Contacts of the helix formed by residues 100 - 116 (chain E) in PDB entry 5LSJ
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 ASN 100 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 6.0 0.2 - - - -
143B GLN* 3.0 28.1 - - - +
96E LYS 4.0 2.6 + - - -
97E GLU 4.4 2.8 + - - -
98E GLU 3.8 1.8 - - - -
99E GLY* 1.3 78.3 - - - +
101E LEU* 1.3 56.9 + - - +
102E GLU* 3.0 27.7 + - - +
103E ALA* 3.0 18.6 + - + +
104E VAL* 3.0 30.1 + - + +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PHE* 4.9 2.2 - - + -
15C PHE* 4.4 27.8 - - + -
91C LEU* 5.3 3.8 - - + -
95E ILE* 3.9 15.0 - - + +
96E LYS* 3.2 21.5 + - + +
98E GLU* 3.2 27.4 - - - +
99E GLY 4.1 6.3 - - - +
100E ASN* 1.3 73.3 - - - +
102E GLU* 1.3 62.1 + - - +
104E VAL* 3.6 19.7 - - + -
105E LEU* 2.9 55.9 + - + +
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Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E VAL* 5.2 15.5 - - + -
96E LYS* 2.8 33.8 + - - +
97E GLU* 4.6 12.4 - - - +
100E ASN* 3.0 18.0 + - - +
101E LEU* 1.3 75.7 + - - +
103E ALA* 1.3 59.9 + - + +
105E LEU* 4.3 2.4 - - - +
106E ASN* 2.9 43.5 + - - +
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Residues in contact with ALA 103 (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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100E ASN* 3.0 29.3 + - + +
102E GLU* 1.3 83.1 - - + +
104E VAL* 1.3 61.3 + - + +
106E ASN* 3.9 5.3 - - - +
107E ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.6 16.5 - - + +
13C PHE* 4.7 13.2 - - + -
15C PHE* 5.9 0.7 - - + -
99E GLY 4.4 6.7 - - - +
100E ASN* 3.0 14.3 + - + +
101E LEU* 3.4 38.6 - - + +
103E ALA* 1.3 78.5 - - + +
105E LEU* 1.3 66.1 + - + +
107E ALA* 3.5 5.0 + - - +
108E LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 105 (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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13C PHE* 3.7 30.7 - - + -
90C ILE* 3.9 29.4 - - + -
91C LEU* 4.5 3.4 - - + -
34E ARG* 4.3 13.1 - - + +
35E VAL* 5.1 16.8 - - + -
38E LEU* 4.9 19.1 - - + -
96E LYS* 6.0 1.6 - - + -
101E LEU* 2.9 38.5 + - + +
102E GLU* 4.3 2.2 - - - +
104E VAL* 1.3 74.1 - - - +
106E ASN* 1.3 62.6 + - - +
108E LEU* 3.4 10.9 + - + +
109E ASP* 2.8 33.0 + - - +
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Residues in contact with ASN 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E SER* 3.9 12.3 - - - +
35E VAL* 4.2 13.6 - - - +
102E GLU* 2.9 29.3 + - - +
103E ALA* 3.9 5.1 - - - +
105E LEU* 1.3 74.8 - - - +
107E ALA* 1.3 59.3 + - - +
109E ASP* 3.1 16.2 + - - +
110E LYS* 2.9 26.9 + - - +
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Residues in contact with ALA 107 (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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12C PHE* 5.0 6.1 - - + -
103E ALA 2.9 20.9 + - - +
104E VAL* 3.7 7.9 - - - +
106E ASN* 1.3 75.1 - - - +
108E LEU* 1.3 57.6 + - - +
110E LYS* 3.2 12.7 + - + +
111E ILE* 2.9 38.7 + - + +
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.6 21.9 - - + -
13C PHE* 3.8 29.8 - - + -
91C LEU 4.9 1.6 - - - +
92C ARG 4.4 10.5 - - - +
93C ILE* 4.3 15.7 - - + -
94C PRO* 5.4 2.0 - - + -
97C ILE* 5.5 0.4 - - + -
99C LEU* 5.4 1.6 - - + -
34E ARG* 3.6 31.0 - - - +
104E VAL 2.9 19.1 + - - +
105E LEU* 3.6 7.9 - - + +
106E ASN 3.2 0.2 - - - -
107E ALA* 1.3 73.4 - - - +
109E ASP* 1.3 61.3 + - - +
111E ILE* 3.3 12.9 + - + -
112E VAL* 2.9 46.0 + - + +
