Contacts of the strand formed by residues 157 - 163 (chain E) in PDB entry 1AO7
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 VAL 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E PHE* 4.6 6.9 - - - -
125E PRO* 4.7 0.9 - - + -
149E ALA* 5.8 1.1 - - + -
152E PHE* 3.3 44.2 - - + -
155E ASP 3.5 3.0 + - - -
156E HIS* 1.3 79.3 - - - +
158E GLU* 1.3 64.9 + - - +
159E LEU* 4.1 3.0 + - + +
178E PRO* 4.5 6.5 - - + -
192E LEU* 3.7 30.6 - - + +
214E VAL* 4.2 20.6 - - + -
215E GLN 3.3 8.3 - - - +
216E PHE* 4.1 11.0 - - + -
217E TYR* 4.7 0.2 - - - -
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Residues in contact with GLU 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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9E LYS* 3.7 22.1 + - - +
10E PHE* 3.7 14.6 - - + -
157E VAL* 1.3 74.9 - - - +
159E LEU* 1.3 59.4 + - - +
160E SER* 4.2 1.9 + - - -
213E GLN* 4.0 1.4 - - - +
214E VAL* 3.6 1.1 + - - -
215E GLN* 2.8 46.8 + - + +
217E TYR* 2.9 39.2 + - + -
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Residues in contact with LEU 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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147E CYS* 5.1 2.9 - - - -
148E LEU 6.1 0.2 - - - +
149E ALA* 5.4 2.2 - - + +
157E VAL* 4.0 2.2 + - + +
158E GLU* 1.3 72.8 - - - +
160E SER* 1.3 86.4 + - - +
161E TRP* 4.8 2.0 - - + +
172E VAL* 5.7 0.3 - - - +
174E THR* 4.1 21.7 - - + +
192E LEU* 3.9 36.5 - - + +
193E SER 4.4 2.7 - - - +
194E SER* 3.8 28.0 - - - +
212E CYS* 3.5 31.0 - - - -
213E GLN 3.3 9.0 - - - +
214E VAL* 3.8 17.3 - - + +
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Residues in contact with SER 160 (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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158E GLU 5.0 1.9 + - - -
159E LEU* 1.3 85.2 - - - +
161E TRP* 1.3 60.4 + - - +
162E TRP* 2.8 25.8 + - - -
167E GLU* 3.2 30.6 + - - -
172E VAL* 5.6 2.9 - - - -
211E ARG 3.7 0.3 - - - +
212E CYS* 3.5 3.6 - - - -
213E GLN* 2.8 45.3 + - - +
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Residues in contact with TRP 161 (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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129E VAL* 4.2 16.2 - - + -
145E LEU* 3.7 27.1 - - + -
146E VAL 3.8 17.3 - - - -
147E CYS* 3.5 26.9 - - + -
159E LEU* 4.8 3.1 - - + +
160E SER* 1.3 76.0 - - - +
162E TRP* 1.3 60.7 + - - +
163E VAL* 4.1 1.1 - - + -
167E GLU* 2.8 26.6 + - - +
168E VAL* 2.8 32.1 + - + -
172E VAL* 3.4 34.4 - - + +
194E SER* 3.0 23.2 + - - -
195E ARG 3.6 7.5 + - - -
196E LEU* 3.6 26.7 - - + -
210E PHE* 4.6 15.5 - - + -
211E ARG 3.4 13.9 - - - -
212E CYS* 4.2 14.4 - - + -
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Residues in contact with TRP 162 (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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160E SER* 2.8 27.6 + - - -
161E TRP* 1.3 77.2 - - - +
163E VAL* 1.3 64.6 + - - +
164E ASN 3.8 0.7 + - - -
165E GLY* 4.1 13.3 + - - -
166E LYS* 4.0 11.4 - - + +
167E GLU* 3.6 38.4 - - + +
209E HIS* 3.8 2.8 + - - +
211E ARG* 2.8 58.5 + - - +
213E GLN* 2.7 42.1 + - + -
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Residues in contact with VAL 163 (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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161E TRP* 4.1 1.3 + - + -
162E TRP* 1.3 71.8 - - - +
164E ASN* 1.3 66.3 + - + +
165E GLY 2.6 18.3 + - - -
166E LYS* 2.7 29.6 + - + +
168E VAL* 3.6 36.1 - - + -
196E LEU* 4.6 5.6 - - + -
198E VAL* 6.5 0.2 - - + -
202E PHE* 4.3 13.9 - - + -
208E ASN* 6.2 0.2 - - + -
209E HIS 3.4 6.1 - - - +
210E PHE* 3.1 37.7 - - + +
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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