Contacts of the strand formed by residues 284 - 291 (chain B) in PDB entry 2OT7
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 ASN 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B TYR 4.6 1.4 - - - +
178B PHE* 3.3 9.5 - - - +
179B GLY* 3.0 35.7 + - - +
200B LEU* 3.7 14.5 - - + +
202B PHE* 3.3 18.6 - - - +
203B GLY* 3.9 1.8 - - - -
204B GLU 2.8 30.5 + - - +
205B PRO 3.5 9.9 + - - -
206B LYS* 4.2 3.3 + - - +
280B ASN* 3.0 25.6 + - - +
282B GLY 3.1 6.9 + - - -
283B PHE* 1.3 79.6 - - - +
285B CYS* 1.3 64.5 + - - +
286B ALA 5.1 0.3 + - - -
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Residues in contact with CYS 285 (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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140B LEU* 3.7 27.4 - - - -
176B LEU* 4.5 3.4 - - - -
177B TYR 3.2 6.3 - - - -
178B PHE* 3.4 30.1 - - + -
200B LEU* 3.6 4.5 - - - +
201B HIS* 2.7 37.3 + - - +
202B PHE* 3.1 34.8 + - + -
284B ASN* 1.3 76.3 - - - +
286B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 286 (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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176B LEU* 3.3 7.3 - - - +
177B TYR* 2.9 40.0 + - + +
198B ASN* 3.6 22.7 - - - +
199B TYR 3.1 11.2 - - - +
200B LEU* 4.2 6.3 - - + -
201B HIS* 4.4 2.9 - - - -
206B LYS* 3.8 23.1 - - - +
284B ASN* 5.1 0.8 + - - +
285B CYS* 1.3 75.3 - - - +
287B GLU* 1.3 62.8 + - - +
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Residues in contact with GLU 287 (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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138B GLY 4.4 0.2 - - - -
139B THR* 2.8 34.7 + - - -
140B LEU 2.9 16.5 + - - -
141B TYR* 3.5 14.0 - - - -
150B ILE* 3.3 25.9 - - + +
151B GLY 4.7 0.2 + - - -
174B PRO* 3.7 11.5 - - + +
175B TYR 3.2 11.4 - - - +
176B LEU* 3.5 5.8 - - + +
198B ASN* 3.4 3.9 - - - -
199B TYR 2.8 30.8 + - - +
201B HIS* 2.7 38.2 + - + +
286B ALA* 1.3 74.9 - - - +
288B SER* 1.3 61.8 + - - +
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Residues in contact with SER 288 (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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150B ILE* 3.8 5.2 - - - -
170B GLY 4.3 1.2 - - - +
173B THR 4.1 0.3 - - - +
174B PRO* 3.6 1.4 - - - +
175B TYR* 2.9 34.9 + - - +
177B TYR* 3.7 22.4 - - - -
196B SER* 4.4 0.5 - - - -
197B ILE 2.7 18.8 + - - -
198B ASN* 4.0 9.2 - - - -
287B GLU* 1.3 75.0 - - - +
289B THR* 1.3 61.9 + - - +
500B OGA 3.2 18.3 + - - -
9D MLZ 3.7 16.0 - - - -
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Residues in contact with THR 289 (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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150B ILE* 3.4 33.4 - - + +
153B LEU* 4.0 15.0 - - + -
170B GLY 3.4 7.1 + - - -
171B VAL 3.1 16.5 + - - +
172B ASN* 4.1 1.8 - - - -
173B THR 2.6 28.6 + - - -
196B SER* 3.4 5.5 - - - -
197B ILE* 3.0 28.4 + - + +
288B SER* 1.3 76.6 + - - +
290B ASN* 1.3 69.6 + - - +
9D MLZ 3.6 7.6 - - - -
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Residues in contact with ASN 290 (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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153B LEU* 4.7 0.3 - - - +
157B LEU* 3.5 6.5 - - + +
170B GLY 3.8 0.4 + - - -
171B VAL* 3.2 39.7 + - - +
172B ASN* 5.2 0.7 - - - -
190B GLU* 2.8 38.0 + - - +
191B ASP* 4.9 4.7 + - - +
194B LEU* 4.1 21.9 - - + +
195B TYR 2.8 20.0 + - - +
196B SER* 3.6 3.8 - - - -
289B THR* 1.3 91.7 + - - +
291B PHE* 1.3 65.9 - - - +
9D MLZ 3.5 14.3 - - - -
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Residues in contact with PHE 291 (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 PHE* 3.8 38.4 - + - -
31B ILE* 4.1 15.5 - - + -
153B LEU* 4.2 13.7 - - + -
155B THR* 3.5 18.6 - - + +
157B LEU* 3.5 9.0 - - - -
194B LEU* 3.2 9.6 - - - +
195B TYR* 3.1 67.0 + + + +
196B SER 3.5 24.9 - - - -
197B ILE* 3.9 5.4 - - + -
269B ILE* 4.1 13.0 - - + -
290B ASN* 1.3 80.4 - - - +
292B ALA* 1.3 71.0 + - - +
293B THR* 4.7 2.0 - - + -
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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