Contacts of the strand formed by residues 49 - 57 (chain D) in PDB entry 3B13


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 LYS 49 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  GLN*     5.0     4.7    -      -       -      +
     45D  MET*     3.3     3.8    -      -       -      +
     46D  VAL*     2.9    34.8    +      -       -      +
     47D  ASP*     3.8     8.7    -      -       +      +
     48D  GLY*     1.3    83.0    -      -       -      +
     50D  PRO*     1.3    70.5    -      -       +      +
     51D  VAL*     3.8     6.3    +      -       +      +
    177D  LEU*     4.2    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1368C  TYR*     3.5    33.2    -      -       +      +
      1D  MET*     3.8    20.6    -      -       +      -
      2D  GLN*     3.3    17.7    +      -       -      +
     44D  VAL      3.5     7.0    -      -       -      +
     45D  MET*     3.9    13.0    -      -       +      -
     48D  GLY      3.8     6.7    -      -       -      +
     49D  LYS*     1.3    82.3    -      -       +      +
     51D  VAL*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET*     4.1     6.9    -      -       -      +
      2D  GLN*     3.1    19.1    -      -       +      +
      4D  ILE*     4.1    13.2    -      -       +      -
     42D  ALA      3.6     0.5    -      -       -      +
     43D  ASN*     3.4     4.0    -      -       -      +
     44D  VAL*     2.8    56.7    +      -       +      +
     46D  VAL*     5.5     0.4    -      -       +      -
     49D  LYS      3.8    11.0    -      -       -      +
     50D  PRO*     1.3    81.4    -      -       -      +
     52D  ASN*     1.3    59.5    +      -       -      +
     53D  LEU*     4.2     8.7    -      -       +      +
    173D  ILE*     3.6    34.8    -      -       +      -
    177D  LEU*     4.5    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 52 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1526C  PRO*     4.1    21.7    -      -       -      +
      1D  MET*     4.1    14.4    -      -       +      -
      2D  GLN      3.0     8.7    +      -       -      +
      3D  ALA*     3.5    10.1    -      -       +      +
      4D  ILE      2.9    27.2    +      -       -      +
     41D  SER*     3.3    24.7    +      -       -      -
     42D  ALA      3.3     5.7    +      -       -      -
     43D  ASN*     2.9    27.8    +      -       -      +
     51D  VAL*     1.3    71.7    -      -       -      +
     53D  LEU*     1.3    60.9    +      -       -      +
     54D  GLY*     3.7     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 53 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  ILE*     3.4    34.8    -      -       +      +
      6D  CYS*     3.9    17.9    -      -       +      -
     23D  TYR*     4.3    10.3    -      -       +      +
     41D  SER*     3.4     3.3    +      -       -      -
     42D  ALA*     2.9    42.2    +      -       +      +
     44D  VAL*     5.0     1.1    -      -       +      -
     51D  VAL*     3.8    10.5    -      -       +      -
     52D  ASN*     1.3    73.1    -      -       -      +
     54D  GLY*     1.3    59.7    +      -       -      +
     55D  LEU*     3.9    30.6    +      -       +      +
     77D  VAL*     5.5     1.3    -      -       +      -
    169D  PHE*     4.2    18.6    -      -       +      -
    172D  ALA*     5.5     2.5    -      -       +      -
    173D  ILE*     4.1    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 54 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1529C  MET*     3.7    19.5    -      -       -      -
      4D  ILE      2.9    10.5    +      -       -      +
      5D  LYS*     3.9     1.6    -      -       -      -
      6D  CYS*     2.9    31.2    +      -       -      +
     40D  TYR      3.7     2.0    -      -       -      -
     41D  SER*     4.5     3.1    -      -       -      -
     52D  ASN*     3.7     6.1    +      -       -      -
     53D  LEU*     1.3    73.4    -      -       -      +
     55D  LEU*     1.3    61.1    +      -       -      -
     56D  TRP*     4.0     4.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1529C  MET*     3.5     1.1    -      -       -      -
      6D  CYS*     3.4    36.3    -      -       +      +
      8D  VAL*     4.7     3.1    -      -       +      -
     20D  LEU*     4.1    27.2    -      -       +      +
     23D  TYR*     4.3     1.3    -      -       +      -
     24D  THR*     3.8    28.5    -      -       +      -
     39D  ASN*     3.1    24.3    -      -       -      +
     40D  TYR*     2.7    19.9    +      -       +      +
     53D  LEU*     4.1    24.0    -      -       +      +
     54D  GLY*     1.3    73.2    -      -       -      +
     56D  TRP*     1.3    62.9    +      -       -      +
     57D  ASP      3.7     0.3    +      -       -      -
    169D  PHE*     4.0    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 56 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1525C  ASN*     3.7    13.1    +      -       -      +
   1528C  SER*     3.6    23.1    -      -       -      -
   1529C  MET*     3.4    46.9    -      -       +      +
   1532C  ASN*     4.6     7.2    -      -       +      -
   1595C  LEU*     5.4     1.3    -      -       +      -
   1598C  PHE*     3.7    29.6    -      +       -      -
      5D  LYS*     3.4    49.5    -      -       +      +
      6D  CYS      2.9    16.2    +      -       -      +
      7D  VAL*     4.0    13.3    -      -       +      +
      8D  VAL*     2.8    34.0    +      -       -      +
     20D  LEU*     4.7     0.2    -      -       -      -
     39D  ASN*     3.6    10.5    -      -       -      -
     54D  GLY*     4.0     6.3    +      -       -      -
     55D  LEU*     1.3    72.1    -      -       -      +
     57D  ASP*     1.3    60.6    +      -       -      +
     58D  THR*     3.6     3.3    +      -       +      -
     71D  SER*     4.0    24.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 57 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1539C  VAL*     3.2    35.3    -      -       -      +
      8D  VAL*     4.3     2.2    -      -       -      +
     16D  LYS*     3.4    28.6    -      -       -      +
     17D  ASN*     3.7    20.7    -      -       -      +
     20D  LEU*     3.4    26.0    -      -       +      +
     38D  ASP*     4.4     7.7    -      -       +      +
     39D  ASN*     3.0    27.9    +      -       -      +
     40D  TYR*     4.7     1.9    -      -       +      -
     55D  LEU      3.7     1.2    +      -       -      -
     56D  TRP*     1.3    71.4    -      -       -      +
     58D  THR*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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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