Contacts of the helix formed by residues 82 - 99 (chain A) in PDB entry 1MUG
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A VAL 5.6 0.9 - - - +
81A SER* 1.3 73.7 - - - +
83A GLN* 1.3 68.2 + - + +
85A LEU* 3.4 8.9 + - + +
86A HIS* 3.1 21.1 + - - +
110A GLN* 3.2 24.4 + - - +
114A GLN* 3.5 39.7 + - + +
119A ARG* 4.9 11.5 - - - +
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Residues in contact with GLN 83 (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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81A SER* 3.5 14.1 - - - +
82A LYS* 1.3 88.1 + - - +
84A GLU* 1.3 64.7 + - + +
86A HIS* 3.5 6.8 + - - +
87A ALA* 3.3 21.0 + - - +
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Residues in contact with GLU 84 (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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70A VAL* 3.7 24.7 - - + +
72A ARG* 3.2 42.4 + - - +
80A VAL* 3.5 14.0 - - + +
81A SER* 2.9 43.6 + - - +
83A GLN* 1.3 76.2 - - + +
85A LEU* 1.3 64.8 + - - +
86A HIS 3.3 0.2 + - - -
87A ALA* 3.3 6.5 + - - +
88A GLY* 3.1 17.3 + - - -
91A LYS* 5.1 1.7 + - - -
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Residues in contact with LEU 85 (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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17A ILE* 4.0 26.5 - - + -
69A LEU* 3.8 23.4 - - + +
70A VAL* 4.0 6.7 - - + -
80A VAL* 4.0 14.6 - - + +
81A SER 3.0 15.5 + - - +
82A LYS* 3.5 9.9 - - + +
84A GLU* 1.3 75.8 - - - +
86A HIS* 1.3 61.4 + - - +
88A GLY* 3.2 3.6 + - - -
89A GLY 3.2 16.5 + - - -
110A GLN* 4.2 16.2 - - + +
111A ALA* 4.3 7.0 - - - -
114A GLN* 3.4 41.3 - - + +
115A GLY* 3.4 12.8 - - - +
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Residues in contact with HIS 86 (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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82A LYS 3.1 15.7 + - - +
83A GLN* 3.8 8.1 - - - +
84A GLU 3.2 0.4 - - - -
85A LEU* 1.3 75.7 - - - +
87A ALA* 1.3 65.3 + - - +
89A GLY* 3.2 13.0 + - - -
90A ARG* 3.3 42.3 + - + +
114A GLN* 3.3 20.8 + - + +
115A GLY* 4.3 5.8 + - - +
117A SER* 2.7 30.1 + - - -
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Residues in contact with ALA 87 (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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83A GLN 3.3 13.6 + - - +
84A GLU* 3.3 5.6 + - - +
86A HIS* 1.3 78.7 + - - +
88A GLY* 1.3 62.1 + - - +
89A GLY 3.4 0.2 + - - -
90A ARG* 3.6 26.1 + - - +
91A LYS* 3.2 27.4 + - - +
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Residues in contact with GLY 88 (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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69A LEU* 3.3 31.8 - - - +
84A GLU 3.1 9.6 + - - -
85A LEU 3.6 4.3 - - - -
86A HIS 3.1 1.0 - - - -
87A ALA* 1.3 77.5 - - - +
89A GLY* 1.3 63.5 - - - +
91A LYS* 3.4 16.6 + - - +
92A LEU* 3.0 23.2 + - - +
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Residues in contact with GLY 89 (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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69A LEU* 3.8 10.7 - - - +
85A LEU 3.2 6.3 + - - -
86A HIS 3.2 7.3 + - - -
88A GLY* 1.3 77.2 - - - +
90A ARG* 1.3 56.0 + - - +
92A LEU* 3.3 4.5 + - - +
93A ILE* 3.0 38.1 + - - +
115A GLY 3.4 24.9 - - - -
116A PHE* 4.9 2.5 - - - -
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Residues in contact with ARG 90 (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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86A HIS* 3.3 47.3 + - + +
87A ALA* 3.6 19.6 + - - +
88A GLY 3.3 0.6 - - - -
89A GLY* 1.3 72.7 - - - +
91A LYS* 1.3 67.8 + - + +
93A ILE* 3.3 10.3 + - + +
94A GLU* 3.1 32.6 + - - +
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Residues in contact with LYS 91 (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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69A LEU 4.1 8.2 + - - +
