Contacts of the strand formed by residues 214 - 220 (chain B) in PDB entry 1U5Y
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 ASP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B VAL 3.6 0.9 - - - +
147B ARG* 3.3 3.3 - - - -
148B VAL* 2.8 40.6 + - + +
175B ARG* 2.8 37.5 + - + -
176B GLU 3.2 4.3 - - - +
177B GLY* 3.4 20.3 - - - -
178B GLN* 4.3 4.9 + - - +
210B LEU* 3.8 1.9 - - - -
211B HIS* 2.9 47.5 + - - +
212B GLN 4.8 0.2 - - - +
213B GLY* 1.3 80.3 - - - +
215B ILE* 1.3 61.5 + - - +
216B ILE* 4.8 1.3 - - + -
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Residues in contact with ILE 215 (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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145B ILE* 3.1 50.7 - - + -
146B VAL 3.3 3.6 - - - +
147B ARG* 4.1 24.7 - - + -
175B ARG* 3.0 7.1 - - - -
176B GLU* 2.9 47.5 + - + +
213B GLY 3.8 8.7 + - - +
214B ASP* 1.3 75.3 - - - +
216B ILE* 1.3 58.1 + - - +
217B THR* 4.1 7.9 + - + +
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Residues in contact with ILE 216 (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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129B TRP* 5.9 0.5 - - - -
144B ASP 4.6 0.2 - - - +
145B ILE* 3.4 5.4 - - - -
146B VAL* 2.7 40.3 + - + +
148B VAL* 4.0 14.8 - - + -
156B LEU* 4.2 13.0 - - + -
173B VAL* 4.2 11.0 - - + -
174B SER 3.2 6.5 - - - +
175B ARG* 3.6 26.7 - - + -
184B LEU* 4.3 4.7 - - + -
210B LEU* 3.8 27.4 - - + -
214B ASP* 4.8 1.1 - - + -
215B ILE* 1.3 73.2 - - - +
217B THR* 1.3 64.4 + - - +
218B VAL* 4.3 0.6 + - + -
236B LEU* 5.2 7.6 - - + +
238B PHE* 3.8 35.7 - - + -
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Residues in contact with THR 217 (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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126B GLU* 4.0 2.9 - - - +
144B ASP 4.7 1.3 - - - -
145B ILE* 3.2 31.9 - - + -
172B VAL 3.4 0.9 - - - +
173B VAL* 3.2 5.9 - - - +
174B SER* 2.8 57.4 + - - +
175B ARG 5.9 0.3 - - - -
176B GLU* 6.2 1.8 - - + +
181B ARG* 4.6 1.9 + - - -
215B ILE* 4.2 9.0 - - + +
216B ILE* 1.3 73.2 - - - +
218B VAL* 1.3 63.5 + - - +
219B LYS* 3.7 33.5 - - - +
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Residues in contact with VAL 218 (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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125B THR 4.3 0.2 - - - +
126B GLU* 3.4 19.4 - - - +
127B VAL* 3.9 11.6 + - + +
129B TRP* 4.0 26.0 - - + +
144B ASP 4.9 3.4 + - - -
158B SER* 4.1 6.1 - - - +
160B VAL* 4.6 7.2 - - + -
171B GLN* 3.9 30.7 - - + -
172B VAL 3.2 4.3 - - - +
173B VAL* 4.0 10.1 - - + -
216B ILE* 4.3 0.6 + - + -
217B THR* 1.3 77.0 - - - +
219B LYS* 1.3 61.3 + - - +
220B ILE* 4.9 4.7 - - + -
236B LEU* 3.8 41.1 - - + -
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Residues in contact with LYS 219 (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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124B VAL* 4.8 24.0 - - + +
125B THR 3.5 7.2 - - - +
126B GLU* 3.4 30.1 + - + +
171B GLN* 3.4 1.9 - - - -
172B VAL* 2.8 47.2 + - + +
181B ARG* 3.7 37.8 - - - +
217B THR* 3.7 29.3 - - - +
218B VAL* 1.3 77.5 - - - +
220B ILE* 1.3 69.7 + - - +
221B PRO* 4.0 0.9 - - + -
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Residues in contact with ILE 220 (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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124B VAL* 3.4 2.1 - - - +
125B THR* 2.9 44.4 + - - +
127B VAL* 4.6 10.3 - - + -
160B VAL* 4.7 5.6 - - + -
162B PHE* 4.0 21.1 - - + -
169B MET* 4.4 16.4 - - - -
170B GLY 3.9 10.1 - - - +
171B GLN* 4.2 12.3 - - + -
218B VAL* 4.9 2.0 - - + -
219B LYS* 1.3 79.5 - - - +
221B PRO* 1.3 66.9 - - + +
222B ARG* 2.9 14.1 + - + +
225B ALA* 3.6 23.1 - - + -
227B LEU* 3.9 27.1 - - + -
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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