Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 6H25


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 47 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ALA*     3.3     3.6    -      -       -      +
     46C  ASP*     1.3    82.5    -      -       -      +
     48C  SER*     1.3    62.0    +      -       -      -
     60C  CYS      4.0     0.3    -      -       -      +
     61C  GLY*     3.5     3.1    -      -       -      -
     62C  VAL*     2.9    35.5    +      -       -      +
    159C  ALA*     4.1    12.6    -      -       -      -
    162C  ASN*     3.4    19.3    -      -       -      -
    163C  VAL*     4.5     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ILE*     4.3     1.9    -      -       -      +
     40C  GLY*     3.3    21.5    +      -       -      -
     41C  SER*     3.1    10.9    +      -       -      -
     42C  ILE*     3.1    55.4    +      -       -      -
     45C  ALA*     5.1     2.7    -      -       -      -
     47C  GLY*     1.3    74.4    -      -       -      -
     49C  ALA*     1.3    61.8    +      -       -      +
     60C  CYS      3.4     7.2    -      -       -      -
     61C  GLY*     5.2     2.0    -      -       -      -
    158C  ALA      4.7     0.9    -      -       -      +
    159C  ALA*     4.4     2.6    -      -       -      -
    162C  ASN*     3.1    14.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ASN      3.6     6.5    -      -       -      +
     39C  ILE*     5.0     0.4    -      -       +      -
     41C  SER*     6.5     0.2    -      -       -      -
     42C  ILE*     6.3     0.7    -      -       -      -
     48C  SER*     1.3    76.6    -      -       -      +
     50C  LEU*     1.3    62.1    +      -       -      +
     51C  VAL      4.2     0.2    -      -       -      -
     58C  VAL      3.9     0.5    -      -       -      +
     59C  ILE*     3.3     8.0    -      -       -      +
     60C  CYS      2.9    31.5    +      -       -      +
    155C  ALA*     3.4    31.2    -      -       -      +
    158C  ALA*     3.7    15.0    -      -       +      -
    159C  ALA*     3.5    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  THR      4.0     0.2    -      -       -      +
     37C  VAL*     3.1     7.3    -      -       -      +
     38C  ASN*     2.9    67.3    +      -       +      +
     41C  SER*     5.2     8.9    -      -       -      +
     49C  ALA*     1.3    74.3    -      -       -      +
     51C  VAL*     1.3    67.6    +      -       -      +
     52C  LYS*     4.5    16.4    -      -       +      -
     57C  THR*     3.7    25.6    -      -       +      -
     58C  VAL      3.7     0.7    -      -       -      +
     59C  ILE*     3.7    28.0    -      -       +      -
    142C  LEU*     5.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  THR*     5.9     0.9    -      -       -      -
     36C  THR      3.6     6.7    -      -       -      +
     37C  VAL*     3.7    16.4    -      -       +      -
     49C  ALA*     5.2     2.0    -      -       +      -
     50C  LEU*     1.3    81.1    -      -       -      +
     52C  LYS*     1.3    64.9    +      -       -      +
     53C  LEU*     4.0    23.3    -      -       +      +
     56C  THR      3.5     1.4    -      -       -      +
     57C  THR*     3.3     4.9    -      -       -      +
     58C  VAL*     2.9    38.6    +      -       +      +
    151C  ALA*     4.4    11.2    -      -       +      +
    154C  PHE*     3.9    20.6    -      -       +      +
    155C  ALA*     3.7    35.4    -      -       +      +
    158C  ALA*     5.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  THR      3.7     2.1    -      -       -      +
     35C  THR*     3.5     1.2    -      -       -      -
     36C  THR*     2.9    53.5    +      -       -      +
     38C  ASN*     5.6     3.4    -      -       -      +
     50C  LEU*     4.2    18.1    -      -       +      -
     51C  VAL*     1.3    76.8    -      -       -      +
     53C  LEU*     1.3    60.5    +      -       -      +
     54C  GLY      4.2     0.4    -      -       -      -
     55C  ASN*     5.4     7.5    -      -       -      +
     56C  THR      3.4     5.6    -      -       -      +
     57C  THR*     3.4    31.8    +      -       +      +
     45F  LEU*     4.5    17.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  PHE*     5.5     2.0    -      -       +      -
     33C  ARG*     5.3     1.8    -      -       +      +
     34C  THR      3.3     4.0    -      -       -      +
     35C  THR*     3.7    26.9    -      -       +      -
     51C  VAL*     4.0    11.7    -      -       +      -
     52C  LYS*     1.3    75.3    -      -       -      +
     54C  GLY*     1.3    61.5    +      -       -      +
     55C  ASN      3.4     0.4    -      -       -      -
     56C  THR*     2.3    56.0    +      -       +      +
    146C  GLY      4.9     6.3    -      -       -      +
    147C  ASN*     4.9     4.5    -      -       +      +
    150C  ASP*     4.5    17.0    -      -       -      +
    151C  ALA*     3.8    33.4    -      -       +      +
    154C  PHE*     5.1     5.2    -      -       +      -
    209C  ASP*     4.0    26.5    -      -       -      +
----------------------------------------------------------
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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