Contacts of the helix formed by residues 150 - 159 (chain E) in PDB entry 6R7H
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 150 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E THR* 4.2 20.0 - - + +
104E GLU* 3.9 39.7 - - + +
107E VAL* 5.7 11.0 - - + -
148E SER* 3.2 3.8 - - - -
149E GLY* 1.3 77.2 - - - +
151E ASP* 1.3 64.7 + - - +
152E VAL 3.2 1.8 - - - -
153E SER* 2.6 21.4 + - - +
154E THR* 3.1 22.5 + - - +
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Residues in contact with ASP 151 (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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103E THR* 3.7 19.2 - - - -
104E GLU* 3.7 13.5 - - - +
136E TRP* 3.5 27.5 - - + -
138E HIS* 4.4 3.2 + - - -
140E HIS* 3.1 36.4 + - - -
147E LEU* 3.9 23.6 - - + -
148E SER* 3.7 8.1 + - - +
150E ILE* 1.3 77.6 - - - +
152E VAL* 1.3 60.7 + - - +
154E THR* 4.4 3.5 - - - -
155E GLN* 3.2 29.7 + - - +
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LEU* 3.9 18.8 - - + +
148E SER 3.3 21.3 + - - +
149E GLY* 3.4 15.5 - - - +
151E ASP* 1.3 76.5 - - - +
153E SER* 1.3 62.9 + - - +
155E GLN 4.3 0.7 - - - -
156E MET* 3.4 30.5 + - + +
188E THR* 3.7 34.6 - - + +
194E LYS* 5.4 0.2 - - - +
220E GLN* 3.7 38.1 - - + +
221E TYR* 4.7 2.5 - - + -
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Residues in contact with SER 153 (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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149E GLY 3.3 13.6 + - - -
150E ILE* 2.6 25.5 + - - +
152E VAL* 1.3 79.5 - - - +
154E THR* 1.3 62.7 + - - +
155E GLN 3.4 0.4 - - - -
156E MET* 3.7 20.2 + - - +
157E LEU* 3.7 20.8 + - - +
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Residues in contact with THR 154 (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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103E THR* 4.9 13.5 - - + +
107E VAL* 5.1 6.0 - - + +
108E ASN* 4.0 39.5 + - + +
109E ALA 4.9 2.9 - - - +
110E GLN* 5.3 1.8 - - + -
136E TRP* 6.0 2.7 - - - -
150E ILE* 3.1 22.7 + - - +
151E ASP* 4.5 3.7 - - - -
153E SER* 1.3 76.9 + - - +
155E GLN* 1.3 63.8 + - - +
157E LEU* 3.3 15.5 + - + +
158E ASN* 2.8 37.1 + - - +
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Residues in contact with GLN 155 (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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136E TRP* 4.1 21.8 - - + +
147E LEU* 3.9 5.7 - - - +
151E ASP 3.2 17.8 + - - +
152E VAL 4.7 1.3 - - - +
153E SER 3.4 0.2 - - - -
154E THR* 1.3 77.5 - - - +
156E MET* 1.3 61.7 + - - +
158E ASN* 3.3 8.6 + - + +
159E GLN* 3.2 50.4 + - + +
165E PHE* 4.7 1.7 + - + -
166E VAL* 4.5 6.5 - - - +
167E ALA* 3.4 39.7 - - - +
187E ARG* 4.0 5.3 - - - +
188E THR* 3.3 35.7 + - - +
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Residues in contact with MET 156 (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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152E VAL* 3.4 22.3 + - + +
153E SER* 3.7 17.6 + - - +
154E THR 3.3 0.6 - - - -
155E GLN* 1.3 77.1 - - - +
157E LEU* 1.3 62.8 + - + +
158E ASN 3.4 0.4 + - - -
159E GLN* 3.9 15.4 + - - +
160E GLN* 3.7 26.3 + - - +
188E THR* 4.5 5.6 - - + -
189E TYR 3.8 23.8 - - - +
190E PRO* 4.1 22.1 - - + +
191E LYS* 3.7 29.6 - - - +
194E LYS* 4.4 12.8 - - - +
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Residues in contact with LEU 157 (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 ASN* 5.9 3.6 - - - +
153E SER* 3.7 17.5 + - - +
154E THR* 3.3 14.2 + - + +
155E GLN 3.2 0.6 - - - -
156E MET* 1.3 79.0 - - + +
158E ASN* 1.3 65.8 + - - +
160E GLN* 4.3 15.2 + - - +
161E PHE* 3.4 32.8 - - + -
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Residues in contact with ASN 158 (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 ASN* 4.3 11.4 - - - +
110E GLN* 3.4 36.4 - - - +
114E TYR* 5.5 2.3 + - - -
136E TRP* 4.9 5.3 - - - +
154E THR* 2.8 30.7 + - - +
155E GLN* 3.3 8.0 + - - +
157E LEU* 1.3 82.9 - - - +
159E GLN* 1.3 58.7 + - - +
160E GLN 3.2 2.5 - - - -
161E PHE* 3.9 3.3 - - - +
162E GLN* 3.0 36.0 + - + +
165E PHE* 3.6 23.4 - - + -
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Residues in contact with GLN 159 (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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155E GLN* 3.2 38.8 + - + +
156E MET* 3.9 12.8 + - - +
157E LEU 3.6 0.4 - - - -
158E ASN* 1.3 77.8 - - - +
160E GLN* 1.3 60.7 + - + +
162E GLN 4.4 4.7 - - - -
163E GLU* 3.1 30.5 - - + +
165E PHE* 4.0 23.0 - - + +
187E ARG* 3.1 48.7 + - - +
188E THR* 3.5 17.0 + - - +
190E PRO* 5.3 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