Contacts of the strand formed by residues 166 - 173 (chain B) in PDB entry 1XUO
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B GLY 5.2 3.6 - - - -
130B VAL* 3.4 45.8 - - + +
132B LEU* 4.2 15.9 - - + -
161B LEU* 3.9 38.5 - - + +
164B THR* 3.2 34.2 + - + +
165B SER* 1.3 83.2 - - - +
167B GLN* 1.3 58.8 + - - +
168B PHE* 3.8 23.7 - + + -
186B TYR* 3.9 14.2 + - - -
227B ARG* 5.2 0.2 - - - -
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Residues in contact with GLN 167 (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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130B VAL 3.0 4.4 + - - -
131B ASP* 3.1 26.6 - - - +
132B LEU* 2.9 26.5 + - - +
166B TYR* 1.3 75.8 - - - +
168B PHE* 1.3 65.4 + - - +
183B PHE* 3.6 21.5 - - + +
186B TYR* 4.1 7.2 - - + -
187B VAL* 3.2 35.2 - - + +
225B GLY 3.0 24.0 + - - +
227B ARG* 3.6 28.3 + - - +
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Residues in contact with PHE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.3 44.4 - - + +
134B PHE* 3.8 14.8 - + + -
157B VAL* 4.8 1.1 - - + -
158B MET* 3.7 40.4 - - + -
161B LEU* 3.9 27.1 - - + -
166B TYR* 3.8 29.6 - + + -
167B GLN* 1.3 77.1 - - - +
169B ALA* 1.3 61.0 + - - +
181B PHE* 3.5 8.1 - - + -
183B PHE* 3.4 15.9 - - - -
186B TYR* 3.4 56.9 - + + +
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Residues in contact with ALA 169 (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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132B LEU 3.2 5.5 + - - +
133B VAL* 3.4 11.5 - - + -
134B PHE* 3.0 27.6 + - - -
168B PHE* 1.3 75.0 - - - +
170B ALA* 1.3 62.0 + - - +
179B THR* 5.6 0.4 - - + -
181B PHE* 3.4 20.2 - - - +
182B ASP* 4.0 9.9 - - - -
183B PHE* 3.9 24.7 - - + +
219B VAL* 4.3 10.1 - - + -
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Residues in contact with ALA 170 (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 PHE* 3.3 17.0 - - + +
136B PHE* 4.2 15.3 - - + -
154B MET* 4.7 3.1 - - - -
169B ALA* 1.3 75.1 - - - +
171B VAL* 1.3 60.2 + - - +
179B THR 3.6 0.9 - - - -
180B GLU* 2.8 32.9 + - + +
181B PHE* 3.1 39.2 + - + +
196B LEU* 4.4 6.7 - - + -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.2 13.9 - - + -
134B PHE 2.8 7.5 + - - +
135B LEU* 3.3 23.6 - - + +
136B PHE* 2.9 30.0 + - - -
170B ALA* 1.3 79.4 - - - +
172B GLN* 1.3 69.8 + - - +
177B TYR* 4.4 2.2 - - + -
178B LYS 3.2 14.1 - - - +
179B THR* 4.0 10.3 - - + +
214B TYR* 3.8 23.3 - - + -
215B VAL* 4.2 3.4 - - + -
219B VAL* 3.8 29.4 - - + -
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Residues in contact with GLN 172 (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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136B PHE* 3.3 28.8 - - + +
138B GLY* 3.4 20.7 - - - -
147B PHE* 3.7 10.3 - - - -
171B VAL* 1.3 75.6 - - - +
173B PHE* 1.3 62.9 + - - +
177B TYR* 3.4 3.1 - - - -
178B LYS* 2.9 32.6 + - - +
180B GLU* 3.0 26.1 - - - +
199B VAL* 3.9 2.8 - - - +
200B LYS 2.9 19.7 + - - +
201B HIS* 3.6 4.9 - - - +
202B MET* 3.0 49.4 - - + +
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Residues in contact with PHE 173 (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 LEU* 3.6 33.0 - - + -
136B PHE 3.0 18.5 + - - -
137B ASP* 3.5 31.4 - - + +
138B GLY 2.8 24.6 + - - -
172B GLN* 1.3 74.7 - - - +
174B SER* 1.3 62.0 + - - +
176B SER 3.4 4.5 - - - -
177B TYR* 3.8 9.0 - - + -
202B MET* 4.0 2.9 - - - -
206B THR* 4.0 12.3 - - + -
207B ASN 4.0 12.8 - - - -
208B THR* 3.6 37.0 - - + -
211B ALA* 3.5 27.8 - - + -
236B ILE* 4.6 3.6 - - + -
237B ILE 4.2 2.2 - - - -
238B THR* 4.3 12.6 - - - -
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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