Contacts of the helix formed by residues 110 - 123 (chain E) in PDB entry 1QZW
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 THR 110 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E GLY 2.7 3.1 + - - +
109E LYS* 1.3 81.7 - - + +
111E THR* 1.3 103.3 + - + +
112E THR* 2.3 13.9 + - - -
113E ALA* 2.9 10.7 + - - +
136E ARG* 5.0 12.6 - - - +
138E ALA 5.6 0.4 - - - +
139E ALA* 5.5 2.9 - - - -
142E GLN* 3.2 29.5 + - - +
143E LEU* 3.9 20.0 - - - +
146E LEU* 5.6 1.0 - - - +
185E ASP* 3.4 13.5 - - - -
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Residues in contact with THR 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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108E GLY* 2.4 33.0 + - - +
110E THR* 1.3 100.2 + - + +
112E THR* 1.3 80.3 + - - +
113E ALA* 2.4 2.9 + - - +
114E GLY* 2.6 14.7 + - - -
115E LYS* 6.3 0.2 - - - -
142E GLN* 3.7 24.5 - - - +
146E LEU* 5.5 7.2 - - - +
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Residues in contact with THR 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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101E LEU* 5.3 5.4 - - - +
108E GLY* 2.5 35.7 + - - +
109E LYS 2.9 7.8 + - - +
110E THR 2.3 26.0 + - - -
111E THR* 1.3 86.6 + - - +
113E ALA* 1.3 56.1 + - - +
114E GLY* 2.4 20.6 + - - -
115E LYS* 3.2 18.4 + - - +
116E LEU* 3.4 8.8 + - - -
217E VAL* 4.9 12.3 - - + -
245E THR* 4.1 17.9 - - + -
279E LEU* 5.6 0.8 - - - +
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Residues in contact with ALA 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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101E LEU* 6.1 3.3 - - + +
110E THR* 3.3 10.5 - - - +
111E THR 2.4 6.7 + - - +
112E THR* 1.3 80.5 + - - +
114E GLY* 1.3 70.5 + - - +
116E LEU* 2.7 20.2 - - - +
117E ALA* 2.5 22.9 + - - +
129E LEU* 4.8 9.0 - - + -
183E ILE* 4.1 15.3 - - + -
185E ASP* 5.2 10.1 - - + +
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Residues in contact with GLY 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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111E THR 2.6 12.4 + - - -
112E THR 2.4 6.2 + - - -
113E ALA* 1.3 81.8 - - - +
115E LYS* 1.3 54.4 + - - -
117E ALA* 3.1 4.0 - - - -
118E TYR* 2.4 34.5 + - - -
129E LEU* 5.2 3.1 - - - +
146E LEU* 4.7 17.3 - - - +
150E ILE* 6.1 2.5 - - - -
276E ILE* 3.8 6.7 - - - -
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Residues in contact with LYS 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 THR 6.3 0.2 - - - -
112E THR* 3.2 10.6 + - - +
114E GLY* 1.3 69.6 - - - -
116E LEU* 1.3 50.5 + - - +
118E TYR* 2.8 16.9 - - + -
119E PHE* 2.3 45.0 + - - +
271E GLY* 4.0 4.0 + - - -
273E GLY 2.3 33.2 + - - +
274E GLU 4.1 0.4 - - - -
275E LYS 2.8 20.9 - - - +
276E ILE* 3.0 27.3 - - + +
277E ASP* 4.2 0.9 - - - -
278E GLU* 2.8 25.0 - - - +
279E LEU* 3.0 40.4 - - + +
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Residues in contact with LEU 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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99E ILE* 4.6 11.7 - - + -
101E LEU* 5.4 8.1 - - + -
112E THR* 3.4 6.2 + - - +
113E ALA* 2.7 19.7 - - - +
114E GLY 2.5 4.2 + - - -
115E LYS* 1.3 76.3 - - - +
117E ALA* 1.3 76.6 - - - +
119E PHE* 2.9 16.0 - - + +
120E TYR* 3.1 31.5 + - + -
