Contacts of the helix formed by residues 85 - 98 (chain E) in PDB entry 6B0B
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 CYS 85 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A CYS* 6.1 0.9 - - - -
87A SER* 4.8 6.1 - - - +
54E HIS* 3.7 9.9 - - + +
83E SER 3.7 1.6 + - - -
84E PRO* 1.3 77.7 - - - +
86E SER* 1.3 67.9 + - - +
87E SER* 3.6 21.8 - - - -
88E CYS* 3.8 0.7 - - - -
89E ALA* 3.2 19.8 + - - +
112E TYR* 4.6 12.0 - - + +
119E GLN* 3.2 33.0 - - - +
122E GLY* 4.9 1.7 - - - +
200E ZN 2.3 37.8 - - - -
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 2.4 30.7 + - - -
87A SER* 4.2 6.1 + - - -
118A PRO* 4.6 8.3 - - - -
85E CYS* 1.3 77.5 - - - +
87E SER* 1.3 68.0 + - - -
89E ALA* 3.2 4.0 + - - +
90E TRP* 3.0 27.6 + - - -
118E PRO* 3.7 33.3 - - - +
119E GLN* 3.7 10.8 - - - +
122E GLY* 4.4 10.8 - - - -
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 6.1 0.2 - - - -
85A CYS* 4.7 7.3 - - - +
86A SER* 4.4 2.6 + - - -
114A HIS* 3.3 23.5 + - - -
116A CYS* 4.3 1.4 - - - -
118A PRO* 4.3 10.8 - - - -
119A GLN* 3.2 38.3 + - - -
54E HIS* 5.3 1.2 - - - -
85E CYS* 3.6 11.6 - - - -
86E SER* 1.3 83.2 + - - +
88E CYS* 1.3 60.3 + - - +
90E TRP* 3.1 5.5 + - - +
91E GLU 2.9 22.2 + - - -
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Residues in contact with CYS 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 4.1 8.5 - - - -
54E HIS* 3.0 22.7 - - - -
56E GLU* 4.1 22.8 - - + +
57E ILE* 3.9 21.7 - - + +
60E ILE* 5.2 0.3 - - - +
84E PRO* 5.5 0.2 - - + -
85E CYS* 3.8 3.7 - - - +
86E SER 3.4 0.4 - - - -
87E SER* 1.3 73.7 - - - +
89E ALA* 1.3 61.1 + - - +
91E GLU* 3.6 8.7 - - - +
92E LEU* 2.8 31.2 + - - +
200E ZN 2.3 35.4 - - - -
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Residues in contact with ALA 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E PRO* 4.8 13.1 - - + +
85E CYS 3.2 21.5 + - - +
86E SER 3.2 3.7 + - - +
87E SER 3.2 0.6 - - - -
88E CYS* 1.3 78.2 - - - +
90E TRP* 1.3 57.2 + - - +
92E LEU* 3.2 11.3 + - - +
93E VAL* 2.9 28.1 + - - +
122E GLY 3.2 26.5 - - - +
123E LEU* 5.1 1.1 - - + -
126E LEU* 3.9 17.2 - - + +
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Residues in contact with TRP 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A CYS* 3.7 23.3 - - + -
117A LYS* 3.5 44.0 - - + -
118A PRO* 3.3 34.9 - - + +
86E SER* 3.0 26.0 + - - +
87E SER 3.1 8.1 + - - +
89E ALA* 1.3 75.8 - - - +
91E GLU* 1.3 60.7 + - - +
93E VAL* 3.1 14.2 - - + +
94E ASP* 2.9 38.3 + - - +
118E PRO 5.6 0.2 + - - -
121E ASP* 5.0 13.3 + - - -
122E GLY* 4.0 20.4 + - - -
125E LEU* 3.6 39.3 - - + -
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Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 3.8 45.6 - - + +
116A CYS* 4.9 1.4 - - - +
0C U 6.1 0.4 - - - -
1C U 4.4 26.4 + - - +
57E ILE* 4.8 16.9 - - + +
60E ILE* 4.0 17.6 - - + +
87E SER 2.9 9.9 + - - +
88E CYS* 3.6 11.7 - - - +
