Contacts of the helix formed by residues 80 - 93 (chain E) in PDB entry 3HB8
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 PHE 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C GLU* 6.2 1.8 - - + -
78E ARG* 4.2 1.4 + - - -
79E VAL* 1.3 70.8 - - - +
81E TRP* 1.3 56.3 + - - +
82E LYS* 3.2 28.5 - - + -
83E GLY* 2.7 45.4 + - - -
84E VAL* 2.9 15.8 + - - +
105E GLY 5.0 3.4 - - - -
106E VAL* 4.3 26.0 - - + -
107E LYS 5.4 0.9 - - - -
108E ILE* 4.6 15.5 - - + -
225E PHE* 3.8 12.6 - + + -
614E EDO 6.5 0.4 - - - -
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Residues in contact with TRP 81 (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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150C GLU 5.9 3.6 - - - -
71E PHE* 3.8 27.6 - + - -
73E LEU* 4.4 21.5 - - + -
79E VAL* 2.8 14.7 + - - +
80E PHE* 1.3 70.5 - - - +
82E LYS* 1.3 67.2 + - - +
84E VAL* 3.0 27.7 + - + +
85E LEU* 2.9 52.3 + - + +
228E ALA* 4.6 0.9 - - + -
232E LEU* 3.8 32.1 - - + -
279E LEU* 4.4 7.4 - - + -
296E PHE* 4.8 4.7 - - + +
297E GLN* 5.8 0.8 - - - +
298E ILE* 3.3 42.5 - - + +
301E TYR* 5.9 2.2 - - + -
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Residues in contact with LYS 82 (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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150C GLU* 3.5 42.4 + - + +
80E PHE* 3.2 19.6 + - + -
81E TRP* 1.3 83.4 - - - +
83E GLY* 1.3 56.8 + - - +
85E LEU* 4.9 3.8 - - - -
86E GLU* 3.1 47.8 + - + +
104E LYS 2.8 29.5 + - - -
105E GLY* 4.2 15.9 - - - -
106E VAL* 3.4 3.3 - - + +
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Residues in contact with GLY 83 (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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80E PHE* 2.7 29.6 + - - -
82E LYS* 1.3 77.6 - - - +
84E VAL* 1.3 63.5 + - - +
86E GLU* 4.2 0.2 - - - +
87E GLU* 3.0 28.6 + - - +
106E VAL* 3.5 21.4 - - - +
225E PHE* 3.7 8.2 - - - -
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Residues in contact with VAL 84 (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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79E VAL* 4.4 4.5 - - + -
80E PHE 2.9 10.0 + - - +
81E TRP* 3.4 32.1 - - + +
83E GLY* 1.3 79.6 - - - +
85E LEU* 1.3 65.3 + - - +
87E GLU* 3.6 2.3 - - - +
88E LEU* 3.0 21.1 + - - +
225E PHE* 3.4 43.0 - - + +
228E ALA* 4.0 9.4 - - + -
229E SER* 3.5 33.4 + - - +
232E LEU* 4.2 7.2 - - + -
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Residues in contact with LEU 85 (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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81E TRP* 2.9 44.4 + - + +
82E LYS* 4.4 4.3 - - - +
84E VAL* 1.3 74.9 - - - +
86E GLU* 1.3 62.6 + - + +
88E LEU* 3.7 1.0 + - - +
89E LEU* 3.3 37.8 + - + +
232E LEU* 3.9 21.8 - - + -
236E MET* 4.8 1.8 - - + -
293E ALA* 3.6 33.0 - - + +
296E PHE* 3.7 34.1 - - + +
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Residues in contact with GLU 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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82E LYS* 3.1 35.5 + - + +
85E LEU* 1.3 75.1 - - + +
87E GLU* 1.3 61.0 + - - +
89E LEU* 3.6 11.3 + - - +
90E TRP* 3.1 24.8 + - - +
101E LEU* 3.5 9.0 - - + +
104E LYS* 3.4 38.8 + - + +
106E VAL* 3.5 20.2 - - + -
293E ALA* 3.8 23.6 - - + +
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Residues in contact with GLU 87 (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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83E GLY 3.0 19.0 + - - +
