Contacts of the strand formed by residues 176 - 184 (chain R) 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 176 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41R PRO* 5.6 5.9 - - - +
110R THR* 6.0 2.6 - - + +
144R ASP* 3.1 21.5 + - - -
145R TYR* 2.9 44.8 + - + +
146R PHE* 4.1 25.9 - + - -
147R PRO* 4.2 2.5 - - + -
148R GLU* 3.4 44.2 - - + +
168R ALA* 4.2 10.1 - - + -
169R VAL 3.7 3.8 - - - -
170R LEU* 3.7 46.8 - - + +
171R GLN* 4.0 0.2 + - - -
175R LEU* 1.3 74.0 - - - +
177R SER* 1.3 62.4 + - - +
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Residues in contact with SER 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141R LEU* 4.2 8.3 - - - +
142R VAL 3.2 12.6 + - - -
143R LYS* 3.1 24.8 - - - +
145R TYR* 3.5 2.9 - - - -
169R VAL* 2.7 43.8 + - - +
171R GLN* 3.1 27.9 + - - -
176R TYR* 1.3 78.8 - - - +
178R LEU* 1.3 58.8 + - - +
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Residues in contact with LEU 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141R LEU* 3.8 2.2 - - - +
142R VAL* 2.8 42.6 + - + +
145R TYR* 3.6 21.5 - - + +
148R GLU* 5.3 0.7 - - - +
150R VAL* 4.0 32.1 - - + +
152R VAL* 4.3 10.8 - - + -
165R THR* 3.8 15.3 - - + -
166R PHE 3.8 13.5 - - - +
167R PRO 3.8 18.4 - - - +
168R ALA* 3.9 6.7 - - + +
169R VAL* 5.1 1.8 - - - -
177R SER* 1.3 75.3 - - - +
179R SER* 1.3 82.5 + - - +
180R SER 4.2 1.1 - - - +
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Residues in contact with SER 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Q VAL* 5.1 9.3 - - - +
176Q SER* 4.6 11.6 + - - -
178Q THR* 5.2 3.1 + - - -
124R LEU* 4.7 11.8 - - - +
140R CYS 3.4 10.3 - - - -
141R LEU* 3.6 17.3 - - - +
166R PHE* 2.9 44.5 + - - +
178R LEU* 1.3 83.4 + - - +
180R SER* 1.3 60.3 + - - +
181R VAL* 5.0 2.7 - - - -
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Residues in contact with SER 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R GLY* 3.2 2.9 - - - -
140R CYS* 2.9 36.4 + - - +
142R VAL* 5.7 1.5 - - - +
152R VAL* 3.5 27.7 - - - +
154R TRP* 2.8 29.8 + - - -
163R VAL* 3.8 1.6 - - - +
164R HIS 3.9 4.3 - - - -
165R THR* 3.1 25.6 + - - +
178R LEU* 4.2 0.8 - - - +
179R SER* 1.3 73.9 - - - +
181R VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q PHE* 5.1 4.0 - - + -
133Q VAL* 6.3 1.1 - - + -
135Q LEU* 3.3 37.2 - - + -
137Q ASN* 4.2 4.7 - - - +
124R LEU* 3.6 25.6 - - + -
138R LEU 3.4 10.8 - - - +
139R GLY* 4.0 0.2 - - - -
154R TRP* 4.6 0.9 - - - -
163R VAL* 3.2 7.4 - - - +
164R HIS* 2.9 47.0 + - + +
166R PHE* 3.8 15.7 - - + -
179R SER* 5.0 2.5 - - - -
180R SER* 1.3 77.6 + - - +
182R VAL* 1.3 69.6 + - - +
183R THR* 6.3 0.2 - - + -
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Residues in contact with VAL 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137R ALA* 4.0 0.4 - - - -
138R LEU* 3.0 46.4 + - + +
154R TRP* 4.2 14.6 - - + -
159R LEU* 3.5 40.4 - - + -
161R SER 4.1 2.0 - - - +
162R GLY 3.5 14.4 - - - -
163R VAL* 3.7 17.7 - - + -
181R VAL* 1.3 83.0 - - - +
183R THR* 1.3 65.1 + - - +
184R VAL* 3.8 13.2 + - + +
194R TYR* 5.4 0.4 - - + -
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Residues in contact with THR 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q SER* 5.9 0.7 - - - -
116Q PHE* 3.9 15.5 - - + -
135Q LEU* 5.4 0.9 - - + -
137Q ASN* 3.6 31.3 + - + +
138Q ASN* 5.1 1.4 + - - -
135R THR* 4.5 10.1 - - - +
136R ALA 3.4 7.4 - - - +
137R ALA* 3.6 24.9 - - + +
161R SER 5.2 0.9 - - - +
162R GLY* 3.9 15.5 + - - -
181R VAL* 6.3 0.2 - - + -
182R VAL* 1.3 75.7 - - - +
184R VAL* 1.3 66.2 - - - +
185R PRO* 4.8 0.7 - - - +
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Residues in contact with VAL 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R THR* 4.6 3.6 - - - -
136R ALA* 3.1 28.7 + - - +
138R LEU* 4.7 13.0 - - + -
159R LEU* 4.7 8.5 - - + -
161R SER 5.8 0.2 - - - +
182R VAL* 4.1 23.8 - - + +
183R THR* 1.3 79.8 - - - +
185R PRO* 1.3 79.5 - - + +
186R SER* 4.3 0.3 - - - -
188R SER 5.1 0.2 - - - +
189R LEU* 5.2 5.1 - - + +
194R TYR* 3.6 46.9 - - + +
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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