Contacts of the strand formed by residues 181 - 188 (chain B) in PDB entry 5X1V
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 ILE 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B LEU* 3.9 21.8 - - + -
174B ILE 3.8 0.5 - - - +
175B TYR* 3.4 5.5 - - - +
176B VAL* 2.8 48.9 + - + +
177B ASP* 5.4 3.1 - - + -
179B GLY 4.5 1.7 - - - -
180B LEU* 1.3 86.3 - - + +
182B SER* 1.3 64.3 + - - +
183B LEU* 4.3 9.9 - - + -
197B VAL* 4.7 2.0 - - + -
199B ASN 3.5 15.0 - - - +
201B GLY* 4.0 20.6 - - - +
202B SER 3.7 25.4 - - - +
203B LEU* 3.9 32.1 - - + -
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Residues in contact with SER 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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173B LYS* 4.4 0.7 + - - +
174B ILE 3.8 2.9 - - - -
175B TYR* 3.6 24.3 - - - -
179B GLY 5.1 2.2 + - - -
180B LEU 4.1 0.2 - - - -
181B ILE* 1.3 72.8 - - - +
183B LEU* 1.3 70.9 + - - +
198B GLU* 3.0 43.7 + - - -
199B ASN* 3.3 38.5 + - - +
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Residues in contact with LEU 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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134B LEU* 5.0 2.0 - - + -
140B LEU* 4.2 12.3 - - + -
142B ILE* 4.1 15.9 - - + -
157B LEU* 5.3 1.1 - - + -
173B LYS* 3.4 16.3 - - - +
174B ILE* 2.9 44.4 + - + +
176B VAL* 4.3 18.2 - - + -
181B ILE* 4.3 11.7 - - + -
182B SER* 1.3 83.9 + - - +
184B GLN* 1.3 62.1 + - - +
195B THR* 3.4 27.1 - - + +
196B GLU 3.6 5.2 - - - +
197B VAL* 3.9 32.5 - - + -
198B GLU* 4.0 4.4 - - - +
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLY* 4.0 24.0 + - - +
172B SER 3.5 12.3 - - - +
173B LYS* 3.6 11.8 - - - -
174B ILE 5.1 0.2 - - - +
183B LEU* 1.3 76.2 - - - +
185B VAL* 1.3 66.7 + - - +
186B LYS* 3.2 35.7 + - - +
195B THR* 2.9 12.6 + - - -
196B GLU* 2.9 24.8 + - + +
198B GLU* 3.0 30.7 - - + +
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Residues in contact with VAL 185 (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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168B VAL* 4.5 8.7 - - + -
169B GLU 3.4 24.7 - - - +
170B VAL* 4.0 2.2 - - - -
171B GLY* 3.0 29.1 + - - -
172B SER* 3.2 22.7 + - - +
174B ILE* 4.0 20.7 - - + +
183B LEU 4.4 0.2 - - - -
184B GLN* 1.3 72.0 - - - +
186B LYS* 1.3 62.4 + - - +
187B GLN 4.6 4.9 - - - +
188B LYS* 5.6 2.7 - - + -
193B LEU* 3.8 33.9 - - + -
194B VAL 3.7 4.9 - - - +
195B THR* 3.9 14.6 - - + -
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Residues in contact with LYS 186 (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 THR* 5.8 3.1 - - + -
170B VAL* 3.6 15.1 - - - +
184B GLN* 3.2 43.4 - - - +
185B VAL* 1.3 73.9 - - - +
187B GLN* 1.3 63.3 + - + +
194B VAL* 3.0 10.3 + - + +
195B THR 4.5 0.9 - - - -
196B GLU* 3.4 51.5 + - + +
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Residues in contact with GLN 187 (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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170B VAL* 4.5 2.7 - - - -
185B VAL* 4.6 2.7 - - - +
186B LYS* 1.3 80.9 + - + +
188B LYS* 1.3 66.4 + - - +
192B PHE* 5.3 8.3 - - + -
193B LEU* 3.6 2.1 - - - +
194B VAL* 2.6 64.3 + - + +
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Residues in contact with LYS 188 (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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165B CYS 4.1 11.0 + - - +
166B LYS 5.6 0.2 + - - -
168B VAL* 3.2 28.5 + - + +
169B GLU* 3.4 37.4 + - - +
170B VAL* 4.0 22.8 - - + +
185B VAL* 5.6 3.4 - - + -
187B GLN* 1.3 83.3 - - - +
189B GLY* 1.3 64.3 + - - +
192B PHE* 3.9 6.3 - - - -
193B LEU* 3.8 19.7 - - + -
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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