Contacts of the strand formed by residues 332 - 336 (chain A) in PDB entry 2B7O
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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A VAL* 3.4 10.1 - - + +
305A VAL* 4.2 7.2 - - + -
319A TYR* 4.1 4.3 - - + +
320A VAL* 3.8 42.8 - - + +
323A LEU* 3.9 32.1 - - + +
324A ASP* 4.4 16.9 - - + +
328A LYS 4.8 0.4 + - - -
330A GLY 4.3 4.6 - - - +
331A ARG* 1.3 80.5 - - - +
333A THR* 1.3 77.4 + - - +
334A LEU* 3.9 21.5 - - + -
360A GLN 5.6 0.2 + - - -
361A VAL* 3.3 17.9 - - + +
362A ILE* 3.0 21.5 + - - +
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Residues in contact with THR 333 (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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71A LEU* 5.2 3.6 - - - +
81A LEU* 4.6 6.2 - - + +
303A VAL 2.9 13.4 + - - -
304A GLY* 3.2 6.4 - - - -
305A VAL 3.0 25.1 + - - -
330A GLY 4.8 2.3 + - - -
332A LEU* 1.3 79.6 - - - +
334A LEU* 1.3 65.2 + - - +
335A VAL* 3.8 4.9 + - + -
362A ILE* 3.4 37.2 - - + +
364A GLN* 3.4 39.7 - - + +
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Residues in contact with LEU 334 (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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305A VAL* 3.8 13.2 - - + -
307A LEU* 3.8 28.0 - - + -
311A MSE 5.8 0.2 - - + -
316A ALA* 4.7 4.3 - - + +
319A TYR* 4.6 9.0 - - + -
320A VAL* 4.3 5.4 - - + -
332A LEU* 3.9 24.4 - - + -
333A THR* 1.3 79.2 - - - +
335A VAL* 1.3 62.2 + - - +
336A SER* 3.7 1.5 + - - -
354A VAL* 4.1 16.4 - - + -
361A VAL* 4.1 18.2 - - + -
362A ILE 2.9 8.4 + - - +
363A TRP* 3.7 39.7 - - + -
364A GLN 3.1 23.4 + - - +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TRP* 5.4 2.7 - - + -
304A GLY* 4.7 4.9 - - - -
305A VAL 2.9 19.7 + - - +
306A LYS* 3.5 29.3 - - + -
307A LEU* 2.7 32.0 + - - +
333A THR* 4.1 10.1 - - + +
334A LEU* 1.3 74.6 - - - +
336A SER* 1.3 59.1 + - - +
337A ARG* 3.5 1.6 + - - +
364A GLN* 3.3 32.8 - - - +
366A ASP* 3.5 30.5 - - + +
409A HIS* 4.3 9.2 - - + -
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Residues in contact with SER 336 (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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307A LEU* 3.7 10.5 - - - +
334A LEU 3.7 2.5 + - - -
335A VAL* 1.3 71.3 - - - +
337A ARG* 1.3 58.5 + - - +
338A MSE 3.5 21.4 - - - +
343A VAL* 3.9 5.5 - - - +
347A LEU* 3.9 33.5 - - - +
363A TRP* 5.9 2.5 - - - -
364A GLN 2.8 14.6 + - - -
365A CYS* 3.8 1.9 - - - +
366A ASP 2.8 29.3 + - - +
390A GLU* 4.1 3.6 + - - +
394A PHE* 4.4 8.8 - - - -
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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