Contacts of the strand formed by residues 173 - 182 (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 TYR 173 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q SER* 5.5 0.9 + - - -
105Q GLU* 3.3 17.9 + - - +
138Q ASN* 3.0 20.6 - - - -
139Q PHE* 2.9 36.8 + - + +
140Q TYR* 3.7 18.6 - + - -
141Q PRO 4.1 0.2 - - - -
142Q ARG* 3.2 64.5 + - + +
163Q VAL* 4.1 6.3 - - + -
164Q THR* 3.4 24.0 - - - -
165Q GLU* 4.9 0.2 - - - -
166Q GLN* 2.5 49.1 + - + -
172Q THR* 1.3 76.0 + - - +
174Q SER* 1.3 72.1 + - - +
164R HIS* 4.7 0.8 + - - -
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Residues in contact with SER 174 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Q LEU 3.1 11.4 - - - -
137Q ASN* 4.5 1.8 - - - -
138Q ASN 3.3 5.0 + - - -
139Q PHE* 3.3 2.0 - - - -
163Q VAL* 4.5 1.1 - - - -
164Q THR* 3.2 32.7 + - - -
173Q TYR* 1.3 86.7 + - - +
175Q LEU* 1.3 59.3 + - - +
164R HIS* 2.8 45.9 + - - -
166R PHE* 2.9 19.8 - - - -
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Residues in contact with LEU 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Q CYS 4.6 0.2 - - - -
135Q LEU* 3.7 1.4 - - - -
136Q LEU* 2.9 57.7 + - + +
139Q PHE* 3.3 16.2 - - + -
142Q ARG 5.4 1.8 - - - +
144Q ALA* 4.5 17.9 - - + +
146Q VAL* 4.1 8.3 - - + -
161Q GLU* 3.1 37.2 - - + +
162Q SER 3.5 8.1 - - - +
163Q VAL* 4.0 17.7 - - + +
174Q SER* 1.3 71.2 - - - +
176Q SER* 1.3 86.2 + - - +
177Q SER 3.8 2.9 - - - +
166R PHE* 3.2 16.1 - - - -
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Residues in contact with SER 176 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q VAL* 4.1 16.0 - - - +
134Q CYS 3.7 5.8 - - - -
135Q LEU* 4.9 1.1 - - - +
160Q GLN 3.7 0.9 - - - +
161Q GLU* 3.2 3.8 - - - -
162Q SER* 2.8 41.2 + - - -
175Q LEU* 1.3 79.7 - - - +
177Q SER* 1.3 61.6 + - - +
178Q THR* 4.4 5.9 + - - -
166R PHE* 3.3 34.6 - - - +
179R SER* 4.6 10.0 + - - -
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Residues in contact with SER 177 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q VAL* 3.3 5.9 - - - +
134Q CYS* 3.1 34.8 + - - -
146Q VAL* 4.0 19.7 + - - +
148Q TRP* 2.8 33.8 + - - -
159Q SER* 4.4 4.2 + - - -
160Q GLN 3.3 8.0 + - - -
161Q GLU* 4.1 10.3 + - - +
175Q LEU* 3.8 8.4 - - - +
176Q SER* 1.3 74.2 - - - +
178Q THR* 1.3 67.2 + - - +
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Residues in contact with THR 178 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q SER* 3.9 30.3 - - - +
132Q VAL 3.2 6.5 - - - +
133Q VAL* 4.1 12.0 - - + +
148Q TRP* 4.6 0.2 - - - -
158Q ASN 3.9 0.2 - - - +
159Q SER* 3.1 6.3 - - - -
160Q GLN* 2.9 40.8 + - - +
176Q SER* 4.4 7.6 + - - -
177Q SER* 1.3 78.3 + - - +
179Q LEU* 1.3 60.9 + - - +
180Q THR* 3.5 13.9 + - - +
141R LEU* 5.9 4.3 - - + +
143R LYS* 6.2 0.4 - - - -
179R SER* 5.2 3.8 + - - -
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Residues in contact with LEU 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q ALA 3.4 5.7 - - - +
131Q SER* 3.5 0.2 - - - -
132Q VAL* 2.8 50.2 + - + +
148Q TRP* 3.9 41.7 - - + -
150Q VAL* 3.9 20.4 - - + -
155Q GLN* 4.1 2.5 - - + -
158Q ASN* 2.9 43.5 - - - +
159Q SER* 4.1 3.6 - - - -
178Q THR* 1.3 70.0 - - - +
180Q THR* 1.3 60.2 + - - +
181Q LEU* 3.5 27.2 + - + +
192Q TYR* 4.3 2.5 - - + -
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Residues in contact with THR 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q THR* 6.0 5.2 - - + -
130Q ALA 3.9 3.4 - - - +
131Q SER* 4.3 9.8 + - - +
158Q ASN* 3.0 25.3 + - - +
160Q GLN* 4.5 11.4 + - - +
178Q THR* 3.5 16.2 + - - +
179Q LEU* 1.3 70.7 - - - +
181Q LEU* 1.3 76.8 + - - +
143R LYS* 5.7 7.4 - - - +
171R GLN* 5.9 2.1 - - - +
172R SER* 6.2 0.2 - - - +
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Residues in contact with LEU 181 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q THR* 3.9 3.6 - - - +
130Q ALA* 2.8 40.7 + - + +
132Q VAL* 4.9 3.1 - - + -
150Q VAL* 4.8 4.9 - - + -
155Q GLN* 5.2 3.4 - - - +
158Q ASN* 3.5 22.9 - - + +
179Q LEU* 3.5 29.8 - - + +
180Q THR* 1.3 87.9 - - - +
182Q SER* 1.3 65.5 + - - +
185Q ASP* 4.7 16.4 - - + +
186Q TYR* 4.8 3.8 - - + -
192Q TYR* 3.7 27.8 - - + +
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Residues in contact with SER 182 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q GLY 4.7 3.8 - - - -
129Q THR* 4.7 7.0 - - - +
130Q ALA 4.5 2.0 - - - +
181Q LEU* 1.3 77.0 - - - +
183Q LYS* 1.3 63.0 + - - +
184Q ALA* 3.7 6.5 + - - +
185Q ASP* 2.9 36.5 + - - +
186Q TYR* 3.1 23.3 + - - +
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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