Contacts of the strand formed by residues 281 - 287 (chain B) in PDB entry 1BO1
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 LEU 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B LEU* 4.5 7.2 - - + -
216B ASP* 3.7 1.7 - - - -
217B LEU* 2.8 39.8 + - + +
260B PHE* 4.4 19.1 - - + -
264B LEU* 4.9 0.9 - - + -
280B SER* 1.3 73.7 - - - +
282B LEU* 1.3 65.3 + - - +
283B VAL* 3.5 29.2 + - + +
365B MET* 4.4 11.0 - - + -
366B ALA* 3.7 25.8 - - - +
367B ILE* 4.2 2.0 - - + +
407B PHE* 3.3 26.2 - - + -
411B MET* 4.0 22.9 - - + -
414B ILE* 4.4 6.7 - - + -
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Residues in contact with LEU 282 (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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204B VAL* 3.6 27.8 - - + -
205B PHE* 3.5 39.0 - - + -
214B LYS* 4.0 11.4 - - + -
215B TYR 3.1 19.7 - - - +
216B ASP* 5.0 8.1 - - + +
237B THR* 5.6 1.1 - - + -
280B SER 4.0 1.4 + - - -
281B LEU* 1.3 72.6 - - - +
283B VAL* 1.3 66.3 + - - +
364B PHE 3.2 12.8 - - - +
365B MET* 3.3 15.9 - - - +
366B ALA 3.1 15.0 + - - +
368B ILE* 4.5 19.6 - - + +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 4.1 3.4 - - - -
213B ARG 3.7 0.2 - - - +
214B LYS* 3.2 8.0 - - - +
215B TYR* 2.8 61.8 + - + -
217B LEU* 3.6 18.6 - - + -
243B PHE* 4.8 8.7 - - + -
250B LEU* 4.9 9.0 - - + -
281B LEU* 3.5 26.9 - - + +
282B LEU* 1.3 80.5 - - - +
284B GLY* 1.3 63.0 + - - +
285B ILE* 4.4 11.9 - - + -
363B TYR* 5.9 0.9 - - + -
364B PHE 3.4 2.5 - - - -
365B MET* 4.2 13.9 - - + -
414B ILE* 5.5 1.1 - - + -
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Residues in contact with GLY 284 (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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205B PHE* 3.7 18.9 - - - -
211B VAL* 3.8 9.4 - - - -
213B ARG 3.6 3.1 - - - -
283B VAL* 1.3 75.9 - - - +
285B ILE* 1.3 63.2 + - - +
363B TYR* 3.4 6.4 - - - +
364B PHE* 2.9 43.9 + - - -
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Residues in contact with ILE 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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211B VAL* 3.4 3.2 - - - +
212B HIS* 2.6 35.5 + - + -
213B ARG* 2.8 32.6 + - + +
215B TYR* 3.5 18.2 - - + -
248B GLN* 3.5 26.5 - - - +
249B LYS 5.5 1.6 - - - +
250B LEU* 5.0 6.3 - - + -
283B VAL* 4.4 9.9 - - + -
284B GLY* 1.3 78.1 - - - +
286B HIS* 1.3 60.7 + - - +
287B ASP* 4.6 2.0 - - + +
361B GLU* 3.5 30.7 - - + +
362B VAL 3.8 4.0 - - - +
363B TYR* 4.5 13.7 - - + -
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Residues in contact with HIS 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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209B LEU* 3.9 15.3 - - + +
210B THR* 2.7 44.8 + - - +
212B HIS* 3.8 9.6 - - - -
285B ILE* 1.3 74.5 - - - +
287B ASP* 1.3 58.4 + - - +
288B VAL* 3.5 12.2 + - + +
291B ALA* 3.5 25.0 - - + +
343B ASP* 3.6 27.1 - - - -
361B GLU* 3.3 10.5 - - - -
362B VAL* 3.1 50.1 + - + +
364B PHE* 4.1 13.5 - - + -
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Residues in contact with ASP 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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212B HIS* 2.8 39.7 + - + +
285B ILE* 4.1 2.7 - - + +
286B HIS* 1.3 71.1 - - - +
288B VAL* 1.3 63.6 + - - +
289B ASP* 3.2 13.3 + - - +
290B ARG* 3.1 28.2 + - + +
291B ALA* 3.0 8.7 + - - +
360B LYS 4.0 7.9 - - - +
361B GLU* 4.1 17.8 - - - +
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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