Contacts of the strand formed by residues 176 - 183 (chain B) in PDB entry 1UZL
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 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B MET* 3.5 41.3 - - + +
128B GLN* 4.0 7.0 - - + +
133B GLY* 3.3 18.2 - - - +
135B MET* 4.2 18.2 - - + -
167B ILE* 4.8 3.2 - - + +
168B ALA* 4.9 0.5 - - - -
171B LEU* 3.0 55.7 + - + +
172B SER* 3.2 5.7 + - - -
174B ALA* 3.1 9.1 - - + +
175B ASN* 1.3 80.4 - - - +
177B THR* 1.3 64.5 + - - +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLY 3.0 3.8 + - - +
134B ARG* 3.3 37.6 - - - +
135B MET* 2.9 28.1 + - - +
167B ILE* 5.5 0.2 - - - -
172B SER* 4.4 5.2 - - - +
175B ASN* 4.8 2.9 - - - +
176B VAL* 1.3 81.8 - - - +
178B ALA* 1.3 62.2 + - - +
179B ASN* 4.1 6.8 + - - -
229B ALA 5.3 0.4 + - - +
230B SER 3.9 13.9 - - - +
232B ILE 3.5 23.8 + - - +
233B SER* 3.5 19.1 - - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B MET* 3.3 14.8 - - + -
137B PHE* 4.2 4.7 - - + -
164B ALA* 3.5 33.3 - - - +
167B ILE* 3.9 22.2 - - + -
168B ALA* 3.9 4.5 - - - +
177B THR* 1.3 75.2 - - - +
179B ASN* 1.3 58.3 + - - +
233B SER* 3.6 4.2 + - - -
234B GLY* 2.8 34.1 + - - -
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Residues in contact with ASN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 6.1 0.6 - - - +
135B MET 3.0 10.2 + - - +
136B ILE* 3.5 8.2 - - + +
137B PHE* 3.0 28.6 + - - -
164B ALA* 5.1 0.4 - - - -
177B THR* 4.1 10.1 + - - -
178B ALA* 1.3 74.4 - - - +
180B VAL* 1.3 67.2 + - - +
224B LEU* 4.1 31.0 + - + +
229B ALA* 5.1 2.4 + - - +
232B ILE* 3.2 31.7 + - - +
233B SER* 3.1 7.3 + - - -
234B GLY 3.1 9.2 + - - -
235B ALA* 3.0 34.2 + - + +
237B ILE* 6.0 0.7 - - + -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PHE* 3.4 21.3 - - + +
139B GLY* 4.6 6.7 - - - +
157B LYS 5.8 0.2 - - - +
160B VAL* 4.5 4.3 - - + +
161B ILE* 3.9 34.1 - - + +
164B ALA* 3.8 24.0 - - + -
179B ASN* 1.3 81.2 - - - +
181B VAL* 1.3 72.7 + - - +
182B ALA* 4.5 2.5 - - + +
224B LEU* 4.9 0.4 - - - +
235B ALA 2.8 12.7 + - - +
236B VAL* 3.3 15.1 - - + -
237B ILE* 2.8 29.5 + - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.9 14.1 - - + -
137B PHE 2.9 5.1 + - - +
138B ILE* 3.7 10.5 - - + -
139B GLY 2.9 26.0 + - - -
180B VAL* 1.3 73.4 - - - +
182B ALA* 1.3 59.9 + - - +
183B PRO* 3.2 7.4 - - + +
217B VAL* 4.3 21.5 - - + -
220B VAL* 4.4 12.6 - - + -
221B VAL* 4.2 11.2 - - + -
224B LEU* 3.4 31.9 - - + -
237B ILE* 3.5 4.0 - - + +
239B VAL* 3.8 26.5 - - + -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLY* 4.8 4.0 - - - +
143B GLY* 5.8 7.9 - - - +
161B ILE* 5.8 3.1 - - + -
180B VAL* 4.0 4.0 - - + -
181B VAL* 1.3 70.6 - - - +
183B PRO* 1.3 67.7 - - - +
184B GLY 3.7 0.3 + - - -
236B VAL* 4.2 20.2 - - + -
237B ILE 2.9 14.3 + - - +
238B PRO* 3.4 9.0 - - + +
239B VAL* 3.0 22.0 + - - -
240B ASP* 4.7 2.4 - - - +
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Residues in contact with PRO 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.8 4.5 - - + -
138B ILE* 4.1 11.0 - - + -
139B GLY 3.0 31.6 - - - +
141B VAL* 3.2 7.6 - - + -
142B SER* 2.7 32.6 + - - -
143B GLY 4.7 0.5 + - - -
181B VAL* 3.2 11.4 - - + +
182B ALA* 1.3 87.0 - - - +
184B GLY* 1.3 56.5 + - - +
186B ILE* 3.8 22.4 - - + -
217B VAL* 4.4 19.1 - - + -
239B VAL* 3.4 10.8 - - + +
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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
------------------------------------------------------------
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