Contacts of the strand formed by residues 119 - 127 (chain A) in PDB entry 3SBW


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 GLY 119 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ARG*     4.5     8.3    -      -       -      -
    117A  ASP      3.3     3.2    +      -       -      -
    118A  SER*     1.3    74.8    -      -       -      +
    120A  ILE*     1.3    66.7    +      -       -      -
    121A  TYR*     3.7    13.5    -      -       -      -
    141A  GLU*     3.4     5.6    +      -       -      +
    142A  LEU      2.9    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ARG*     3.7     4.9    -      -       -      +
     70A  LEU*     2.8    54.0    +      -       +      +
    119A  GLY*     1.3    73.5    -      -       -      -
    121A  TYR*     1.3    66.3    +      -       -      +
    139A  GLY*     4.3     2.5    -      -       -      -
    140A  ALA      3.5     7.0    -      -       -      +
    141A  GLU*     3.5    42.8    -      -       +      +
     93B  ALA*     3.8    34.5    -      -       +      +
     94B  ARG      4.3     0.4    -      -       -      +
     96B  GLN*     4.4    15.7    -      -       +      +
    111B  LEU*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     3.8     9.0    -      -       +      -
     52A  PHE*     4.6     7.0    -      +       +      -
     67A  TRP*     3.3    28.5    -      +       -      +
     68A  ASN      3.1    15.9    -      -       -      +
     69A  ARG*     3.6    35.7    +      -       +      -
     70A  LEU*     4.7     1.1    -      -       -      +
     79A  GLN*     4.0    11.9    -      -       +      -
     95A  PHE*     4.1    17.5    -      +       -      -
    110A  ILE*     4.2     8.2    -      -       +      +
    117A  ASP*     2.5    34.8    +      -       -      -
    119A  GLY      3.7    19.3    -      -       -      -
    120A  ILE*     1.3    79.4    -      -       -      +
    122A  LEU*     1.3    63.1    +      -       -      +
    139A  GLY*     3.2     6.1    -      -       -      -
    140A  ALA*     2.8    38.5    +      -       -      +
    142A  LEU*     4.1    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     3.8     9.4    -      -       -      -
     67A  TRP*     3.6     2.9    -      -       -      -
     68A  ASN*     2.8    51.2    +      -       +      +
     70A  LEU*     4.2    26.0    -      -       +      +
     76A  THR*     6.2     0.4    -      -       +      -
    121A  TYR*     1.3    77.1    -      -       -      +
    123A  CYS*     1.3    73.4    +      -       -      +
    124A  GLY*     5.1     0.2    -      -       -      -
    136A  GLU*     3.9    23.8    -      -       +      +
    137A  SER*     3.4    13.7    -      -       -      +
    138A  PRO      3.7     4.0    -      -       -      +
    139A  GLY      4.7     2.0    -      -       -      +
     94B  ARG*     4.4     5.4    -      -       -      -
    112B  ASP*     3.6    16.2    -      -       -      +
    114B  ARG*     3.5    28.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.6     8.6    -      -       -      +
     36A  THR      4.2     0.9    -      -       -      -
     37A  PHE*     3.6    17.1    -      -       +      -
     54A  CYS*     2.1    54.3    -      -       +      -
     65A  LEU*     4.8     1.1    -      -       +      -
     66A  ASN      3.2     8.5    -      -       -      +
     67A  TRP*     4.5     0.7    -      -       -      +
    108A  MET*     4.0    11.4    -      -       +      -
    122A  LEU*     1.3    79.5    -      -       -      +
    124A  GLY*     1.3    58.7    +      -       -      +
    136A  GLU*     3.6     1.2    -      -       -      -
    137A  SER*     2.9    44.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     4.0     1.3    -      -       -      -
     64A  MET      3.8     0.7    -      -       -      +
     65A  LEU*     3.3     8.0    -      -       -      +
     66A  ASN*     2.7    47.7    +      -       -      +
     68A  ASN*     5.1     2.5    +      -       -      -
    122A  LEU*     4.2     1.9    +      -       -      +
    123A  CYS*     1.3    76.7    -      -       -      +
    125A  ALA*     1.3    61.7    +      -       -      -
    126A  ILE*     5.0     2.7    -      -       -      -
    134A  ILE*     5.9     1.6    -      -       -      -
    135A  GLU      3.3     9.4    -      -       -      -
    136A  GLU*     4.2     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.9    15.3    -      -       +      +
     56A  LEU*     4.3    12.8    -      -       +      -
     63A  LEU*     4.8    12.1    -      -       +      -
     64A  MET      3.4     5.6    -      -       -      +
     65A  LEU*     4.1    13.9    -      -       +      -
    124A  GLY*     1.3    75.1    -      -       -      -
    126A  ILE*     1.3    62.2    +      -       -      +
    133A  LYS      3.8     0.9    -      -       -      +
    134A  ILE*     3.4     4.5    -      -       -      +
    135A  GLU*     2.7    39.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ASP      4.5     0.7    -      -       -      +
     63A  LEU*     3.6     9.0    -      -       -      -
     64A  MET*     2.7    65.6    +      -       +      +
     66A  ASN*     3.3    36.1    -      -       +      +
    124A  GLY      4.8     2.7    -      -       -      +
    125A  ALA*     1.3    81.4    -      -       -      +
    127A  SER*     1.3    70.1    +      -       -      +
    128A  LEU*     4.1     3.5    +      -       +      -
    132A  LEU*     4.1    18.4    -      -       +      -
    133A  LYS      3.4     6.1    -      -       -      +
    134A  ILE*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ASP*     4.5     8.4    +      -       -      -
     63A  LEU*     3.8    22.4    -      -       -      +
    126A  ILE*     1.3    77.2    -      -       -      +
    128A  LEU*     1.3    59.8    +      -       -      +
    129A  HIS      3.4    18.9    +      -       -      -
    131A  LYS      3.2     3.9    +      -       -      +
    132A  LEU*     3.5     4.0    -      -       -      +
    133A  LYS*     2.8    54.9    +      -       -      +
----------------------------------------------------------
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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