Contacts of the strand formed by residues 26 - 33 (chain H) in PDB entry 3STJ


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 26 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  VAL*     4.7     6.1    -      -       +      +
     23H  LEU*     3.0    10.2    +      -       -      +
     24H  PRO*     3.8     3.5    -      -       -      +
     25H  ALA*     1.4    79.5    -      -       +      +
     27H  VAL*     1.3    69.2    +      -       -      +
     67H  GLY      3.4    12.8    -      -       -      +
     68H  VAL*     4.6     3.6    -      -       +      +
     95H  ASN      4.8     7.1    +      -       -      -
    127H  ILE*     5.3     3.6    -      -       +      -
    144H  VAL*     3.6    44.4    -      -       +      +
    145H  GLY*     4.4     4.9    -      -       -      +
    152H  GLN*     3.0    28.1    -      -       +      +
    189H  GLY*     4.6     1.8    -      -       -      -
    190H  ALA*     3.7    28.3    -      -       +      +
    192H  LEU*     5.2     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24H  PRO      4.3     0.9    -      -       -      +
     25H  ALA      3.8     1.3    -      -       -      +
     26H  VAL*     1.3    81.8    -      -       -      +
     28H  SER*     1.3    59.1    +      -       -      +
     29H  VAL*     4.0     3.4    -      -       +      -
     66H  SER*     3.1     9.4    -      -       -      -
     67H  GLY*     2.8    51.4    +      -       -      +
     69H  ILE*     3.6    34.1    -      -       +      -
     77H  VAL*     3.9     8.7    -      -       +      -
     92H  ILE*     3.9    29.8    -      -       +      -
     93H  GLN      3.6    11.0    -      -       -      +
     94H  LEU*     3.7    17.5    -      -       +      -
    146H  ASN*     5.4     0.4    -      -       -      -
    152H  GLN*     6.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 28 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  VAL*     1.3    74.3    -      -       -      +
     29H  VAL*     1.3    63.3    +      -       -      +
     30H  ARG*     4.0     2.9    +      -       -      +
     64H  LEU*     3.4    24.3    -      -       -      +
     65H  GLY      3.6     4.9    -      -       -      -
     66H  SER*     4.4     0.2    -      -       -      +
     91H  SER      3.9     0.2    -      -       -      +
     92H  ILE*     3.4     5.2    -      -       -      -
     93H  GLN*     2.9    55.8    +      -       -      +
    146H  ASN*     3.3    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  VAL*     4.0     7.0    -      -       +      -
     28H  SER*     1.3    77.2    +      -       -      +
     30H  ARG*     1.3    60.5    +      -       -      +
     31H  VAL*     4.0     3.9    +      -       +      +
     63H  GLY      3.9     0.3    -      -       -      +
     64H  LEU*     3.5     5.8    -      -       -      -
     65H  GLY      2.8    37.4    +      -       -      +
     66H  SER      3.4    29.2    -      -       -      +
     67H  GLY*     3.9     5.6    -      -       -      +
     77H  VAL*     4.7     1.1    -      -       +      -
     79H  THR*     4.6     0.9    -      -       -      +
     83H  VAL*     3.9    10.6    -      -       +      +
     84H  ILE*     3.7    29.8    -      -       +      -
     90H  ILE*     4.2    14.1    -      -       +      -
     91H  SER      3.6     2.5    -      -       -      -
     92H  ILE*     3.9    15.5    -      -       +      -
    116H  LEU*     4.4     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28H  SER*     4.0     3.9    -      -       -      +
     29H  VAL*     1.3    72.7    -      -       -      +
     31H  VAL*     1.3    66.5    +      -       -      +
     32H  GLU*     5.2     9.4    +      -       +      +
     62H  GLU*     3.1    35.7    +      -       +      +
     63H  GLY      3.6     7.6    -      -       -      +
     64H  LEU*     4.4    18.6    -      -       +      +
     89H  LYS      4.0     0.3    -      -       -      +
     90H  ILE*     3.4     4.2    -      -       -      +
     91H  SER*     2.8    55.5    +      -       -      +
     93H  GLN*     6.4     2.0    -      -       +      -
     99H  GLU*     5.7     5.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  VAL*     4.3     6.5    -      -       +      +
     30H  ARG*     1.3    79.8    -      -       -      +
     32H  GLU*     1.3    66.7    +      -       -      +
     61H  PHE*     3.7    24.0    -      -       +      -
     62H  GLU*     3.3     6.2    -      -       -      +
     63H  GLY*     2.8    40.2    +      -       -      +
     83H  VAL*     3.7    26.5    -      -       +      +
     84H  ILE*     3.9    11.9    -      -       +      -
     86H  GLN      5.8     0.2    -      -       -      +
     87H  ALA*     3.6    32.5    -      -       +      +
     89H  LYS      3.4     2.7    -      -       -      -
     90H  ILE*     3.9    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 32 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30H  ARG*     5.2    11.1    +      -       +      +
     31H  VAL*     1.3    81.5    -      -       -      +
     33H  GLY*     1.3    52.3    +      -       -      +
     61H  PHE      3.4     5.8    -      -       -      +
     62H  GLU*     3.2    33.8    -      -       +      +
     87H  ALA      3.7     0.2    -      -       -      -
     88H  GLN*     2.7    31.1    +      -       -      +
     89H  LYS*     2.9    44.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  GLU*     1.3    76.0    -      -       -      +
     34H  THR*     1.3    58.6    +      -       -      -
     60H  PRO*     3.3    23.9    -      -       -      +
     61H  PHE*     3.2    26.7    +      -       -      +
     86H  GLN      3.7     9.4    -      -       -      -
     88H  GLN*     3.7    19.9    -      -       -      +
----------------------------------------------------------
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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