* 5.5 1.0 - - - -
81A THR* 2.6 34.2 + - + +
82A LEU 5.3 0.2 + - - -
83A SER* 3.7 18.8 - - - +
117A GLU 4.7 7.8 + - - +
118A SER* 4.6 6.9 - - - -
119A GLN 5.1 0.3 + - - -
144A GOL 5.4 0.2 - - - -
77C THR* 3.2 7.9 + - - +
78C ALA* 1.3 80.6 - - - +
80C VAL* 1.3 62.3 + - + +
82C GLU* 3.6 9.9 + - - +
83C THR* 3.2 24.3 + - - -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 4.0 33.4 - - + -
26A THR* 4.7 18.6 - - + -
65A THR 4.4 13.9 - - - +
66A THR* 5.3 1.3 - - - -
67A PRO* 4.3 8.5 - - + -
81A THR* 4.9 2.7 - - + -
76C PHE* 3.7 30.1 - - + -
77C THR* 3.1 20.8 + - + +
79C GLU* 1.3 74.6 - - + +
81C ALA* 1.3 65.8 + - - +
83C THR* 3.1 8.3 + - - -
84C LYS* 2.9 25.5 + - + +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.6 27.8 - - + -
30C VAL* 3.8 22.4 - - + -
76C PHE* 3.9 8.4 - - + +
77C THR 2.8 21.7 + - - +
78C ALA 3.7 2.7 - - - +
80C VAL* 1.3 71.8 - - - +
82C GLU* 1.3 65.2 + - - +
84C LYS* 3.3 3.0 + - - +
85C VAL* 3.0 28.4 + - - +
103C LEU* 3.8 7.6 - - + -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.9 21.9 - - + +
83A SER* 4.4 4.5 + - - -
86A ARG* 3.1 42.4 + - - -
144A GOL 3.5 34.8 + - - +
78C ALA 3.0 18.4 + - - +
79C GLU* 3.8 7.3 - - - +
80C VAL 3.3 0.2 - - - -
81C ALA* 1.3 77.0 - - - +
83C THR* 1.3 61.5 + - - +
85C VAL* 3.5 4.4 + - - +
86C ALA* 3.1 22.0 + - - +
103C LEU* 3.6 10.0 - - - +
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 33.0 - - + -
79A GLN* 4.2 13.0 - - - +
80A PRO 4.3 0.4 - - - +
81A THR* 3.4 12.6 - - - -
82A LEU* 3.2 33.7 + - + +
79C GLU 3.2 12.3 + - - -
80C VAL* 3.1 9.5 + - - -
82C GLU* 1.3 75.6 - - - +
84C LYS* 1.3 67.4 + - - +
86C ALA* 3.2 3.2 + - + +
87C MET* 2.9 29.1 + - + +
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Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.6 34.6 + - - -
24A PHE* 4.1 16.1 - - + -
67A PRO* 4.8 2.0 - - - -
76A ARG* 4.3 3.0 - - - +
30C VAL* 4.8 3.8 - - + -
50C PHE* 2.7 31.5 + - + +
51C PHE* 3.9 17.9 - - + +
76C PHE* 3.7 46.0 - - + -
80C VAL* 2.9 18.9 + - + +
81C ALA* 3.8 5.8 - - - +
83C THR* 1.3 75.8 - - - +
85C VAL* 1.3 64.6 + - - +
87C MET* 3.2 9.7 + - - +
88C VAL* 2.9 29.7 + - + +
101C CYS* 5.1 0.7 - - - -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.1 7.4 - - + -
81C ALA 3.0 20.8 + - - +
82C GLU* 3.7 7.0 - - - +
84C LYS* 1.3 77.4 - - - +
86C ALA* 1.3 59.2 + - - +
88C VAL* 3.4 1.4 + - - +
89C ASN* 3.0 46.7 + - - +
101C CYS* 3.6 24.4 - - - +
102C THR* 3.7 29.6 - - - +
103C LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.7 24.5 - - + -
82C GLU 3.1 14.9 + - - +
83C THR* 3.7 7.4 - - + +
85C VAL* 1.3 78.7 - - - +
87C MET* 1.3 57.0 + - + +
89C ASN* 3.4 5.4 + - - +
90C LYS* 2.9 31.5 + - - +
