Contacts of the strand formed by residues 284 - 291 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TYR 4.6 1.6 - - - +
178A PHE* 3.3 8.5 - - - +
179A GLY* 3.0 40.4 + - - +
200A LEU* 4.0 13.5 - - + +
202A PHE* 3.1 21.1 - - - +
203A GLY* 3.8 1.1 - - - -
204A GLU 2.8 28.1 + - - +
205A PRO 3.4 11.9 + - - -
206A LYS* 4.8 2.4 + - - -
280A ASN* 3.3 25.8 + - - +
282A GLY 3.0 10.5 + - - -
283A PHE* 1.3 79.4 - - - +
285A CYS* 1.3 64.3 + - - +
286A ALA 5.0 0.3 + - - -
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.7 26.0 - - - -
176A LEU* 4.5 3.8 - - - -
177A TYR 3.3 6.1 - - - -
178A PHE* 3.4 29.4 - - + -
200A LEU* 3.8 4.4 - - - +
201A HIS* 2.9 34.0 + - - +
202A PHE* 2.9 39.8 + - + +
284A ASN* 1.3 74.7 - - - +
286A ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.3 5.4 - - - +
177A TYR* 2.8 45.7 + - + +
198A ASN* 3.6 27.6 - - - +
199A TYR 3.3 6.5 - - - +
200A LEU* 3.9 6.1 - - + -
201A HIS* 4.3 3.4 - - - -
206A LYS* 3.8 23.8 - - - +
284A ASN* 5.0 0.6 + - - +
285A CYS* 1.3 74.3 - - - +
287A GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY 4.3 0.2 - - - -
139A THR* 2.6 33.7 + - - -
140A LEU 2.8 24.1 + - - -
141A TYR* 3.6 11.1 - - - -
150A ILE* 3.4 28.0 - - + +
151A GLY 4.5 0.2 + - - -
174A PRO* 3.5 13.9 - - + +
175A TYR 3.3 10.5 - - - +
176A LEU* 3.6 6.4 - - + +
198A ASN* 3.3 5.0 - - - -
199A TYR* 2.9 33.2 + - + +
201A HIS* 2.9 30.6 + - + +
286A ALA* 1.3 73.2 - - - +
288A SER* 1.3 64.1 + - - +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.8 4.9 - - - -
170A GLY 4.3 1.4 - - - +
173A THR 4.2 0.2 - - - +
174A PRO* 3.5 2.1 - - - +
175A TYR* 2.9 33.8 + - - +
177A TYR* 3.6 24.2 - - - -
196A SER* 4.7 0.2 - - - -
197A ILE 2.7 18.8 + - - -
198A ASN* 4.0 7.2 - - - -
287A GLU* 1.3 76.8 - - - +
289A THR* 1.3 63.1 + - - +
500A OGA 3.1 19.0 + - - -
9C MLZ 3.7 15.3 - - - -
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.6 33.0 - - + +
153A LEU* 3.8 16.6 - - + -
170A GLY 3.3 7.7 + - - -
171A VAL 3.2 10.2 + - - -
172A ASN* 4.2 1.5 - - - -
173A THR* 2.7 28.0 + - - -
196A SER* 3.4 4.3 - - - -
197A ILE* 3.0 29.2 + - + +
288A SER* 1.3 75.5 + - - +
290A ASN* 1.3 74.4 + - - +
9C MLZ 3.7 7.4 - - - -
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Residues in contact with ASN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.7 0.3 - - - +
157A LEU* 3.5 5.6 - - + +
170A GLY 3.9 0.2 + - - -
171A VAL* 3.3 45.0 + - - +
172A ASN* 5.2 0.5 - - - -
190A GLU* 2.9 37.4 + - - +
191A ASP* 4.9 3.8 + - - +
194A LEU* 3.8 23.6 - - + +
195A TYR 3.1 17.6 + - - +
196A SER* 3.7 0.8 - - - -
289A THR* 1.3 91.4 + - - +
291A PHE* 1.3 64.5 + - - +
9C MLZ 3.2 16.1 - - - +
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.8 39.3 - + - -
31A ILE* 4.0 14.8 - - + -
153A LEU* 4.2 7.9 - - + -
155A THR* 3.6 19.3 - - + +
157A LEU* 3.8 8.5 - - - -
194A LEU* 3.6 9.4 - - - +
195A TYR* 3.1 68.2 + + + +
196A SER 3.5 23.8 - - - -
197A ILE* 3.9 11.9 - - + -
269A ILE* 4.1 14.8 - - + -
290A ASN* 1.3 79.9 - - - +
292A ALA* 1.3 71.4 + - - +
293A THR* 4.5 3.8 - - + -
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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