Contacts of the helix formed by residues 92 - 102 (chain E) in PDB entry 2FRV
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 MET 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E HIS 4.7 0.4 - - - +
14E ASN* 2.9 46.8 - - - +
15E ALA 3.8 2.7 - - - -
76E ILE* 4.3 1.6 - - + -
77E PRO* 4.1 17.5 - - + -
82E GLY 4.6 0.2 + - - -
85E GLY* 3.0 44.0 + - - +
86E LYS* 3.7 6.7 - - - +
87E VAL* 4.4 11.4 - - + -
90E ARG 3.4 0.4 + - - -
91E ASN* 1.3 67.9 - - - +
93E TYR* 1.3 67.6 + - - +
95E ILE* 3.3 9.8 + - + +
96E CYS* 3.1 26.7 + - - -
20F HIS* 3.6 43.5 - - + +
41F LEU* 4.0 6.7 - - + -
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Residues in contact with TYR 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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76E ILE* 3.5 25.0 - - + +
77E PRO 4.2 11.9 + - - +
78E MET* 3.7 26.7 - - + -
81E GLY 5.8 1.6 - - - +
82E GLY* 5.7 1.8 - - - -
91E ASN* 3.2 6.9 - - + +
92E MET* 1.3 78.2 - - - +
94E ASP* 1.3 72.1 + - - +
96E CYS* 3.5 1.6 + - - +
97E ALA* 2.9 38.6 + - + +
134E ALA 3.7 9.9 - - - -
135E LEU* 3.3 27.4 - - + -
137E LYS* 2.8 34.3 + - - -
138E LEU* 3.9 10.0 - - - +
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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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90E ARG* 3.8 19.4 + - + +
91E ASN* 2.8 36.5 + - - +
93E TYR* 1.3 87.6 - - - +
95E ILE* 1.3 64.7 + - - +
97E ALA* 3.3 5.9 + - - +
98E GLU* 3.1 23.2 + - - +
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Residues in contact with ILE 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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12E LEU* 4.3 18.8 - - + -
57E GLU* 5.7 3.6 - - - +
60E LEU* 4.3 11.9 - - + -
87E VAL* 3.6 36.8 - - + +
90E ARG* 3.4 57.0 - - + +
91E ASN 3.1 10.5 + - - +
92E MET* 3.9 7.9 - - + +
94E ASP* 1.3 77.4 - - - +
96E CYS* 1.3 56.3 + - - +
98E GLU* 3.2 2.0 + - - +
99E VAL* 2.9 41.7 + - + +
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Residues in contact with CYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.0 21.8 - - - -
14E ASN* 3.4 31.4 - - - -
72E ILE* 4.4 7.9 - - + -
76E ILE* 3.9 17.0 - - + -
92E MET 3.1 20.0 + - - +
93E TYR 3.8 3.4 - - - +
95E ILE* 1.3 72.4 - - - +
97E ALA* 1.3 62.7 + - - +
99E VAL 4.4 0.2 - - - +
100E ALA* 2.9 36.3 + - - +
135E LEU* 3.7 18.8 - - + +
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Residues in contact with ALA 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 TYR* 2.9 36.6 + - + +
94E ASP* 3.3 6.5 + - - +
96E CYS* 1.3 76.7 - - - +
98E GLU* 1.3 56.5 + - - +
101E PRO* 2.9 25.3 - - - +
135E LEU* 4.4 1.8 - - - +
138E LEU* 3.4 28.8 - - + +
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Residues in contact with GLU 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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60E LEU* 6.5 0.2 - - - -
61E HIS* 4.8 10.6 + - - -
64E ILE* 3.7 25.4 - - + +
90E ARG* 2.7 38.1 + - - +
94E ASP 3.1 10.7 + - - +
95E ILE* 3.5 8.3 - - - +
96E CYS 3.1 0.4 - - - -
97E ALA* 1.3 78.7 - - - +
99E VAL* 1.3 65.9 + - + +
101E PRO* 3.8 1.7 - - - +
102E LYS* 3.1 38.0 + - - +
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Residues in contact with VAL 99 (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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10E VAL* 4.2 6.7 - - + -
12E LEU* 4.1 13.2 - - + -
60E LEU* 4.4 11.4 - - + -
64E ILE* 3.9 31.0 - - + -
68E PHE* 3.7 16.2 - - + -
70E CYS* 4.0 20.2 - - - -
95E ILE* 2.9 35.5 + - + +
98E GLU* 1.3 77.6 - - + +
100E ALA* 1.3 68.6 + - - +
102E LYS* 3.0 22.4 + - - +
103E ALA 3.6 4.2 + - - -
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Residues in contact with ALA 100 (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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12E LEU* 5.9 0.2 - - + -
70E CYS* 4.3 8.5 - - - -
72E ILE* 4.1 17.5 - - + -
96E CYS 2.9 20.8 + - - +
99E VAL* 1.3 76.3 - - - +
101E PRO* 1.3 66.2 - - + +
103E ALA* 3.2 20.8 + - - +
106E VAL* 3.6 14.2 - - + +
135E LEU* 4.0 12.1 - - + -
140E VAL* 3.9 18.7 - - + +
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Residues in contact with PRO 101 (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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96E CYS 3.4 1.3 - - - +
97E ALA 2.9 28.7 - - - +
98E GLU 3.8 2.7 - - - +
99E VAL 3.4 3.6 - - - -
100E ALA* 1.3 94.5 - - + +
102E LYS* 1.3 59.9 + - + +
103E ALA 3.5 4.3 + - - +
138E LEU* 4.0 35.9 - - + +
139E GLY 6.3 0.2 - - - -
140E VAL* 4.2 9.9 - - + -
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Residues in contact with LYS 102 (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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64E ILE* 3.9 42.8 - - + +
66E GLY 4.4 5.2 - - - +
68E PHE* 3.6 16.3 - - + -
98E GLU* 3.1 33.1 + - - +
99E VAL 3.0 7.8 + - - +
101E PRO* 1.3 78.2 - - + +
103E ALA* 1.3 60.6 + - - +
104E LYS* 4.1 7.4 + - - -
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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
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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