Contacts of the helix formed by residues 120 - 135 (chain E) in PDB entry 2PWZ
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 PRO 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E PHE* 3.9 36.6 - - + -
94E ASN* 5.6 1.6 - - + -
95E ALA 6.2 0.2 - - - +
119E ASN* 1.3 84.5 - - + +
121E VAL* 1.3 56.9 + - - +
122E ASN* 3.4 4.0 - - + +
123E THR* 3.0 14.5 + - - +
124E THR* 2.8 38.8 + - + -
178E SER* 5.6 8.5 - - - +
302E ASP* 6.4 0.7 - - - -
305E LEU* 6.1 0.9 - - + -
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Residues in contact with VAL 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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116E ILE* 3.6 22.0 - - + +
117E ILE 3.6 13.9 - - - +
118E THR 3.6 4.9 - - - +
119E ASN* 3.0 25.6 - - - +
120E PRO* 1.3 67.5 - - - +
122E ASN* 1.3 68.1 + - - +
123E THR 3.0 0.9 + - - -
124E THR* 3.4 6.5 - - - +
125E VAL* 3.2 25.3 + - + +
145E GLY* 3.8 27.6 - - - -
146E VAL 4.3 3.1 - - - +
147E THR* 4.7 0.4 - - + -
177E HIS* 3.8 29.1 - - + +
253E TYR* 3.7 10.8 - - + -
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Residues in contact with ASN 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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120E PRO* 3.4 3.2 + - + -
121E VAL* 1.3 74.4 - - - +
123E THR* 1.3 57.8 + - - +
126E ALA* 4.4 4.9 + - - +
176E GLY* 3.4 3.6 - - - -
177E HIS* 2.7 28.0 + - - +
178E SER* 3.5 14.2 + - - +
181E THR* 3.0 24.9 + - - -
253E TYR* 2.8 35.0 + - - +
263E PHE* 5.2 0.2 - - - +
299E LEU* 3.5 13.2 - - + +
302E ASP* 2.9 37.8 + - + +
303E ILE* 4.0 12.1 + - - +
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Residues in contact with THR 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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91E PHE* 3.5 33.9 - - + -
120E PRO* 3.0 16.8 + - - +
122E ASN* 1.3 76.7 - - - +
124E THR* 1.3 65.1 + - - +
125E VAL 3.3 1.8 - - - -
126E ALA* 3.2 7.6 + - - +
127E ILE* 3.1 22.6 + - + +
302E ASP* 3.0 28.8 + - - +
305E LEU* 4.1 9.9 - - + +
306E GLY* 3.4 25.7 - - - +
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Residues in contact with THR 124 (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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91E PHE* 5.4 0.7 - - + -
94E ASN 5.0 3.4 - - - +
95E ALA* 5.0 3.8 - - - +
98E VAL* 3.7 26.4 - - + +
116E ILE* 3.3 16.8 - - - +
118E THR* 2.7 29.3 + - + +
119E ASN 4.2 3.1 - - - +
120E PRO* 2.8 36.0 + - + +
121E VAL* 3.4 5.4 - - - -
123E THR* 1.3 74.3 - - - +
125E VAL* 1.3 57.7 + - - +
127E ILE* 3.2 19.2 + - + +
128E ALA* 2.9 26.5 + - - +
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Residues in contact with VAL 125 (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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116E ILE* 3.8 20.4 - - + -
121E VAL* 3.2 18.1 + - + +
124E THR* 1.3 74.7 - - - +
126E ALA* 1.3 60.5 + - - +
128E ALA* 3.4 6.6 + - - +
129E ALA* 2.9 29.6 + - - +
143E LEU* 3.5 11.4 - - + +
145E GLY* 3.5 32.1 - - - +
253E TYR* 3.6 32.3 - - + +
263E PHE* 3.6 19.5 - - + -
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Residues in contact with ALA 126 (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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122E ASN 4.4 3.0 + - - +
123E THR 3.2 12.3 + - - +
125E VAL* 1.3 79.4 - - - +
127E ILE* 1.3 61.4 + - - +
129E ALA* 3.4 1.0 + - - +
130E GLU* 3.2 30.8 + - - +
262E ARG* 4.7 0.2 + - - -
263E PHE* 3.9 26.9 - - + -
303E ILE* 3.6 34.1 - - + +
306E GLY* 4.1 4.7 - - - -
307E GLU* 4.2 5.2 - - + +
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Residues in contact with ILE 127 (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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91E PHE* 4.5 0.2 - - + -
95E ALA* 3.7 34.8 - - + +
98E VAL* 4.1 5.4 - - + -
99E LYS* 4.0 31.4 - - + +
123E THR* 3.1 27.2 + - + +
