Contacts of the strand formed by residues 168 - 174 (chain E) in PDB entry 5AQP
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 ASN 168 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E THR* 2.7 19.0 + - + +
141E ASN* 2.8 29.2 + - - +
142E ALA 3.0 24.4 + - - -
166E GLY 4.0 1.0 + - - -
167E LEU* 1.3 70.2 - - - +
169E VAL* 1.3 60.5 + - - +
170E LEU* 3.2 19.3 + - - +
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Residues in contact with VAL 169 (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 ALA 3.4 7.9 - - - +
144E VAL* 4.3 15.0 - - + -
158E THR 5.5 0.2 - - - +
159E LYS* 4.2 17.5 - - + +
162E GLY* 3.8 32.3 - - - -
163E THR* 4.5 2.4 + - - +
167E LEU* 3.6 6.8 + - + +
168E ASN* 1.3 74.0 + - - +
170E LEU* 1.4 65.1 + - - +
171E ARG* 3.7 21.9 - - - +
172E ILE* 3.9 25.6 - - + -
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Residues in contact with LEU 170 (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* 3.8 29.2 - - + -
141E ASN* 3.9 18.4 - - + +
142E ALA 2.9 15.3 + - - +
143E VAL* 4.3 16.2 - - + -
168E ASN* 3.2 24.5 + - - +
169E VAL* 1.4 71.7 - - - +
171E ARG* 1.3 63.9 + - + +
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Residues in contact with ARG 171 (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 ALA 4.1 0.8 + - - -
143E VAL* 3.5 14.6 - - + +
144E VAL 3.3 22.0 + - - -
169E VAL* 3.4 7.1 - - - +
170E LEU* 1.3 84.9 - - + +
172E ILE* 1.3 64.9 + - - +
173E ILE* 4.3 14.8 - - + -
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Residues in contact with ILE 172 (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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144E VAL* 3.3 29.4 - - + +
146E VAL* 3.7 30.3 - - + -
155E ARG* 4.6 20.0 + - + +
158E THR* 4.3 18.4 - - + -
159E LYS* 4.5 20.0 - - + +
169E VAL* 3.9 16.2 - - + -
171E ARG* 1.3 76.0 - - - +
173E ILE* 1.3 64.9 + - - +
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Residues in contact with ILE 173 (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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143E VAL* 4.0 20.2 - - + -
144E VAL 3.3 5.3 + - - -
145E THR* 3.2 33.9 - - + -
146E VAL* 3.2 6.7 + - - -
155E ARG* 5.4 0.4 - - - +
171E ARG* 4.3 15.9 - - + -
172E ILE* 1.3 80.2 - - - +
174E ASN* 1.3 67.4 + - - +
177E THR* 4.9 8.1 - - + -
178E ALA* 3.7 29.4 - - + +
181E ILE* 4.4 13.7 - - + -
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Residues in contact with ASN 174 (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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146E VAL 3.2 5.4 - - - +
147E PRO 4.0 1.0 - - - +
148E ALA* 3.7 11.0 + - - +
155E ARG* 2.9 38.2 + - - +
173E ILE* 1.3 76.0 - - - +
175E GLU* 1.3 59.8 + - - +
176E PRO* 3.8 12.6 - - + -
177E THR* 3.2 20.8 + - - +
178E ALA* 2.9 25.8 + - - +
219E VAL* 3.5 27.5 - - - +
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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