Contacts of the strand formed by residues 70 - 78 (chain B) in PDB entry 2N0A


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.
For CSU analysis of other PDB entry

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 VAL 70 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  VAL*     4.2     7.2    -      -       +      -
     69A  ALA      3.2     2.4    +      -       -      +
     70A  VAL*     3.2    28.4    -      -       +      +
     71A  VAL      3.2    20.8    +      -       -      -
     64B  THR*     5.4     7.2    -      -       +      -
     66B  VAL*     3.9    23.1    -      -       +      -
     69B  ALA*     1.3    77.9    -      -       -      +
     71B  VAL*     1.3    66.1    +      -       -      +
     72B  THR*     4.0    20.6    -      -       +      -
     70C  VAL*     3.2    33.4    -      -       +      +
     71C  VAL*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  VAL*     5.6     0.2    -      -       -      -
     71A  VAL*     3.3    18.8    -      -       +      +
     92A  THR*     3.0    34.8    -      -       +      +
     70B  VAL*     1.3    78.4    -      -       -      +
     72B  THR*     1.3    69.1    +      -       -      +
     75B  THR*     4.2    18.6    -      -       -      +
     92B  THR*     3.5    18.6    -      -       +      +
     93B  GLY*     3.4    21.5    -      -       -      +
     70C  VAL      3.2     6.5    +      -       -      -
     71C  VAL*     3.3    12.5    -      -       +      +
     72C  THR      3.1    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  VAL      3.1     6.2    +      -       -      +
     72A  THR*     3.1    26.8    -      -       +      +
     73A  GLY      3.2    21.0    +      -       -      +
     61B  GLU*     4.9     8.1    +      -       -      +
     70B  VAL*     4.0    18.8    -      -       +      -
     71B  VAL*     1.3    83.1    -      -       -      +
     73B  GLY*     1.3    60.5    +      -       -      +
     74B  VAL      4.3     0.2    -      -       -      -
     61C  GLU*     5.2     7.6    -      -       -      +
     70C  VAL*     6.2     0.2    -      -       +      -
     72C  THR*     3.1    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLY*     3.3     9.6    -      -       -      -
     71B  VAL*     6.4     0.2    -      -       -      -
     72B  THR*     1.3    75.2    -      -       -      +
     74B  VAL*     1.3    62.0    +      -       -      +
     75B  THR*     5.5     0.2    -      -       -      -
     72C  THR      3.2     7.5    +      -       -      +
     73C  GLY*     3.3     7.1    -      -       -      -
     74C  VAL*     3.1    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLY      3.1     5.9    +      -       -      +
     74A  VAL*     3.3    29.9    -      -       +      +
     75A  THR      3.1    23.2    +      -       -      +
     51B  GLY*     4.7    18.2    -      -       -      -
     52B  VAL      5.2     2.7    -      -       -      +
     53B  ALA*     3.8    27.1    -      -       +      +
     72B  THR      4.3     0.4    +      -       -      -
     73B  GLY*     1.3    73.5    -      -       -      -
     75B  THR*     1.3    71.8    +      -       -      +
     76B  ALA*     5.0     4.5    -      -       +      +
     51C  GLY*     4.8     8.3    -      -       -      +
     53C  ALA*     5.4     0.7    -      -       +      -
     74C  VAL*     3.3    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  THR*     3.3    17.2    -      -       +      +
     90A  ALA*     6.4     0.2    -      -       +      -
     92A  THR*     4.1    22.7    -      -       +      +
     71B  VAL*     4.2    20.1    -      -       -      +
     73B  GLY      5.5     0.2    -      -       -      -
     74B  VAL*     1.3    77.0    +      -       -      +
     76B  ALA*     1.3    64.9    +      -       -      +
     77B  VAL*     4.5    13.5    -      -       +      -
     92B  THR*     4.7    10.5    -      -       +      -
     74C  VAL*     3.1     7.3    +      -       -      +
     75C  THR*     3.3    18.6    +      -       +      +
     76C  ALA      3.1    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  THR      3.1     8.4    +      -       -      +
     76A  ALA*     3.3     6.6    -      -       +      -
     77A  VAL      3.2    19.4    +      -       -      -
     49B  VAL*     3.3    24.6    -      -       +      +
     50B  HIS      5.3     6.3    -      -       -      +
     51B  GLY*     5.4     2.7    -      -       -      -
     74B  VAL*     4.4     7.8    -      -       +      +
     75B  THR*     1.3    75.2    -      -       -      +
     77B  VAL*     1.3    67.8    +      -       -      +
     49C  VAL*     3.9    12.6    -      -       +      -
     51C  GLY*     5.4     3.6    -      -       -      +
     76C  ALA*     3.3    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  THR*     5.5     0.9    -      -       +      +
     77A  VAL*     3.4    29.6    -      -       +      +
     90A  ALA*     3.8    16.4    -      -       +      -
     49B  VAL*     4.7     0.2    -      -       -      -
     75B  THR*     4.5    12.6    -      -       +      -
     76B  ALA*     1.3    84.8    -      -       -      +
     78B  ALA*     1.3    57.6    +      -       -      +
     79B  GLN*     4.3    17.5    -      -       +      +
     90B  ALA*     4.0    14.6    -      -       +      -
     49C  VAL*     3.2    11.3    -      -       -      +
     76C  ALA      3.2     4.0    +      -       -      -
     77C  VAL*     3.4    29.6    -      -       +      -
     78C  ALA      3.1    18.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  VAL      3.1    12.2    +      -       -      +
     78A  ALA*     4.4     2.0    -      -       -      -
     79A  GLN*     2.3    38.9    +      -       -      +
     47B  GLY      3.9     4.0    -      -       -      -
     48B  VAL      3.5    43.1    -      -       -      +
     77B  VAL*     1.3    72.5    -      -       -      +
     79B  GLN*     1.3    59.0    +      -       -      +
     47C  GLY      3.7    10.8    -      -       -      +
     49C  VAL*     4.1     5.4    -      -       +      -
     78C  ALA*     4.1     4.0    -      -       -      -
----------------------------------------------------------
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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
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
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