Contacts of the helix formed by residues 135 - 147 (chain E) in PDB entry 3PRJ
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 ARG 135 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E LEU* 3.8 8.7 - - + +
133E PRO 4.0 0.4 + - - -
134E VAL* 1.3 78.1 - - + +
136E ALA* 1.3 61.4 + - - +
137E ALA 3.5 2.2 - - - -
138E GLU* 3.2 54.9 + - - +
139E SER* 3.3 23.2 + - - -
142E ARG* 5.9 1.6 - - - +
214E TRP* 4.8 18.2 - - + -
217E GLU* 3.5 13.8 + - - -
287E LEU* 4.7 20.0 - - - -
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Residues in contact with ALA 136 (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 THR* 6.1 0.9 - - + -
106E LEU* 4.7 6.7 - - + -
109E ILE* 4.5 11.2 - - + -
128E GLU* 3.6 35.0 - - + +
133E PRO* 4.7 0.9 - - + -
134E VAL 3.7 15.0 - - - +
135E ARG* 1.3 75.4 - - - +
137E ALA* 1.3 68.9 + - - +
139E SER* 3.2 8.2 + - - -
140E ILE* 3.2 26.4 + - - +
217E GLU* 3.3 6.5 + - - +
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Residues in contact with ALA 137 (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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128E GLU* 4.9 3.6 - - + +
135E ARG 3.5 0.4 - - - -
136E ALA* 1.3 75.6 - - - +
138E GLU* 1.3 63.4 + - - +
140E ILE* 3.2 10.7 + - - +
141E ARG* 3.0 28.9 + - - +
156E VAL* 4.1 11.8 - - + +
157E LEU 5.3 0.9 - - - +
158E SER* 4.6 8.1 - - - -
213E THR* 3.9 30.3 - - + +
217E GLU* 3.1 23.9 + - - +
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Residues in contact with GLU 138 (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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135E ARG* 3.2 54.4 + - - +
136E ALA 3.2 0.6 - - - -
137E ALA* 1.3 79.1 - - - +
139E SER* 1.3 57.5 + - - +
141E ARG* 3.5 25.6 + - - +
142E ARG* 2.9 55.7 + - - +
214E TRP* 5.8 2.3 - - - -
217E GLU* 4.9 0.6 + - - +
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Residues in contact with SER 139 (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* 3.8 22.3 - - - +
109E ILE* 4.1 12.6 - - - +
110E GLU* 4.6 16.2 - - - +
135E ARG 3.3 12.6 + - - -
136E ALA 3.2 10.0 + - - -
137E ALA 3.2 0.4 - - - -
138E GLU* 1.3 76.7 - - - +
140E ILE* 1.3 70.0 + - - +
142E ARG* 3.6 5.8 + - - +
143E ILE* 3.5 24.5 + - - +
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Residues in contact with ILE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 3.8 23.8 - - + -
109E ILE* 3.7 18.2 - - + -
110E GLU* 6.4 0.2 - - - +
113E ALA* 4.2 13.0 - - + -
126E VAL* 4.4 7.0 - - + -
128E GLU* 3.8 28.0 - - + +
136E ALA 3.2 16.6 + - - +
137E ALA* 3.6 7.2 - - - +
139E SER* 1.3 80.8 + - - +
141E ARG* 1.3 63.6 + - - +
143E ILE* 3.0 14.7 + - - +
144E PHE* 3.1 47.3 + - + -
156E VAL* 4.2 14.4 - - + -
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Residues in contact with ARG 141 (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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137E ALA* 3.0 21.6 + - - +
138E GLU* 3.6 27.5 + - - +
140E ILE* 1.3 76.9 - - - +
142E ARG* 1.3 56.8 + - - +
144E PHE* 3.3 4.0 + - + +
145E ASP* 2.9 52.1 + - - +
156E VAL* 3.9 27.9 - - + +
183E ASP* 4.1 25.8 + - - -
213E THR* 2.9 36.0 + - - +
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Residues in contact with ARG 142 (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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135E ARG* 5.9 1.6 - - - +
138E GLU* 2.9 51.5 + - - +
139E SER* 3.6 6.5 + - - +
140E ILE 3.2 0.4 - - - -
141E ARG* 1.3 76.3 - - - +
143E ILE* 1.3 62.9 + - + +
145E ASP* 4.0 8.6 - - + +
146E ALA* 3.4 23.4 + - + +
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Residues in contact with ILE 143 (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 GLU* 3.6 51.1 - - + +
113E ALA* 3.9 20.2 - - + +
114E ARG* 4.0 40.2 - - + +
117E VAL* 4.8 2.9 - - + -
139E SER 3.5 9.6 + - - +
140E ILE 3.0 9.2 + - - +
142E ARG* 1.3 76.7 - - + +
144E PHE* 1.3 66.9 + - + +
146E ALA* 3.4 1.7 + - - -
147E ASN* 2.9 43.9 + - - +
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Residues in contact with PHE 144 (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* 3.3 34.1 - - + -
116E ILE* 4.0 13.0 - - + -
117E VAL* 3.6 22.0 - - + -
126E VAL* 3.5 37.7 - - + -
140E ILE* 3.1 27.8 + - + +
141E ARG* 3.7 7.9 - - + +
143E ILE* 1.3 77.3 - - + +
145E ASP* 1.3 65.5 + - - +
146E ALA 3.2 1.0 + - - -
147E ASN 3.3 18.9 + - - +
148E THR* 4.0 4.9 + - - -
152E LEU* 5.9 0.7 - - - +
154E LEU* 3.6 31.6 - - + +
156E VAL* 3.9 18.4 - - + -
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Residues in contact with ASP 145 (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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141E ARG* 2.9 41.5 + - - +
142E ARG* 4.0 10.4 - - + +
143E ILE 3.3 0.2 - - - -
144E PHE* 1.3 78.7 - - - +
146E ALA* 1.3 58.0 + - - +
148E THR* 4.1 14.8 - - - +
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Residues in contact with ALA 146 (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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142E ARG* 3.4 16.7 + - + +
143E ILE* 3.4 3.7 + - - +
144E PHE 3.2 0.6 - - - -
145E ASP* 1.3 81.2 - - + +
147E ASN* 1.3 67.2 + - - +
148E THR* 3.4 8.4 + - - +
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Residues in contact with ASN 147 (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 ARG* 4.2 16.7 + - - +
117E VAL* 3.6 37.5 - - + +
143E ILE* 2.9 40.4 + - - +
144E PHE 3.3 6.7 + - - +
146E ALA* 1.3 80.3 - - - +
148E THR* 1.3 60.4 + - - +
149E LYS* 3.8 2.6 + - - +
152E LEU* 4.1 7.1 - - - +
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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