Contacts of the helix formed by residues 99 - 113 (chain E) in PDB entry 5WC9
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 SER 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B GLU 5.3 1.1 - - - -
127B GLU 3.7 3.6 - - - -
128B LEU* 3.6 29.4 + - - -
129B ASN* 3.6 17.7 - - - +
97E THR 3.9 2.2 + - - -
98E ILE* 1.3 79.3 - - - +
100E ILE* 1.3 64.1 + - - +
101E ALA* 3.8 3.3 + - - +
102E ALA* 3.0 27.1 + - - +
103E LYS* 3.1 20.3 + - - +
130E LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 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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126B GLU 4.6 10.5 + - - +
127B GLU* 3.4 20.2 + - + +
98E ILE 3.7 1.3 + - - +
99E SER* 1.3 73.5 - - - +
101E ALA* 1.3 62.5 + - - +
103E LYS* 3.3 29.0 + - + +
104E ASP* 3.1 33.4 + - - +
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Residues in contact with ALA 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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101B ALA* 6.1 4.5 - - + +
105B ALA* 5.8 4.3 - - + -
127B GLU* 3.1 18.7 + - + +
128B LEU* 4.0 19.5 - - + -
99E SER* 3.1 3.6 - - - +
100E ILE* 1.3 78.7 - - - +
102E ALA* 1.3 56.9 + - - +
104E ASP* 3.4 8.6 + - - +
105E ALA* 2.9 27.4 + - - +
128E LEU* 5.6 0.2 - - - -
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 3.6 15.0 - - + -
99E SER* 3.0 24.4 + - - +
101E ALA* 1.3 76.2 - - - +
103E LYS* 1.3 54.8 + - - +
105E ALA* 3.1 6.8 + - - +
106E LEU* 2.7 41.8 + - + +
128E LEU* 4.2 25.6 - - + +
130E LEU* 4.6 9.0 - - + -
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Residues in contact with LYS 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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97E THR* 6.3 0.4 - - - -
98E ILE* 3.7 24.7 - - + -
99E SER 3.1 11.2 + - - +
100E ILE* 3.3 27.5 + - + +
102E ALA* 1.3 76.1 - - - +
104E ASP* 1.3 59.5 + - - +
106E LEU* 4.0 6.1 - - - +
107E GLU* 2.9 34.1 + - - +
138E TRP* 4.5 10.5 - - + +
182G T 3.9 27.9 + - - -
183G C 3.5 26.4 + - - +
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Residues in contact with ASP 104 (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 ILE* 3.1 24.5 + - - +
101E ALA* 3.7 10.6 - - - +
103E LYS* 1.3 77.3 - - - +
105E ALA* 1.3 57.2 + - - +
107E GLU* 4.2 4.2 - - - +
108E ARG* 3.1 27.4 + - - +
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Residues in contact with ALA 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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101B ALA* 5.7 2.7 - - + -
101E ALA 2.9 16.7 + - - +
102E ALA 3.1 4.5 + - - +
104E ASP* 1.3 75.4 - - - +
106E LEU* 1.3 60.2 + - - +
108E ARG* 3.0 19.3 + - - +
109E HIS* 2.8 35.5 + - + +
127E GLU* 5.0 5.6 - - - +
128E LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 106 (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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98E ILE* 4.5 15.9 - - + -
102E ALA 2.7 27.0 + - - +
103E LYS* 4.0 0.7 - - - +
105E ALA* 1.3 72.0 - - - +
107E GLU* 1.3 59.4 + - - +
109E HIS* 3.1 7.6 + - - +
110E PHE* 2.8 28.4 + - - +
124E MET* 4.7 6.1 - - - -
128E LEU* 3.6 26.0 - - + -
130E LEU* 4.8 5.4 - - + -
135E VAL* 3.9 15.0 - - + -
138E TRP* 3.6 46.3 - - + +
139E PHE* 3.8 28.3 - - + -
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Residues in contact with GLU 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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103E LYS 2.9 19.2 + - - +
104E ASP* 4.2 4.5 - - - +
106E LEU* 1.3 76.7 - - - +
108E ARG* 1.3 62.3 + - - +
110E PHE* 3.3 4.9 + - - +
111E GLY* 3.3 17.0 + - - -
138E TRP* 3.6 10.6 - - + -
142E ARG* 2.2 55.5 + - - +
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Residues in contact with ARG 108 (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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104E ASP 3.1 19.8 + - - +
105E ALA* 3.0 15.0 + - - +
107E GLU* 1.3 76.2 - - - +
109E HIS* 1.3 91.4 + - - +
111E GLY* 3.4 10.6 + - - -
112E GLU* 3.7 32.5 + - - +
127E GLU* 4.7 7.1 + - - -
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Residues in contact with HIS 109 (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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105E ALA* 2.8 17.7 + - + +
106E LEU* 3.6 10.1 - - - +
108E ARG* 1.3 102.8 + - - +
110E PHE* 1.3 59.4 + - - +
112E GLU* 3.1 23.1 + - - +
113E GLN* 3.0 28.9 + - - +
124E MET* 3.3 52.6 - - + +
127E GLU* 3.6 28.1 + - - -
128E LEU* 5.9 1.9 - - + +
139E PHE* 4.4 4.4 - - + -
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Residues in contact with PHE 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 LEU 2.8 20.0 + - - +
107E GLU* 3.6 12.8 - - - +
108E ARG 3.2 0.4 - - - -
109E HIS* 1.3 72.3 - - - +
111E GLY* 1.3 62.1 + - - +
112E GLU 3.3 0.5 + - - -
113E GLN 3.4 8.0 + - - -
114E ASN* 2.8 71.0 + - + +
138E TRP* 4.4 2.9 - - + -
139E PHE* 3.7 23.5 - + + -
142E ARG* 3.5 59.7 - - + -
143E ARG* 3.9 20.0 - - + -
146E GLU* 4.7 10.1 - - + -
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Residues in contact with GLY 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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107E GLU* 3.3 10.3 + - - -
108E ARG* 3.4 5.5 + - - -
109E HIS 3.2 0.6 - - - -
110E PHE* 1.3 81.5 - - - +
112E GLU* 1.3 60.7 + - - +
114E ASN* 4.8 3.0 - - - +
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Residues in contact with GLU 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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108E ARG* 3.7 34.4 + - - +
109E HIS* 3.1 24.1 + - - +
111E GLY* 1.3 81.4 - - - +
113E GLN* 1.3 60.9 + - + +
114E ASN* 5.2 0.7 - - - -
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Residues in contact with GLN 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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109E HIS 3.0 14.6 + - - +
110E PHE* 3.4 8.6 + - - +
112E GLU* 1.3 82.8 - - + +
114E ASN* 1.3 67.4 + - - +
115E LYS 3.3 4.0 - - - +
116E PRO* 4.1 20.4 - - + +
124E MET* 5.9 4.9 - - + +
139E PHE* 4.0 9.4 - - - -
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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