70A VAL* 5.2 4.9 - - - +
71A ASP* 5.3 10.7 + - - +
84A GLU 5.1 1.8 + - - -
87A ALA* 3.2 28.7 - - - +
88A GLY* 3.4 21.1 + - - +
90A ARG* 1.3 76.8 - - + +
92A LEU* 1.3 64.4 + - - +
94A GLU* 3.2 16.2 + - - +
95A LYS* 3.0 36.5 + - - +
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Residues in contact with LEU 92 (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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15A CYS* 3.9 15.7 - - + -
67A THR* 3.9 29.6 - - + +
68A LYS 5.3 4.0 - - - +
69A LEU* 3.8 21.8 - - + -
88A GLY 3.0 17.4 + - - +
89A GLY 3.6 4.3 - - - +
90A ARG 3.2 0.2 - - - -
91A LYS* 1.3 76.3 - - - +
93A ILE* 1.3 64.1 + - - +
95A LYS* 3.0 12.3 + - + +
96A ILE* 3.0 39.1 + - + +
104A LEU* 4.0 18.8 - - + -
106A ILE* 4.8 2.7 - - + -
116A PHE* 3.7 27.6 - - + -
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Residues in contact with ILE 93 (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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89A GLY 3.0 23.5 + - - +
90A ARG* 3.7 9.6 - - + +
92A LEU* 1.3 76.2 - - - +
94A GLU* 1.3 63.6 + - + +
96A ILE* 3.3 1.2 + - - +
97A GLU* 2.9 53.3 + - + +
115A GLY 5.7 1.1 - - - +
116A PHE* 3.7 33.4 - - + -
130A ILE* 4.2 18.8 - - + -
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Residues in contact with GLU 94 (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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90A ARG* 3.1 23.3 + - - +
91A LYS* 3.5 14.4 - - - +
93A ILE* 1.3 77.7 - - + +
95A LYS* 1.3 56.6 + - + +
97A GLU* 3.4 13.5 + - - +
98A ASP* 3.0 27.7 + - - +
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Residues in contact with LYS 95 (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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4A ASP* 2.8 30.6 + - - +
6A LEU* 4.4 10.1 - - + -
67A THR* 3.4 21.6 + - + +
68A LYS* 4.8 6.7 + - - +
71A ASP* 5.5 4.6 + - - -
91A LYS* 3.0 27.5 + - - +
92A LEU* 3.0 14.6 + - + +
94A GLU* 1.3 76.4 - - + +
96A ILE* 1.3 62.1 + - + +
98A ASP* 3.0 7.4 + - - +
99A TYR* 2.9 44.6 + - + +
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Residues in contact with ILE 96 (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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6A LEU* 5.9 1.3 - - + -
13A VAL* 4.2 15.0 - - + -
67A THR* 5.6 0.7 - - + -
92A LEU* 3.0 23.3 + - + +
93A ILE 3.9 2.9 - - - +
95A LYS* 1.3 77.7 - - + +
97A GLU* 1.3 56.6 + - - +
99A TYR* 5.2 0.9 - - + -
100A GLN* 2.8 31.2 + - - +
101A PRO* 3.9 21.8 - - + -
104A LEU* 3.9 37.0 - - + -
130A ILE* 3.8 20.6 - - + +
133A THR* 3.5 37.6 + - + +
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Residues in contact with GLU 97 (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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93A ILE* 2.9 40.9 + - - +
94A GLU* 3.6 12.6 - - - +
96A ILE* 1.3 75.5 - - - +
98A ASP* 1.3 57.0 + - - +
100A GLN* 3.1 26.4 + - - +
130A ILE* 3.5 20.4 - - + +
131A GLY* 5.7 0.9 - - - +
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Residues in contact with ASP 98 (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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94A GLU 3.0 13.4 + - - +
95A LYS* 3.0 10.7 + - - +
97A GLU* 1.3 80.6 - - - +
99A TYR* 1.3 86.0 + - + +
100A GLN* 3.5 11.5 + - - +
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Residues in contact with TYR 99 (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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6A LEU* 3.7 49.1 + - + +
7A ALA* 3.6 37.7 - - - +
8A PRO* 4.1 23.1 - - + +
9A GLY 4.4 2.9 + - - -
10A LEU* 5.7 0.4 - - + -
13A VAL* 5.6 2.5 - - + -
95A LYS* 2.9 30.9 + - + +
96A ILE* 5.2 0.7 - - + -
98A ASP* 1.3 90.3 + - + +
100A GLN* 1.3 71.1 + - - +
101A PRO* 3.5 9.2 - - + +
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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