Contacts of the strand formed by residues 38 - 45 (chain D) in PDB entry 5IXG


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 SER 38 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13D  PRO*     3.4    27.5    +      -       -      +
     16D  THR*     3.9    31.0    +      -       -      -
     18D  PRO*     3.6    18.5    -      -       -      +
     35D  PHE      4.7     0.2    +      -       -      -
     36D  ASP      4.2     1.2    +      -       -      -
     37D  LYS*     1.3    79.9    +      -       -      +
     39D  SER*     1.3    64.6    +      -       -      +
     55D  VAL*     4.4     6.3    -      -       -      -
     56D  THR      3.2    11.2    -      -       -      -
     57D  THR*     2.9    21.7    +      -       -      +
    201D  OTP      4.7     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 39 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  PHE*     4.2    14.6    -      -       -      -
     13D  PRO*     5.0     8.3    -      -       -      -
     37D  LYS*     6.4     1.3    -      -       -      -
     38D  SER*     1.3    77.1    -      -       -      +
     40D  GLY*     1.3    58.8    +      -       -      +
     55D  VAL*     3.4     4.0    -      -       -      +
     56D  THR*     2.9    38.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 40 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  GLN*     3.4     4.5    -      -       -      +
     11D  PHE*     3.0    32.2    +      -       -      +
     39D  SER*     1.3    78.7    +      -       -      +
     41D  THR*     1.3    71.9    +      -       -      +
     54D  ASP      3.2    12.1    -      -       -      -
     55D  VAL*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  THR*     4.7     6.7    -      -       -      -
      9D  TYR      3.2     8.7    -      -       -      -
     10D  GLN*     2.7    35.9    -      -       -      +
     11D  PHE*     3.6     3.4    -      -       -      -
     40D  GLY*     1.3    77.3    -      -       -      -
     42D  VAL*     1.3    69.2    +      -       -      +
     43D  THR*     5.7     2.6    -      -       -      +
     52D  THR      4.2     0.2    -      -       -      +
     53D  VAL*     3.7     0.3    -      -       -      -
     54D  ASP*     2.9    43.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  THR*     3.5     3.9    -      -       -      +
      9D  TYR*     2.7    44.9    +      -       +      +
     11D  PHE*     3.1    39.9    -      -       +      -
     41D  THR*     1.3    73.5    -      -       -      +
     43D  THR*     1.3    74.5    +      -       -      +
     44D  LEU*     4.7     3.8    -      -       +      +
     52D  THR      3.3    12.6    -      -       -      +
     53D  VAL*     4.2     5.4    -      -       +      -
     93D  ILE*     3.7    17.0    -      -       +      -
    171D  ALA*     4.7     2.5    -      -       +      -
    201D  OTP      3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  SER*     5.2     5.2    -      -       -      -
      7D  ALA      3.3     8.5    -      -       -      -
      8D  THR*     3.7    24.2    -      -       +      +
     41D  THR*     5.7     3.1    -      -       -      +
     42D  VAL*     1.3    80.9    -      -       -      +
     44D  LEU*     1.3    61.7    +      -       -      +
     51D  GLY*     3.0     5.5    -      -       -      -
     52D  THR*     2.5    62.4    +      -       -      +
     93D  ILE*     3.9     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  SER*     3.5     2.9    +      -       -      -
      7D  ALA*     2.9    33.3    +      -       -      +
      9D  TYR*     4.0    26.2    -      -       +      +
     42D  VAL*     4.8     2.7    -      -       +      -
     43D  THR*     1.3    74.8    -      -       -      +
     45D  ASP*     1.3    60.7    +      -       -      +
     46D  ARG*     4.0    24.5    -      -       +      +
     50D  THR      3.8     7.6    -      -       -      +
     51D  GLY*     4.9     0.2    -      -       -      -
     93D  ILE*     4.1    20.2    -      -       +      -
     95D  PHE*     3.8    27.4    -      -       +      -
    100D  PRO*     4.5     8.3    -      -       +      -
    123D  PHE*     3.9    29.6    -      -       +      -
    136D  CYS*     4.6     3.1    -      -       -      -
    201D  OTP      4.7     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 45 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  SER*     3.8    33.1    +      -       -      +
     44D  LEU*     1.3    74.3    -      -       -      +
     46D  ARG*     1.3    58.1    +      -       -      +
     47D  ALA*     3.2    11.4    +      -       -      +
     48D  ALA*     2.9    28.9    +      -       -      +
     49D  LYS      2.9    23.0    +      -       -      -
     50D  THR*     2.9    30.3    +      -       -      +
     51D  GLY*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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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