93C ARG* 5.4 0.7 + - - -
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Residues in contact with MET 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.7 32.8 - - + -
76A ARG* 3.1 42.8 - - - +
79A GLN* 3.6 26.7 - - + +
50C PHE* 3.9 23.1 - - + -
83C THR* 2.9 24.8 + - + +
84C LYS* 3.2 8.0 + - - +
86C ALA* 1.3 78.1 - - + +
88C VAL* 1.3 62.2 + - - +
90C LYS* 3.4 8.1 + - - +
91C TYR* 3.0 23.9 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.2 6.5 - - + -
46C VAL* 3.9 23.0 - - + +
50C PHE* 4.0 21.5 - - + -
51C PHE* 3.8 30.3 - - + -
84C LYS* 2.9 20.1 + - - +
85C VAL 3.9 3.1 - - - +
87C MET* 1.3 74.4 - - - +
89C ASN* 1.3 59.8 + - - +
91C TYR* 3.1 8.5 + - - +
92C ALA* 2.9 26.4 + - + +
99C LEU* 4.7 7.9 - - + +
101C CYS* 3.6 26.2 - - + -
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.0 29.4 + - - +
86C ALA* 4.0 5.1 - - - +
88C VAL* 1.3 76.6 - - - +
90C LYS* 1.3 55.9 + - - +
92C ALA* 3.3 5.8 + - - +
93C ARG* 2.9 41.8 + - - +
99C LEU 3.5 11.5 - - - +
100C LEU* 3.9 10.2 - - - +
101C CYS* 3.0 43.9 + - - +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 2.9 19.1 + - - +
87C MET* 3.8 7.6 - - - +
89C ASN* 1.3 75.4 - - - +
91C TYR* 1.3 58.1 + - - +
93C ARG* 3.3 31.0 + - - +
94C GLU* 2.9 55.5 + - + +
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.4 31.7 - + - -
45C ASP* 2.6 32.4 + - - -
46C VAL* 3.9 11.9 - - + -
49C LYS* 3.6 26.3 - - + +
50C PHE* 3.6 32.1 - + + -
87C MET 3.0 17.4 + - - +
88C VAL 3.5 3.6 - - - +
90C LYS* 1.3 78.8 - - - +
92C ALA* 1.3 59.7 + - - +
94C GLU* 3.5 14.0 + - - +
95C ASN* 2.9 49.0 + - - -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.8 15.0 - - + -
88C VAL* 2.9 13.6 + - + +
89C ASN 3.7 6.7 - - - +
91C TYR* 1.3 76.9 - - - +
93C ARG* 1.3 63.7 + - - +
95C ASN* 3.2 2.9 + - - +
96C GLU 3.0 4.9 + - - -
97C HIS 2.8 39.3 + - - +
99C LEU* 3.6 35.9 - - + +
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA 5.4 0.6 + - - -
89C ASN* 2.9 38.1 + - - +
90C LYS* 3.3 39.3 + - - +
92C ALA* 1.3 77.7 - - - +
94C GLU* 1.3 57.0 + - - +
96C GLU* 2.8 25.5 + - - +
97C HIS 4.4 4.0 - - - -
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS* 2.9 51.8 + - + +
91C TYR* 3.6 21.5 - - - +
93C ARG* 1.3 76.6 - - - +
95C ASN* 1.3 64.4 + - - +
96C GLU* 3.5 6.2 + - - +
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Residues in contact with ASN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.7 23.0 - - + -
91C TYR* 2.9 54.7 + - - +
92C ALA 4.0 0.9 - - - +
93C ARG 3.1 0.6 - - - -
94C GLU* 1.3 81.5 - - - +
96C GLU* 1.3 69.3 + - - +
97C HIS* 3.4 22.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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