Contacts of the strand formed by residues 183 - 188 (chain B) in PDB entry 2YD7
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B MET* 4.6 12.8 - - + -
146B LEU* 3.9 25.8 - - + -
147B CYS 3.5 5.2 - - - +
148B ALA* 3.9 23.6 - - + -
178B LEU* 5.0 10.1 - - + -
179B ARG* 3.0 7.7 + - - -
180B SER* 2.7 50.0 + - - +
182B SER* 1.3 75.9 - - - +
184B GLY* 1.3 63.2 + - - +
185B ALA* 4.4 3.4 - - + +
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Residues in contact with GLY 184 (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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147B CYS* 2.6 46.8 + - - +
157B ILE* 3.8 21.2 - - - +
159B TRP* 3.7 7.2 - - - -
178B LEU 3.4 9.0 - - - -
179B ARG* 3.9 5.4 - - - -
183B ILE* 1.3 74.8 - - - +
185B ALA* 1.3 60.1 + - - -
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Residues in contact with ALA 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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144B THR* 4.2 11.9 - - + -
145B MET 3.2 7.2 - - - +
146B LEU* 3.4 26.5 - - + -
159B TRP* 4.1 4.8 + - - -
177B GLN* 3.2 7.6 - - - +
178B LEU* 2.8 48.9 + - + +
183B ILE* 4.3 3.3 - - + +
184B GLY* 1.3 73.6 - - - -
186B LEU* 1.3 60.5 + - - +
187B GLN* 4.1 2.7 - - + +
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Residues in contact with LEU 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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143B ALA 3.5 2.4 - - - +
144B THR* 3.3 3.0 - - - -
145B MET* 2.7 44.1 + - + +
159B TRP* 3.7 32.9 - - + -
166B VAL* 4.1 10.3 - - + -
175B ILE* 3.7 23.1 - - + -
176B LYS 3.6 14.4 - - - +
177B GLN* 3.7 24.7 - - + +
185B ALA* 1.3 72.5 - - - +
187B GLN* 1.3 59.1 + - - +
188B ILE* 4.4 10.6 - - + +
199B TYR* 3.8 35.2 - - + -
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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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142B THR* 3.5 19.6 - - + +
143B ALA 3.5 3.4 - - - -
144B THR* 3.9 23.2 - - + +
174B ARG 3.6 2.3 - - - +
175B ILE* 3.4 5.1 - - - +
176B LYS* 2.8 44.8 + - + +
178B LEU* 4.1 28.6 - - + +
185B ALA* 4.1 4.4 - - + +
186B LEU* 1.3 73.6 - - - +
188B ILE* 1.3 62.0 + - - +
189B GLU* 3.8 11.4 - - + +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.3 2.0 - - - +
143B ALA* 2.7 41.9 + - + +
145B MET* 5.1 5.2 - - + -
174B ARG* 3.8 6.7 - - - +
175B ILE* 4.3 23.8 - - + -
186B LEU* 4.4 11.2 - - + +
187B GLN* 1.3 74.1 - - - +
189B GLU* 1.3 67.1 + - - +
191B SER* 3.4 8.5 + - - +
195B ASP* 3.3 33.4 - - + +
199B TYR* 3.5 35.7 - - + +
217B LEU* 3.8 18.4 - - + -
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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