Contacts of the strand formed by residues 361 - 367 (chain A) 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 GLU 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LYS* 4.9 5.7 - - - +
251A HIS* 5.1 5.2 + - - -
285A ILE* 3.5 22.2 - - + +
286A HIS 3.2 13.9 - - - +
287A ASP* 3.8 18.1 - - - +
288A VAL* 4.2 4.1 - - - +
355A GLU* 3.9 2.9 - - - +
356A SER* 3.0 35.4 + - - +
360A LYS* 1.3 111.3 + - + +
362A VAL* 1.3 69.7 + - - +
363A TYR* 3.5 25.9 + - + -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.3 12.8 - - + -
284A GLY 3.7 0.7 - - - +
285A ILE* 3.6 2.3 - - - -
286A HIS* 2.8 59.1 + - + +
288A VAL* 4.6 7.4 - - + -
344A PRO* 4.9 12.3 - - + -
345A SER* 4.7 7.0 - - - +
353A SER* 4.0 24.5 - - - -
354A HIS 3.3 13.0 - - - +
355A GLU* 4.9 5.8 - - + +
361A GLU* 1.3 79.8 - - - +
363A TYR* 1.3 66.1 + - - +
364A PHE* 4.0 13.9 - - + -
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Residues in contact with TYR 363 (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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249A LYS 4.2 1.9 + - - -
250A LEU* 3.5 39.6 - - + -
251A HIS* 3.0 59.7 + - - -
252A VAL* 3.8 11.2 - - + -
283A VAL* 5.8 1.6 - - + -
284A GLY 3.3 3.8 - - - +
285A ILE* 4.1 16.6 - - + -
352A LYS 3.6 0.7 - - - +
353A SER* 3.0 7.8 - - - -
354A HIS* 2.8 48.5 + - + +
356A SER* 3.8 16.4 - - - -
361A GLU* 3.5 26.3 + - + -
362A VAL* 1.3 76.4 - - - +
364A PHE* 1.3 61.4 + - - +
365A MET* 4.0 14.6 - - + -
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Residues in contact with PHE 364 (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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204A VAL* 3.8 21.5 - - - +
205A PHE* 3.7 18.8 - + + -
206A SER* 3.3 36.3 - - - -
209A LEU* 4.1 13.9 - - + -
210A THR 4.9 0.7 - - - -
211A VAL* 3.7 29.6 - - + -
282A LEU 3.2 6.6 - - - +
283A VAL* 3.3 0.9 - - - -
284A GLY 2.7 48.3 + - - +
286A HIS* 3.9 21.3 - + + -
345A SER* 5.3 0.7 - - - -
350A ALA* 5.3 0.9 - - + -
352A LYS 3.7 4.3 - - - -
353A SER* 3.9 25.1 - - - -
362A VAL* 4.0 16.4 - - + -
363A TYR* 1.3 77.2 - - - +
365A MET* 1.3 60.3 + - - +
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Residues in contact with MET 365 (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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179A LEU* 3.9 16.5 - - - +
204A VAL* 4.1 1.5 - - - +
250A LEU* 4.2 20.4 - - - -
252A VAL* 4.3 5.6 - - + -
260A PHE* 4.3 24.1 - - + -
281A LEU* 4.3 11.4 - - + -
282A LEU 3.1 6.1 - - - +
283A VAL* 4.0 22.9 - - + -
352A LYS* 3.3 22.0 + - - +
354A HIS* 2.8 43.7 - - + +
363A TYR* 4.0 13.4 - - + +
364A PHE* 1.3 82.2 - - - +
366A ALA* 1.3 64.0 + - - +
414A ILE* 5.2 3.1 - - - -
415A LEU* 4.7 7.9 - - + -
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Residues in contact with ALA 366 (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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179A LEU* 3.3 19.5 - - - +
180A LEU 5.7 0.2 - - - -
181A PRO* 6.3 0.2 - - + -
204A VAL* 3.7 14.9 - - + +
281A LEU* 3.9 8.1 - - - +
282A LEU* 2.8 33.8 + - - +
352A LYS* 3.3 33.0 - - + +
365A MET* 1.3 74.3 - - - +
367A ILE* 1.3 62.1 + - - +
368A ILE* 4.3 0.6 - - + +
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Residues in contact with ILE 367 (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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179A LEU* 2.7 25.7 + - + +
180A LEU* 3.8 16.6 - - + -
181A PRO* 3.5 12.7 - - + +
264A LEU* 4.4 4.0 - - + -
267A ASP* 3.6 35.2 - - + +
268A VAL* 4.1 17.9 - - + -
271A LEU* 4.1 12.8 - - + -
279A TYR* 3.9 25.1 - - + -
280A SER 3.3 11.0 - - - +
281A LEU* 4.2 5.2 - - + +
366A ALA* 1.3 72.2 - - - +
368A ILE* 1.3 75.7 + - - +
370A ILE* 5.4 1.8 - - + +
407A PHE* 3.9 17.0 - - + -
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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