Contacts of the helix formed by residues 102 - 116 (chain E) in PDB entry 4Z07
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 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E LYS* 1.3 76.7 - - - +
103E PRO* 1.3 74.7 - - - +
104E GLN* 3.6 13.0 + - - +
105E SER* 3.1 27.5 + - - -
106E LYS* 3.1 19.6 + - - +
203E LYS* 5.8 0.2 + - - -
205E TRP* 5.5 0.2 - - - -
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Residues in contact with PRO 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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101E LYS 4.3 2.0 - - - +
102E SER* 1.3 83.8 - - - +
104E GLN* 1.3 65.6 + - - +
106E LYS* 3.3 14.0 + - + +
107E ASP* 3.1 35.7 + - - +
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Residues in contact with GLN 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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102E SER* 3.2 11.3 + - - +
103E PRO* 1.3 79.9 - - - +
105E SER* 1.3 62.3 + - - +
107E ASP* 3.4 6.4 + - - +
108E LEU* 3.0 24.1 + - + +
159E GLU* 3.1 20.8 - - - +
160E ASP* 5.5 1.7 - - - +
203E LYS* 5.7 0.2 + - - -
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LYS* 4.2 7.6 - - - -
102E SER* 3.1 21.1 + - - -
104E GLN* 1.3 74.7 - - - +
106E LYS* 1.3 61.1 + - - +
108E LEU* 3.1 2.5 + - - +
109E ILE* 2.8 37.2 + - - +
159E GLU* 2.6 35.0 + - - -
203E LYS* 4.2 4.2 + - - -
205E TRP* 3.4 26.4 - - - -
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Residues in contact with LYS 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 PHE* 4.6 13.3 - - - -
100E PRO* 5.9 0.2 - - - +
101E LYS* 3.4 41.1 + - + +
102E SER 3.1 9.7 + - - +
103E PRO* 3.6 14.3 - - + +
105E SER* 1.3 76.4 - - - +
107E ASP* 1.3 63.2 + - - +
109E ILE* 3.3 3.0 + - - +
110E LYS* 3.0 28.8 + - - +
128E GLN* 5.3 5.6 - - - +
131E VAL* 3.7 30.5 - - + +
132E ASP* 4.5 14.7 + - - +
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Residues in contact with ASP 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PRO* 3.1 22.6 + - - +
104E GLN* 3.8 5.6 + - - +
106E LYS* 1.3 76.8 - - - +
108E LEU* 1.3 63.0 + - - +
110E LYS* 3.4 11.4 + - - +
111E GLU* 2.9 38.6 + - + +
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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
----------------------------------------------------------
104E GLN* 3.0 19.3 + - + +
105E SER* 3.1 6.0 + - - +
107E ASP* 1.3 74.9 - - - +
109E ILE* 1.3 63.4 + - + +
111E GLU* 3.3 5.3 + - - +
112E ALA* 2.8 28.6 + - - +
157E VAL* 3.9 12.6 - - + -
158E MET 3.8 7.4 - - - +
159E GLU* 3.6 49.6 - - + +
177E PRO* 4.8 3.4 - - + -
178E GLY* 4.0 24.1 - - - +
205E TRP* 4.7 0.4 - - + -
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Residues in contact with ILE 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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101E LYS* 3.8 26.9 - - + -
105E SER 2.8 20.3 + - - +
106E LYS 3.6 4.0 - - - +
108E LEU* 1.3 75.7 - - + +
110E LYS* 1.3 64.7 + - - +
112E ALA* 3.1 3.6 + - - +
113E ILE* 3.0 34.7 + - + +
131E VAL* 3.6 21.5 - - + +
134E MET* 3.6 28.0 - - + -
157E VAL* 4.2 15.2 - - + +
205E TRP* 3.6 41.1 - - + +
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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 LYS 3.0 16.6 + - - +
107E ASP* 3.6 12.8 - - - +
109E ILE* 1.3 77.6 - - - +
111E GLU* 1.3 74.5 + - - +
113E ILE* 3.4 3.1 + - - +
114E LEU* 3.1 36.6 + - + +
124E LEU* 3.8 31.3 - - - +
127E ILE* 3.9 27.8 - - + +
128E GLN* 6.1 0.7 - - - +
131E VAL* 4.0 4.0 - - + +
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Residues in contact with GLU 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 ASP* 2.9 25.6 + - + +
108E LEU* 3.9 4.5 - - - +
110E LYS* 1.3 95.7 - - - +
112E ALA* 1.3 66.1 + - - +
114E LEU* 3.3 19.9 + - - +
115E ASP* 3.1 23.9 + - - +
178E GLY 4.9 0.2 - - - -
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Residues in contact with ALA 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 LEU 2.8 18.4 + - - +
109E ILE 3.1 4.2 + - - +
111E GLU* 1.3 75.2 - - - +
113E ILE* 1.3 62.4 + - - +
115E ASP* 3.1 14.7 + - - +
116E ASN* 3.2 10.2 + - - +
157E VAL* 3.7 19.5 - - + -
178E GLY* 3.2 35.8 - - - +
179E LYS 3.9 6.3 - - - +
180E VAL* 3.8 12.7 + - + +
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Residues in contact with ILE 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 ILE* 3.0 28.0 + - + +
110E LYS 3.6 6.7 - - - +
111E GLU 3.2 0.2 - - - -
112E ALA* 1.3 76.4 - - - +
114E LEU* 1.3 61.8 + - - +
115E ASP 3.1 1.2 + - - -
116E ASN* 3.1 14.9 + - - +
119E MET* 3.6 35.7 - - + +
120E LYS* 3.5 11.1 + - - -
122E LEU* 4.5 2.0 - - + -
127E ILE* 3.7 36.8 - - + -
130E ILE* 3.8 35.0 - - + -
157E VAL* 4.8 3.6 - - + -
180E VAL* 4.1 17.5 - - + -
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Residues in contact with LEU 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* 3.1 35.3 + - + +
111E GLU* 3.3 29.6 + - - +
113E ILE* 1.3 74.8 - - - +
115E ASP* 1.3 57.7 + - - +
120E LYS* 3.2 43.2 - - + +
122E LEU 5.6 0.9 - - - +
124E LEU* 5.0 7.4 - - + -
127E ILE* 3.8 18.8 - - + -
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Residues in contact with ASP 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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111E GLU 3.1 16.4 + - - +
112E ALA* 3.4 7.0 - - - +
113E ILE 3.0 1.0 - - - -
114E LEU* 1.3 77.3 - - - +
116E ASN* 1.3 64.9 + - - +
117E ASP* 3.6 9.7 + - - +
120E LYS* 5.2 1.9 - - - +
178E GLY 3.9 3.3 - - - +
179E LYS* 3.2 37.5 - - - +
180E VAL 5.6 0.2 + - - -
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Residues in contact with ASN 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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112E ALA 3.2 10.2 + - - +
113E ILE 3.1 9.6 + - - +
115E ASP* 1.3 78.6 - - - +
117E ASP* 1.3 64.8 + - - +
118E PHE* 2.7 31.8 + - - +
119E MET* 3.0 26.1 + - + +
120E LYS* 3.1 27.0 + - - +
180E VAL* 3.7 22.1 + - + +
183E GLU* 2.8 31.4 + - - +
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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