Contacts of the strand formed by residues 159 - 163 (chain Q) in PDB entry 2WUB
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 SER 159 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146Q VAL 5.7 0.3 + - - -
148Q TRP* 3.6 33.5 - - - -
155Q GLN 5.6 1.0 + - - -
156Q SER* 5.6 1.7 - - - -
157Q GLY* 4.7 3.5 + - - +
158Q ASN* 1.3 89.3 + - - +
160Q GLN* 1.3 70.2 + - - +
161Q GLU* 6.0 1.0 - - - +
177Q SER* 4.4 3.4 + - - -
178Q THR 3.1 12.8 - - - -
179Q LEU* 4.1 2.5 - - - -
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Residues in contact with GLN 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158Q ASN 5.6 1.3 - - - +
159Q SER* 1.3 80.6 - - - +
161Q GLU* 1.3 64.0 + - - +
176Q SER 3.7 0.7 - - - +
177Q SER* 3.3 3.9 + - - -
178Q THR* 2.9 38.5 + - - +
180Q THR* 4.5 11.7 + - - +
169R VAL* 3.9 25.7 - - + +
170R LEU 3.1 26.9 + - - -
171R GLN* 4.0 20.4 - - - +
172R SER 4.9 1.2 + - - +
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Residues in contact with GLU 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144Q ALA 4.7 5.6 - - - +
145Q LYS* 5.2 0.3 - - - -
146Q VAL* 3.9 27.7 + - - +
159Q SER* 6.0 1.6 - - - +
160Q GLN* 1.3 77.8 - - - +
162Q SER* 1.3 64.0 + - - +
163Q VAL* 5.0 4.5 - - + +
175Q LEU* 3.1 34.8 - - + +
176Q SER 3.2 5.2 - - - +
177Q SER* 4.1 12.0 + - - +
169R VAL* 4.4 11.6 - - - +
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Residues in contact with SER 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161Q GLU* 1.3 76.5 - - - +
163Q VAL* 1.3 61.0 + - - +
175Q LEU* 3.5 0.3 - - - -
176Q SER* 2.8 43.6 + - - +
166R PHE* 3.1 35.2 - - - +
167R PRO* 3.3 17.2 + - - +
169R VAL* 3.8 20.2 - - - -
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Residues in contact with VAL 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Q PHE* 5.1 2.5 - - + -
142Q ARG* 3.8 37.0 + - + +
161Q GLU* 5.0 3.8 - - + +
162Q SER* 1.3 79.8 + - - +
164Q THR* 1.3 79.0 + - - +
165Q GLU* 5.4 0.9 - - - +
173Q TYR* 4.1 15.9 - - + -
174Q SER 3.6 10.3 - - - +
175Q LEU* 4.0 24.2 - - + -
167R PRO* 3.3 21.3 - - - +
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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