Contacts of the strand formed by residues 287 - 294 (chain B) in PDB entry 2P80
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 ALA 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.2 6.5 - - - +
247B GLN 3.3 17.4 + - - +
267B THR* 5.2 6.3 - - - +
283B ILE* 2.9 22.4 - - + +
284B PRO* 3.1 25.0 + - + +
286B GLY* 1.3 82.8 - - - +
288B ALA* 1.3 63.0 + - - +
279C GLU* 3.5 18.8 - - + +
280C THR* 4.0 13.0 - - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 2.9 28.2 - - + +
132B PHE 4.1 14.1 - - - -
133B VAL* 3.8 8.0 - - + +
153B ALA* 4.2 5.8 - - + -
244B VAL* 4.7 1.6 - - + -
245B HIS 3.2 8.5 - - - +
246B SER* 3.4 24.9 - - - +
266B ALA 5.0 0.4 - - - -
267B THR 3.9 2.5 - - - +
268B GLY* 3.1 11.1 + - - -
283B ILE* 4.3 2.2 - - - -
287B ALA* 1.3 74.1 - - - +
289B GLY* 1.3 60.2 + - - +
279C GLU* 3.2 7.7 + - - -
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Residues in contact with GLY 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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131B VAL* 3.3 11.5 - - - +
244B VAL* 3.4 3.8 - - - +
245B HIS* 2.9 27.1 + - - -
265B TRP 3.5 13.5 - - - -
266B ALA* 3.9 8.3 - - - -
268B GLY* 3.7 5.2 - - - -
283B ILE* 3.7 15.8 - - - +
288B ALA* 1.3 73.7 - - - +
290B ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 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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131B VAL* 4.4 10.5 - - + -
242B LEU* 4.1 18.6 - - + -
243B ILE 3.7 8.1 - - - -
244B VAL* 4.2 14.1 - - + -
264B VAL* 3.4 6.4 - - - +
265B TRP* 2.9 48.0 + - + +
270B PHE* 5.3 5.8 - - + -
283B ILE* 5.1 0.6 - - - +
289B GLY* 1.3 75.8 - - - +
291B ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 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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241B VAL 3.6 1.2 - - - +
242B LEU* 3.3 4.5 - - - -
243B ILE* 2.9 44.0 + - + +
261B GLY* 4.6 6.7 - - - -
263B TYR 3.5 5.2 - - - -
264B VAL* 3.5 24.9 - - + -
281B TRP* 4.2 17.0 - - + +
290B ALA* 1.3 74.5 - - - +
292B PHE* 1.3 61.7 + - - +
293B TYR* 4.2 1.3 + - + -
303B TYR* 6.3 2.0 - - + -
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Residues in contact with PHE 292 (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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162B LEU* 6.0 1.1 - - + -
170B LEU* 4.6 18.2 - - + -
171B THR 3.5 13.5 - - - -
172B TYR* 3.1 42.0 - + + -
240B LYS* 2.7 47.1 - - + -
241B VAL 3.5 4.3 - - - -
242B LEU* 3.8 19.7 - - + +
262B ASP* 3.1 28.1 + - + +
263B TYR* 2.9 27.3 + + + +
265B TRP* 4.2 11.0 - + + -
291B ALA* 1.3 74.2 - - - +
293B TYR* 1.3 66.8 + - - +
294B THR* 3.8 11.7 - - - -
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Residues in contact with TYR 293 (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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103A THR* 3.5 28.1 + - - +
128A LYS* 5.2 4.7 - - - -
239B GLU 3.7 2.1 - - - +
241B VAL* 3.2 27.1 + - - +
243B ILE* 6.2 3.4 - - + -
256B LEU* 4.2 19.7 - - + -
259B GLY* 4.3 4.1 - - - -
260B HIS* 2.7 42.4 - - + +
261B GLY* 4.4 2.2 - - - -
262B ASP* 3.1 33.9 - - - +
291B ALA* 4.2 1.3 + - + -
292B PHE* 1.3 82.8 - - - +
294B THR* 1.3 83.8 + - - +
295B PHE* 3.4 32.6 + + + -
296B GLN* 3.6 12.2 + - + +
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Residues in contact with THR 294 (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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238B GLY* 4.0 18.8 - - - +
239B GLU 3.3 11.0 - - - +
240B LYS* 3.9 11.1 - - + +
262B ASP* 3.1 13.6 + - - +
292B PHE* 3.8 15.4 - - - -
293B TYR* 1.3 89.8 - - - +
295B PHE* 1.3 70.5 + - - +
296B GLN* 3.4 25.8 + - - +
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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