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Residues in contact with ASP 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E THR* 4.5 9.2 + - - +
33E SER* 2.7 39.6 - - - +
34E ARG* 3.2 30.7 + - - +
105E LEU 2.8 25.5 + - - +
106E ASN* 3.1 13.8 + - - +
108E LEU* 1.3 76.0 - - - +
110E LYS* 1.3 62.9 + - - +
112E VAL* 3.2 7.5 + - - +
113E GLU* 2.9 28.9 + - + +
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Residues in contact with LYS 110 (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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106E ASN 2.9 12.6 + - - +
107E ALA* 3.4 14.6 - - + +
109E ASP* 1.3 76.1 - - - +
111E ILE* 1.3 65.4 + - + +
113E GLU* 3.0 6.5 + - - +
114E GLU* 2.9 56.3 + - + +
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Residues in contact with ILE 111 (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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12C PHE* 4.2 24.9 - - + -
97C ILE* 3.7 24.5 - - + +
98C LEU 4.2 5.6 - - - +
99C LEU* 4.7 7.4 - - + -
100C PRO* 3.6 42.6 - - + -
107E ALA* 2.9 25.3 + - + +
108E LEU* 3.3 9.2 + - + +
110E LYS* 1.3 79.8 - - + +
112E VAL* 1.3 55.9 + - - +
114E GLU* 4.4 8.2 - - - +
115E GLY* 3.1 24.1 + - - -
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Residues in contact with VAL 112 (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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94C PRO* 4.0 24.5 - - + -
97C ILE* 3.6 19.5 - - + +
34E ARG* 3.6 24.7 - - - +
108E LEU* 2.9 34.5 + - + +
109E ASP* 3.6 4.5 - - - +
110E LYS 3.1 0.2 - - - -
111E ILE* 1.3 75.9 - - - +
113E GLU* 1.3 70.4 + - - +
115E GLY 3.6 0.2 + - - -
116E LYS* 3.2 35.4 + - + +
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Residues in contact with GLU 113 (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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31E THR* 5.0 19.6 + - - +
109E ASP* 2.9 19.0 + - + +
110E LYS* 3.6 6.1 - - - +
112E VAL* 1.3 82.2 - - + +
114E GLU* 1.3 64.8 + - + +
116E LYS* 3.3 27.9 + - - +
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Residues in contact with GLU 114 (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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110E LYS* 2.9 41.9 + - + +
111E ILE* 4.4 7.0 - - - +
113E GLU* 1.3 77.1 - - + +
115E GLY* 1.3 60.9 + - - +
116E LYS 3.5 7.1 + - - +
117E VAL* 5.2 2.8 - - - +
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Residues in contact with GLY 115 (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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96C ASN* 4.5 4.7 - - - +
97C ILE* 4.1 15.4 - - - +
98C LEU 5.7 2.5 - - - -
111E ILE 3.1 20.2 + - - -
112E VAL 4.0 1.1 - - - -
113E GLU 3.2 0.6 - - - -
114E GLU* 1.3 75.4 - - - +
116E LYS* 1.3 64.2 + - - +
117E VAL* 3.6 0.8 + - - +
118E ARG* 3.6 27.1 + - - +
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Residues in contact with LYS 116 (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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94C PRO* 5.6 3.4 - - - -
96C ASN* 3.2 28.3 - - - +
97C ILE* 4.0 10.1 - - + -
112E VAL* 3.2 25.8 + - - +
113E GLU* 3.6 21.9 + - - +
114E GLU 3.3 7.9 - - - +
115E GLY* 1.3 77.5 - - - +
117E VAL* 1.3 70.1 + - - +
118E ARG 4.2 0.4 - - - +
119E LYS* 3.4 20.3 - - - +
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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