Contacts of the helix formed by residues 136 - 149 (chain E) in PDB entry 2R6C
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 ILE 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B GLU* 3.5 48.2 - - + +
112B LYS* 6.1 2.0 - - - -
114B VAL* 4.5 12.1 - - + -
115B LEU* 4.1 27.5 - - + +
133E GLU* 3.5 25.3 - - - +
134E ASP 5.0 1.1 - - - -
135E GLU* 1.3 75.5 - - - +
137E ASP* 1.3 67.0 + - - +
138E VAL 3.6 0.9 - - - -
139E LEU* 3.4 17.6 - - - +
140E LEU* 2.7 53.5 + - + +
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Residues in contact with ASP 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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111B GLU* 5.1 3.9 - - - +
135E GLU 2.5 17.2 + - - +
136E ILE* 1.3 83.1 - - - +
138E VAL* 1.3 61.4 + - + +
139E LEU 3.2 0.2 - - - -
140E LEU* 3.9 8.9 - - - +
141E ASP* 2.9 39.2 + - - +
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ARG* 5.4 0.2 - - - +
135E GLU* 3.6 32.4 + - + +
137E ASP* 1.3 76.6 - - + +
139E LEU* 1.3 57.1 + - - +
141E ASP* 4.5 3.6 - - + -
142E GLU* 2.8 62.4 + - + +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.8 26.2 - - + -
118B LEU* 4.3 17.8 - - + +
125E ILE* 4.6 5.8 - - + +
128E ASP* 3.7 33.4 - - + +
129E GLY* 4.4 7.0 - - - +
132E ARG* 3.5 39.7 - - + +
133E GLU* 4.5 4.0 - - - +
135E GLU* 3.9 3.4 - - - +
136E ILE* 3.4 21.9 + - - +
137E ASP 3.2 0.2 - - - -
138E VAL* 1.3 80.0 - - - +
140E LEU* 1.3 57.8 + - - +
142E GLU* 4.1 9.3 + - + +
143E ALA* 3.0 25.0 + - + +
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 3.8 30.3 - - + -
115B LEU* 6.3 1.1 - - + -
118B LEU* 4.1 28.3 - - + -
147B ILE 5.6 6.1 - - - +
149B GLU 6.2 0.4 - - - +
136E ILE* 2.7 31.0 + - + +
137E ASP* 4.2 9.2 - - - +
138E VAL 3.3 0.2 - - - -
139E LEU* 1.3 72.0 - - - +
141E ASP* 1.3 66.7 + - - +
143E ALA* 3.6 4.9 - - + +
144E ASP* 3.6 28.6 + - - +
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Residues in contact with ASP 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ASP* 2.9 24.4 + - - +
138E VAL* 4.0 4.0 - - + +
140E LEU* 1.3 77.1 - - - +
142E GLU* 1.3 57.9 + - - +
143E ALA 2.9 9.8 + - - -
144E ASP* 3.0 12.3 + - - +
145E ARG* 2.9 22.6 + - - +
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Residues in contact with GLU 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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132E ARG* 3.2 39.7 + - - +
135E GLU* 3.9 0.9 - - - +
138E VAL* 2.8 49.8 + - + +
139E LEU* 4.1 7.2 - - + +
141E ASP* 1.3 70.8 - - - +
143E ALA* 1.3 56.5 + - - +
144E ASP 3.6 0.2 - - - -
145E ARG* 3.8 27.0 + - - +
146E LYS* 3.0 59.4 + - - +
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Residues in contact with ALA 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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118B LEU* 4.6 14.1 - - + -
147B ILE* 4.3 5.1 - - + +
125E ILE* 3.7 27.3 - - + +
139E LEU 3.0 20.3 + - - +
140E LEU* 3.6 10.8 - - + +
141E ASP 2.9 0.8 - - - -
142E GLU* 1.3 78.1 - - - +
144E ASP* 1.3 65.9 + - - +
146E LYS 3.9 1.8 - - - +
147E ILE* 3.3 29.5 + - - +
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Residues in contact with ASP 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.4 24.7 - - - +
148B MET* 3.5 26.2 - - + +
306B ARG* 6.3 0.2 - - - +
140E LEU* 3.6 18.8 + - - +
141E ASP* 3.0 11.7 + - - +
143E ALA* 1.3 77.1 - - - +
145E ARG* 1.3 65.8 + - - +
146E LYS 3.2 0.2 - - - -
147E ILE* 3.1 4.0 + - - +
148E MET* 2.9 38.8 + - + +
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Residues in contact with ARG 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 ASP 2.9 16.3 + - - +
142E GLU* 3.8 22.4 + - - +
144E ASP* 1.3 78.6 - - - +
146E LYS* 1.3 64.2 + - + +
148E MET* 3.6 7.2 + - - +
149E GLU* 3.2 40.9 + - - +
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Residues in contact with LYS 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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121E THR* 3.8 39.5 + - + +
124E SER* 4.4 20.5 + - - +
125E ILE* 4.8 11.3 - - + +
128E ASP* 4.4 13.3 + - - +
132E ARG* 5.1 0.4 - - - +
142E GLU* 3.0 60.3 + - + +
143E ALA* 4.4 3.8 - - - +
144E ASP 3.2 0.4 - - - -
145E ARG* 1.3 83.2 - - + +
147E ILE* 1.3 61.6 + - - +
149E GLU* 3.7 20.6 + - - +
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Residues in contact with ILE 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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125B ILE* 4.8 13.0 - - + -
140B LEU* 5.2 9.5 - - - +
143B ALA* 4.2 11.7 - - + +
144B ASP* 3.2 24.1 - - - +
147B ILE* 4.3 20.6 - - + -
118E LEU* 4.3 21.9 - - + +
121E THR* 4.0 16.4 - - - +
122E ALA* 5.1 9.0 - - + +
125E ILE* 4.1 16.2 - - + -
143E ALA 3.3 18.9 + - - +
144E ASP* 3.1 4.5 + - - +
146E LYS* 1.3 78.0 - - - +
148E MET* 1.3 68.4 + - + +
149E GLU 3.2 5.7 + - - +
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Residues in contact with MET 148 (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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144B ASP* 3.3 38.6 - - - +
148B MET* 5.8 7.6 - - - +
299B SER 5.7 2.2 - - - +
302B ARG* 5.2 4.5 - - - -
303B ALA* 5.3 13.1 - - + +
306B ARG* 3.4 53.4 - - - +
307B ARG* 4.1 12.5 + - - -
144E ASP* 2.9 33.2 + - + +
145E ARG* 4.1 5.2 - - - +
146E LYS 3.4 0.4 - - - -
147E ILE* 1.3 80.0 - - + +
149E GLU* 1.3 63.9 + - + +
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Residues in contact with GLU 149 (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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140B LEU* 5.5 6.2 - - - +
307B ARG* 3.7 19.2 + - - +
117E ARG* 4.4 17.8 + - - -
121E THR* 6.2 2.5 - - + -
145E ARG* 3.2 40.5 + - - +
146E LYS* 3.7 17.5 + - - +
147E ILE 3.2 5.6 - - - +
148E MET* 1.3 83.2 - - + +
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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