89E ALA 3.4 0.2 - - - -
90E TRP* 1.3 75.4 - - - +
92E LEU* 1.3 58.1 + - - +
94E ASP* 3.4 10.9 + - - +
95E PHE* 2.9 30.7 + - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLU* 4.1 26.5 - - + -
59E PHE* 3.8 23.1 - - + -
60E ILE* 3.6 24.4 - - + +
84E PRO* 5.7 4.5 - - + -
88E CYS 2.8 14.1 + - - +
89E ALA* 3.3 8.1 - - - +
90E TRP 3.2 0.2 - - - -
91E GLU* 1.3 76.6 - - - +
93E VAL* 1.3 57.7 + - - +
95E PHE* 3.2 3.4 + - + +
96E ILE* 2.9 36.1 + - + +
104E LEU* 3.9 26.7 - - + -
106E ILE* 4.5 10.1 - - + -
126E LEU* 4.4 21.3 - - + -
131E VAL* 5.8 0.9 - - + -
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Residues in contact with VAL 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ALA 2.9 15.3 + - - +
90E TRP* 3.1 33.4 - - + +
92E LEU* 1.3 76.2 - - - +
94E ASP* 1.3 65.9 + - - +
96E ILE* 3.3 6.1 + - + -
97E LYS* 2.9 37.3 + - + +
125E LEU* 4.4 14.1 - - + -
126E LEU* 4.3 16.8 - - + +
129E SER* 4.2 18.8 - - - +
130E GLN* 4.6 15.7 - - + +
131E VAL* 6.5 1.3 - - + -
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Residues in contact with ASP 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS 5.6 0.7 - - - +
115A TRP 5.6 0.5 - - - +
116A CYS* 4.5 16.1 - - - +
90E TRP* 2.9 26.2 + - - +
91E GLU* 3.8 12.7 - - - +
93E VAL* 1.3 87.4 - - - +
95E PHE* 1.3 59.3 + - - +
97E LYS* 3.5 15.6 + - - +
98E ALA* 3.5 20.1 + - - +
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Residues in contact with PHE 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PHE* 5.9 4.3 - + - -
60E ILE* 3.9 46.0 - - + -
63E ILE* 4.0 30.1 - - + -
64E LYS* 4.4 26.5 - - + -
68E LEU* 4.9 1.3 - - + -
91E GLU* 2.9 18.9 + - - +
92E LEU* 3.7 4.5 - - + +
94E ASP* 1.3 76.1 - - - +
96E ILE* 1.3 74.0 + - + +
97E LYS 3.4 0.2 - - - -
98E ALA* 3.6 3.2 + - + +
99E HIS* 3.1 58.1 + + + +
102E LEU* 5.6 4.5 - - + -
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E VAL* 5.9 0.9 - - + -
92E LEU* 2.9 23.9 + - + +
93E VAL* 3.7 8.3 - - - +
94E ASP 3.2 0.2 - - - -
95E PHE* 1.3 89.1 - - + +
97E LYS* 1.3 63.2 + - - +
98E ALA 3.2 0.7 - - - -
99E HIS* 2.9 24.2 + - + +
100E ASP* 4.7 0.9 - - - -
102E LEU* 4.1 35.9 - - + +
103E ASN* 6.2 0.2 - - - -
104E LEU* 4.6 30.5 - - + +
130E GLN* 3.9 32.8 - - + -
131E VAL* 4.9 9.4 - - + -
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Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E VAL* 2.9 31.1 + - + +
94E ASP* 3.5 17.6 + - - +
95E PHE 3.4 0.2 - - - -
96E ILE* 1.3 77.4 - - - +
98E ALA* 1.3 60.5 + - - +
99E HIS 3.6 2.3 + - - -
100E ASP* 4.7 3.6 + - - +
130E GLN* 4.8 17.7 - - - +
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ASP 3.5 13.6 + - - +
95E PHE* 3.6 3.8 + - + +
96E ILE 3.2 0.8 - - - -
97E LYS* 1.3 77.2 - - - +
99E HIS* 1.3 79.2 + - + +
100E ASP 3.9 2.0 + - - -
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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