Contacts of the helix formed by residues 137 - 148 (chain E) in PDB entry 6B0B
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 GLY 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136E MET* 1.3 74.4 - - - +
138E PHE* 1.3 65.3 + - - -
139E PRO* 4.5 0.2 - - - -
140E GLU* 2.8 17.9 + - - +
141E PHE* 3.0 28.0 - - - +
166E LEU* 3.6 5.5 - - - +
170E SER* 3.9 17.7 - - - -
174E LYS* 5.3 4.0 - - - -
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Residues in contact with PHE 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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137E GLY* 1.3 72.0 - - - +
139E PRO* 1.4 70.5 - - + +
142E ALA* 2.9 30.9 + - + +
162E MET* 4.5 7.2 - - + -
163E LEU* 3.5 29.6 - - + -
166E LEU* 3.4 36.7 - - + +
167E ASP* 5.7 4.7 - - + -
170E SER* 5.0 1.6 - - - -
36H ARG* 3.0 41.7 - - - -
39H GLU* 3.1 25.8 - - - +
41H THR* 4.0 20.6 - - + -
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Residues in contact with PRO 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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137E GLY* 4.5 0.2 - - - -
138E PHE* 1.4 94.6 - - + +
140E GLU* 1.3 72.6 + - + +
142E ALA* 3.1 6.4 + - + +
143E ASP* 2.6 46.7 + - - +
39H GLU* 3.8 24.2 - - + +
74H LYS* 6.0 3.8 - - - +
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Residues in contact with GLU 140 (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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79E TYR* 3.6 22.8 - - + +
105E ARG* 5.7 0.9 - - - +
107E PHE* 3.5 30.6 - - + -
135E VAL 3.3 19.1 - - - +
136E MET* 3.5 29.7 - - + +
137E GLY* 2.8 24.4 + - - -
139E PRO* 1.3 89.3 - - + +
141E PHE* 1.3 61.6 + - - +
143E ASP* 4.3 5.8 - - - -
144E CYS 3.3 15.4 + - - -
174E LYS* 3.9 8.7 + - - -
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Residues in contact with PHE 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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9E PHE* 4.0 20.5 - + + -
13E PHE* 4.0 20.4 - + + -
14E ASN* 5.4 1.1 - - - -
109E SER* 3.1 35.0 - - - -
136E MET* 3.5 42.6 - - + -
137E GLY 3.0 26.4 + - - +
138E PHE 3.5 0.8 + - - -
139E PRO 3.2 0.2 - - - -
140E GLU* 1.3 76.3 - - - +
142E ALA* 1.3 59.3 + - - +
144E CYS* 3.2 4.3 + - - +
145E TRP* 2.9 29.2 + - - +
162E MET* 5.5 3.1 - - + -
166E LEU* 3.4 29.8 - - + -
169E ASN* 4.1 27.1 - - + -
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Residues in contact with ALA 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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138E PHE* 2.9 32.9 + - + +
139E PRO* 3.7 6.1 - - + +
141E PHE* 1.3 75.6 - - - +
143E ASP* 1.3 65.4 - - - +
145E TRP* 3.4 17.1 + - + +
146E GLU* 3.6 6.2 - - - +
162E MET* 5.5 4.9 - - + -
166E LEU* 4.5 2.6 - - + +
39H GLU* 5.5 4.0 - - + +
41H THR* 5.2 4.5 - - + -
216H ARG* 3.4 31.5 + - - +
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Residues in contact with ASP 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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79E TYR* 3.4 31.6 + - + +
105E ARG* 5.2 1.4 + - - -
139E PRO* 2.6 28.7 + - - +
140E GLU* 3.8 1.2 - - - +
142E ALA* 1.3 75.5 - - - +
144E CYS* 1.3 62.7 + - - +
145E TRP 3.2 0.5 + - - -
146E GLU* 3.4 4.6 - - - +
147E ASN* 2.7 43.2 + - - +
74H LYS* 4.4 15.9 + - - -
216H ARG* 5.8 1.2 + - - -
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Residues in contact with CYS 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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9E PHE* 4.5 3.8 - - + -
13E PHE* 3.7 31.2 - - + -
31E CYS* 3.8 9.9 - - - -
79E TYR* 3.5 30.2 - - + -
136E MET* 4.2 6.3 - - + -
140E GLU 3.3 7.2 + - - +
141E PHE 3.2 4.9 + - - +
143E ASP* 1.3 79.0 - - - +
145E TRP* 1.3 64.6 + - - +
147E ASN 4.1 0.7 - - - -
148E PHE* 3.3 41.3 + - - +
149E VAL* 3.6 8.1 + - - +
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Residues in contact with TRP 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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6E ALA* 3.9 26.2 - - + -
9E PHE* 3.4 42.0 - + + -
141E PHE 2.9 17.1 + - - +
142E ALA* 3.5 8.7 - - + +
143E ASP 3.1 0.6 - - - -
144E CYS* 1.3 81.6 - - - +
146E GLU* 1.3 62.8 + - - +
149E VAL* 3.1 44.2 - - + +
150E ASP 5.1 3.8 - - - -
151E HIS* 3.0 37.1 - + - -
155E LEU* 4.4 14.4 - - + -
158E ASN* 4.3 20.0 - - - -
159E PRO* 4.8 8.6 + - + -
162E MET* 5.5 15.0 - - + -
214H TYR* 4.6 10.7 + - - -
216H ARG* 4.0 18.2 - - - -
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Residues in contact with GLU 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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44E ARG* 4.9 0.7 + - - -
142E ALA 3.6 8.4 - - - +
143E ASP* 3.4 6.9 - - - +
145E TRP* 1.3 76.7 - - + +
147E ASN* 1.3 105.5 + - - +
149E VAL 3.3 8.6 - - - +
150E ASP* 5.3 0.2 - - - -
151E HIS* 3.4 39.7 + - + +
216H ARG* 3.4 32.3 + - + +
218H GLU* 5.1 7.1 - - - +
220H ARG* 5.2 7.6 + - - -
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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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33E GLN* 5.0 6.8 - - - +
44E ARG* 2.7 50.5 + - - +
79E TYR* 5.4 2.2 - - - -
143E ASP* 2.7 37.7 + - - +
146E GLU* 1.3 105.1 + - - +
148E PHE* 1.3 76.3 + - + +
149E VAL 4.4 0.5 - - - +
150E ASP* 5.8 0.2 - - - -
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Residues in contact with PHE 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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3E LEU 3.4 22.7 + - - +
4E LEU* 3.9 9.7 + - + -
31E CYS* 3.5 30.7 - - + -
32E TYR 3.2 36.1 - - - -
33E GLN* 3.8 22.0 - - + -
44E ARG* 4.1 8.7 - - + +
45E GLY* 3.3 31.4 - - - -
46E TYR* 4.4 3.8 - - + -
79E TYR* 4.7 10.5 - + - -
144E CYS* 3.3 33.0 + - - +
147E ASN* 1.3 91.7 - - + +
149E VAL* 1.3 66.4 + - - +
150E ASP* 3.4 5.4 + - - +
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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