181E ILE* 6.4 0.2 - - + -
183E ILE* 3.2 36.3 - - + -
269E PHE* 5.0 12.1 - - + -
279E LEU* 3.7 17.6 - - + +
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Residues in contact with ALA 117 (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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113E ALA 2.5 6.3 + - - +
114E GLY* 2.5 9.5 + - - +
116E LEU* 1.3 82.1 - - - +
118E TYR* 1.3 71.1 + - - +
120E TYR* 2.5 19.5 + - - +
121E LYS 3.4 3.1 + - - -
127E VAL* 4.5 13.9 - - + -
129E LEU* 3.4 35.4 - - + -
150E ILE* 5.3 5.2 - - + -
183E ILE* 4.1 16.2 - - + -
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Residues in contact with TYR 118 (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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114E GLY* 2.4 17.4 + - - +
115E LYS* 2.8 15.7 - - + -
117E ALA* 1.3 77.3 - - - +
119E PHE* 1.3 84.4 + + + +
121E LYS* 3.2 14.9 + - - +
122E LYS* 3.5 44.0 + - + +
150E ILE* 4.3 24.4 - - + +
276E ILE* 2.8 46.9 - - + -
277E ASP* 2.9 37.8 - - + +
279E LEU* 6.1 0.2 - - + -
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Residues in contact with PHE 119 (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 VAL* 5.2 4.5 - - + -
115E LYS* 2.3 34.9 + - + +
116E LEU* 2.9 8.1 - - + +
117E ALA 2.5 1.6 + - - -
118E TYR* 1.3 84.2 - - + +
120E TYR* 1.3 105.4 + + - -
122E LYS* 3.2 13.0 + - - +
123E ARG* 2.7 64.0 - - - +
269E PHE* 4.7 12.6 - + - -
279E LEU* 4.7 11.7 - - + -
281E THR* 5.9 3.8 - - - -
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Residues in contact with TYR 120 (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 VAL* 2.4 48.1 + - - +
91E ASN* 4.4 9.0 - - - -
92E PRO* 5.3 4.7 - - + -
116E LEU* 3.1 29.6 + - + -
117E ALA* 2.5 14.3 + - - +
119E PHE* 1.3 112.0 - + - +
121E LYS* 1.3 58.5 + - - +
123E ARG* 2.6 49.0 + - + +
125E TYR* 3.3 20.8 + + + -
127E VAL* 4.8 8.3 - - + -
181E ILE* 5.4 20.9 - - + -
183E ILE* 6.3 0.2 - - + -
269E PHE* 4.1 5.4 - + - -
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Residues in contact with LYS 121 (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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148C ASN 5.6 0.6 + - - -
151C GLY* 5.5 0.6 - - - -
117E ALA 3.4 2.0 + - - -
118E TYR* 3.2 12.1 + - - +
120E TYR* 1.3 72.6 - - - +
122E LYS* 1.3 55.8 + - + +
123E ARG 2.7 5.6 + - - -
124E GLY* 2.5 27.7 + - - -
125E TYR 4.0 16.8 - - - +
127E VAL* 4.1 16.0 - - + +
150E ILE* 2.7 27.6 + - + +
151E GLY* 3.6 15.5 + - - -
152E VAL* 3.6 22.7 - - + -
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Residues in contact with LYS 122 (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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118E TYR* 3.5 37.7 + - + +
119E PHE* 3.2 9.7 + - - +
121E LYS* 1.3 77.1 - - + +
123E ARG* 1.3 69.4 + - - +
124E GLY 3.5 0.2 - - - -
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Residues in contact with ARG 123 (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 VAL* 5.2 1.0 - - - +
91E ASN* 3.6 30.9 + - - +
119E PHE* 2.7 60.8 - - - +
120E TYR* 2.6 35.3 - - - +
122E LYS* 1.3 83.1 - - - +
124E GLY* 1.3 60.1 + - - +
125E TYR* 2.9 32.5 + - + -
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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