Contacts of the strand formed by residues 50 - 56 (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 ALA 50 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU*     4.0     4.3    -      -       +      -
     44A  VAL*     3.9    19.5    -      -       +      -
     48A  ALA      3.9     0.6    +      -       -      -
     49A  ASN*     1.3    72.8    -      -       -      +
     51A  THR*     1.3    67.4    +      -       -      +
     52A  PHE*     5.5     2.7    -      -       +      -
    108A  MET      3.8     0.6    -      -       -      +
    109A  ASN*     3.3     2.9    -      -       -      +
    110A  ILE*     2.8    38.4    +      -       +      +
    113A  THR*     3.9    20.4    -      -       +      -
    142A  LEU*     4.0    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  PRO*     4.0    10.2    -      -       -      +
     42A  LEU*     3.7    17.3    -      -       -      +
     49A  ASN*     4.4     3.0    +      -       -      +
     50A  ALA*     1.3    75.9    +      -       -      +
     52A  PHE*     1.3    78.4    +      -       -      +
     53A  THR*     4.6     1.3    -      -       -      +
    107A  HIS*     3.6    26.9    -      -       +      +
    108A  MET      3.6     2.9    -      -       -      -
    109A  ASN*     2.7    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     3.6    33.0    -      +       +      -
     38A  TYR      3.3    11.0    -      -       -      +
     39A  PRO      3.3    28.5    -      -       -      -
     42A  LEU*     3.8    25.8    -      -       +      -
     50A  ALA*     5.5     1.8    -      -       +      -
     51A  THR*     1.3    81.8    -      -       -      +
     53A  THR*     1.3    62.5    +      -       -      +
     54A  CYS      4.1     0.4    -      -       -      -
     67A  TRP*     4.7    10.5    -      +       -      -
    107A  HIS*     3.4     5.5    -      -       -      -
    108A  MET      2.9    37.0    +      -       -      +
    110A  ILE*     5.3     2.9    -      -       +      -
    121A  TYR*     4.6    12.3    -      +       -      -
    140A  ALA*     3.6    16.6    -      -       +      -
    141A  GLU      3.5    21.8    -      -       -      -
    142A  LEU*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     3.2     5.7    -      -       -      -
     38A  TYR*     2.6    82.3    +      -       +      +
     51A  THR*     4.6     1.4    -      -       -      +
     52A  PHE*     1.3    71.7    -      -       -      +
     54A  CYS*     1.3    66.2    +      -       -      +
     55A  SER      4.5     0.2    -      -       -      +
    100A  LEU*     4.8     3.6    -      -       +      -
    105A  ASP*     4.3    15.7    -      -       +      +
    106A  PHE      3.2    10.5    -      -       -      +
    107A  HIS*     3.3    22.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.9     4.5    -      -       -      -
     36A  THR      3.4     3.6    -      -       -      -
     37A  PHE*     3.6     9.6    -      -       +      -
     52A  PHE      4.1     0.2    -      -       -      -
     53A  THR*     1.3    72.1    -      -       -      +
     55A  SER*     1.3    60.2    +      -       -      +
     56A  LEU*     3.6    23.1    -      -       -      -
     65A  LEU*     4.0     7.2    -      -       -      -
    104A  HIS      3.8     2.1    -      -       -      +
    105A  ASP*     3.4     1.9    -      -       -      -
    106A  PHE*     2.8    38.8    +      -       +      +
    108A  MET*     3.7    20.9    -      -       +      -
    123A  CYS*     2.1    46.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.4     3.3    -      -       -      -
     36A  THR*     2.8    47.6    +      -       -      -
     38A  TYR*     3.7    20.8    +      -       -      -
     53A  THR*     3.8     0.6    +      -       -      -
     54A  CYS*     1.3    73.8    -      -       -      +
     56A  LEU*     1.3    65.5    +      -       -      +
     57A  SER      4.0     0.2    +      -       -      -
    104A  HIS*     4.5     2.3    +      -       -      -
    105A  ASP*     2.8    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  SER      3.7     4.5    -      -       -      +
     35A  LEU*     4.0    15.5    -      -       +      +
     54A  CYS*     3.6    29.2    -      -       -      -
     55A  SER*     1.3    76.8    +      -       -      +
     57A  SER*     1.3    63.4    +      -       -      +
     58A  ASN      3.3    23.7    +      -       -      +
     59A  TRP*     3.8    24.9    -      -       +      -
     63A  LEU*     4.2     9.9    -      -       +      -
     65A  LEU*     3.7    20.6    -      -       +      -
    104A  HIS*     2.9    43.6    +      -       +      +
    106A  PHE*     4.1     7.4    -      -       +      -
    125A  ALA*     4.3     7.0    -      -       +      -
----------------------------------------------------------
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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