124E THR* 3.3 18.4 - - + +
125E VAL 3.2 0.4 - - - -
126E ALA* 1.3 73.2 - - - +
128E ALA* 1.3 66.8 + - - +
129E ALA 3.2 0.3 + - - -
130E GLU 3.2 1.9 + - - -
131E VAL* 3.1 26.3 + - + +
306E GLY* 3.5 20.2 - - - +
309E PHE* 4.2 9.2 - - + -
310E VAL* 3.7 20.8 - - + +
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Residues in contact with ALA 128 (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 VAL* 4.4 0.2 - - - +
102E VAL* 3.6 32.0 - - + +
114E ILE* 5.6 0.2 - - + -
116E ILE* 4.1 6.7 - - + -
124E THR 2.9 13.1 + - - +
125E VAL* 3.4 9.0 - - - +
127E ILE* 1.3 75.8 - - - +
129E ALA* 1.3 57.4 + - - +
131E VAL* 3.2 3.1 + - - +
132E LEU* 3.0 34.7 + - + +
143E LEU* 3.7 24.9 - - + -
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Residues in contact with ALA 129 (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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125E VAL 2.9 17.9 + - - +
126E ALA 3.8 2.5 - - - +
127E ILE 3.2 0.2 - - - -
128E ALA* 1.3 76.6 - - - +
130E GLU* 1.3 57.2 + - - +
132E LEU* 3.4 2.1 + - - +
133E LYS* 3.0 34.6 + - - +
138E TYR* 3.7 20.8 - - + +
143E LEU* 3.7 15.2 - - + +
262E ARG* 4.4 5.2 - - - +
263E PHE* 3.5 25.4 - - + -
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Residues in contact with GLU 130 (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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126E ALA 3.2 17.6 + - - +
127E ILE 3.8 3.1 - - - +
129E ALA* 1.3 73.4 - - - +
131E VAL* 1.3 60.3 + - - +
133E LYS* 2.6 33.1 + - - +
134E LYS* 3.1 32.6 + - - +
262E ARG* 2.6 29.5 + - - +
307E GLU* 4.1 22.6 - - + +
310E VAL* 3.8 21.1 - - + -
311E ASN* 2.7 27.5 + - - +
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Residues in contact with VAL 131 (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 LYS* 3.8 36.6 - - + -
102E VAL* 3.6 21.1 - - + +
103E GLN* 3.5 34.8 - - + +
106E ALA* 5.0 2.0 - - + -
127E ILE 3.1 14.2 + - - +
128E ALA* 3.4 7.6 - - - +
130E GLU* 1.3 77.9 - - - +
132E LEU* 1.3 61.2 + - - +
134E LYS* 3.4 7.5 - - - +
135E ALA* 3.2 22.3 + - + +
310E VAL* 4.1 15.0 - - + -
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Residues in contact with LEU 132 (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 VAL* 3.7 16.6 - - + +
105E VAL* 5.1 0.9 - - + -
106E ALA* 4.1 13.9 - - + +
110E PRO 5.4 3.6 - - - +
114E ILE* 3.9 33.2 - - + -
128E ALA 3.0 28.5 + - - +
129E ALA 3.8 0.2 - - - +
130E GLU 3.3 0.2 - - - -
131E VAL* 1.3 77.9 - - - +
133E LYS* 1.3 61.6 + - - +
135E ALA* 3.2 7.0 + - - +
136E GLY 3.1 16.3 + - - -
137E VAL* 3.2 31.3 + - + +
138E TYR* 3.7 33.7 - - + -
139E ASP 5.8 0.4 - - - +
143E LEU* 4.2 15.3 - - + -
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Residues in contact with LYS 133 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E ALA 3.0 26.8 + - - +
130E GLU* 2.6 39.1 + - - +
132E LEU* 1.3 71.8 - - - +
134E LYS* 1.3 66.7 + - - +
135E ALA 3.1 1.3 - - - -
136E GLY* 3.0 14.9 + - - +
138E TYR* 3.5 29.5 - - + +
262E ARG* 3.6 18.3 - - - +
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Residues in contact with LYS 134 (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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130E GLU 3.1 21.9 + - - +
131E VAL* 3.4 8.3 - - - +
133E LYS* 1.3 76.6 - - - +
135E ALA* 1.3 59.8 + - - +
136E GLY 3.5 0.3 + - - -
310E VAL* 4.7 14.1 - - + -
311E ASN* 4.6 17.9 - - - +
312E LYS* 5.6 6.5 - - - +
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Residues in contact with ALA 135 (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 ALA* 3.9 25.6 - - + +
131E VAL* 3.2 14.4 + - + +
132E LEU 3.5 6.3 - - - +
133E LYS 3.1 0.6 - - - -
134E LYS* 1.3 77.7 - - - +
136E GLY* 1.3 60.9 + - - +
137E VAL* 3.4 12.4 + - + +
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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