84E VAL 3.6 2.1 - - - +
86E GLU* 1.3 75.6 - - - +
88E LEU* 1.3 59.4 + - - +
90E TRP* 2.9 24.7 + - + +
91E PHE* 2.9 46.4 + - + -
101E LEU* 3.9 11.8 - - + +
108E ILE* 3.6 17.0 - - + +
109E TRP* 3.3 26.1 + - - +
196E HIS* 5.9 0.9 + - - -
225E PHE* 3.6 24.2 - - + -
229E SER* 4.0 9.9 + - - -
614E EDO 4.8 2.6 + - - -
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Residues in contact with LEU 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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84E VAL* 3.0 16.3 + - + +
85E LEU 4.1 3.8 - - - +
87E GLU* 1.3 77.2 + - - +
89E LEU* 1.3 58.2 + - - +
91E PHE* 3.1 11.6 + - + +
92E ILE* 2.9 34.5 + - + +
139E TRP* 3.8 30.1 - - + -
229E SER* 3.9 17.7 - - - +
230E TYR* 6.4 0.9 - - + -
232E LEU* 3.5 26.2 - - + -
233E LEU* 3.7 25.6 - - + +
236E MET* 3.3 33.0 - - + -
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Residues in contact with LEU 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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85E LEU* 3.3 31.0 + - + +
86E GLU* 3.7 15.9 - - - +
87E GLU 3.1 0.4 - - - -
88E LEU* 1.3 75.1 - - - +
90E TRP* 1.3 65.7 + - - +
92E ILE* 3.5 10.1 + - + +
93E LYS* 3.2 32.8 + - + +
236E MET* 4.2 10.3 - - + -
288E ILE 5.8 0.2 - - - +
291E PHE* 3.3 39.9 - - + +
292E LYS* 4.6 1.6 - - - -
293E ALA* 3.6 36.3 - - + +
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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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86E GLU 3.1 14.8 + - - +
87E GLU* 2.9 17.0 + - + +
89E LEU* 1.3 79.1 - - - +
91E PHE* 1.3 83.5 + + - +
93E LYS* 3.5 13.6 + - - +
95E SER* 2.7 62.9 + - - +
96E THR* 4.8 0.4 - - - -
97E ASN 3.2 39.6 + - - -
98E ALA* 3.9 2.9 - - - -
100E GLU* 4.4 6.7 - - + -
101E LEU* 3.8 37.8 - - + +
109E TRP* 3.6 33.7 - + + -
131E LEU* 3.2 26.2 - - + -
134E VAL* 5.1 3.4 - - + -
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Residues in contact with PHE 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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87E GLU* 2.9 50.6 + - - -
88E LEU* 3.1 14.6 + - + +
90E TRP* 1.3 100.6 - + - +
92E ILE* 1.3 57.6 + - - +
93E LYS 2.9 1.8 - - - -
94E GLY* 2.6 28.9 + - - -
95E SER 5.3 1.1 - - - -
109E TRP* 4.6 2.2 - + - -
135E TYR* 3.4 49.4 - + + -
136E GLY* 3.7 13.9 - - - +
139E TRP* 3.5 39.5 - + + -
140E ARG* 4.4 3.6 - - - +
196E HIS* 5.8 4.9 - + - -
229E SER* 5.1 4.3 - - - -
230E TYR* 5.9 2.7 - + - -
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Residues in contact with ILE 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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88E LEU* 2.9 31.4 + - + +
89E LEU* 3.8 12.8 - - + +
91E PHE* 1.3 75.9 - - - +
93E LYS* 1.3 57.5 + - + +
139E TRP* 3.8 17.7 - - + -
140E ARG* 3.1 26.9 + - - +
161E LEU* 3.8 15.9 - - + -
233E LEU* 4.3 9.2 - - + -
236E MET* 4.9 7.4 - - + -
288E ILE* 3.6 60.8 - - + +
289E ASP* 3.7 12.6 - - - +
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Residues in contact with LYS 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 LEU* 3.2 22.1 + - + +
90E TRP* 3.5 13.6 - - - +
91E PHE 2.9 1.0 - - - -
92E ILE* 1.3 75.8 - - + +
94E GLY* 1.3 63.4 + - - +
95E SER* 3.2 10.1 + - - +
100E GLU* 3.4 38.3 + - - +
104E LYS* 4.6 8.3 - - - +
140E ARG* 4.8 1.3 - - - -
141E HIS* 5.9 0.2 + - - -
289E ASP* 5.1 3.8 - - - +
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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