Contacts of the strand formed by residues 235 - 242 (chain E) in PDB entry 4KYI


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 ASN 235 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67E  THR      2.8    20.1    +      -       -      +
     68E  HIS*     3.6    34.1    +      -       +      +
     69E  VAL*     3.1    21.5    +      -       -      +
    222E  ARG*     4.2     4.9    +      -       -      +
    234E  LYS*     1.3    70.3    -      -       -      +
    236E  LEU*     1.3    64.7    +      -       -      +
    237E  SER*     3.6     8.6    +      -       -      -
    252E  SER*     4.9     1.0    -      -       -      -
    253E  GLU*     3.2    35.2    -      -       -      +
    254E  ASP*     3.4    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69E  VAL      3.6    12.6    -      -       -      +
     76E  ALA      4.7     0.2    -      -       -      +
     79E  ALA*     3.9    28.5    -      -       +      +
     80E  SER*     3.7    19.7    -      -       -      +
     83E  ALA*     3.6    16.2    -      -       +      -
    215E  LEU*     3.8    18.4    -      -       +      +
    218E  LEU*     4.3    10.0    -      -       +      +
    234E  LYS      3.4     4.2    +      -       -      -
    235E  ASN*     1.3    72.0    -      -       -      +
    237E  SER*     1.3    68.3    +      -       -      +
    238E  VAL*     3.8    24.0    -      -       +      -
    251E  TYR      4.1     0.7    -      -       -      +
    252E  SER      3.7     2.6    -      -       -      -
    253E  GLU*     3.4    29.0    +      -       -      +
    261E  ILE*     3.7    29.8    -      -       +      -
    265E  VAL*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 237 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68E  HIS*     6.0     1.6    -      -       -      +
     69E  VAL      3.3     6.9    +      -       -      +
     70E  SER*     3.1    43.3    +      -       -      -
     71E  GLY      3.2     2.3    +      -       -      -
    235E  ASN*     4.3     7.8    +      -       -      -
    236E  LEU*     1.3    75.4    -      -       -      +
    238E  VAL*     1.3    64.2    +      -       -      +
    239E  VAL*     5.4     0.2    -      -       -      -
    250E  ARG*     4.3    11.8    +      -       -      -
    251E  TYR      3.2     5.6    -      -       -      -
    252E  SER*     3.2    27.1    -      -       -      -
    297E  GLU      5.7     0.5    +      -       -      -
    298E  ILE*     5.2     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 238 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71E  GLY      3.2    13.0    -      -       -      +
     76E  ALA*     4.2    12.1    -      -       +      +
    215E  LEU*     5.8     0.9    -      -       +      -
    236E  LEU*     3.8    25.6    -      -       +      -
    237E  SER*     1.3    77.9    -      -       -      +
    239E  VAL*     1.3    64.1    +      -       -      +
    240E  VAL*     4.3     4.3    +      -       +      -
    250E  ARG*     3.7     2.4    -      -       -      +
    251E  TYR*     2.9    36.6    +      -       +      +
    264E  VAL*     3.4    46.2    -      -       +      +
    265E  VAL*     4.3    18.6    -      -       +      -
    268E  SER*     4.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 239 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70E  SER*     4.5     4.9    -      -       -      +
     71E  GLY      3.3     5.3    +      -       -      -
     72E  ALA*     3.6     6.8    -      -       +      +
    237E  SER      5.4     0.2    -      -       -      -
    238E  VAL*     1.3    80.2    -      -       -      +
    240E  VAL*     1.3    71.9    +      -       -      +
    248E  LEU*     4.0    21.8    -      -       +      -
    249E  GLU      3.4    13.2    -      -       -      +
    250E  ARG*     3.9    18.4    -      -       +      -
    268E  SER*     3.0    19.6    +      -       -      -
    289E  GLY*     3.4    11.5    -      -       -      +
    294E  ASN*     4.3     9.2    -      -       -      +
    296E  PRO*     3.7    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238E  VAL*     4.5     1.8    -      -       +      -
    239E  VAL*     1.3    77.7    -      -       -      +
    241E  THR*     1.3    65.2    +      -       -      +
    248E  LEU*     3.5    12.1    -      -       -      +
    249E  GLU*     3.0    36.3    +      -       +      +
    251E  TYR*     3.5    35.0    -      -       +      -
    264E  VAL      3.7    11.7    -      -       -      +
    267E  TRP*     3.7     8.3    -      -       +      -
    268E  SER*     3.5    27.8    -      -       -      +
    286E  ILE*     3.7    15.9    -      -       +      -
    287E  ALA      3.8     7.0    -      -       -      +
    289E  GLY*     3.6     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 241 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240E  VAL*     1.3    78.8    -      -       -      +
    242E  ASN*     1.3    60.8    +      -       -      +
    243E  GLN*     3.1    19.0    +      -       +      +
    247E  GLU      3.8     3.6    -      -       -      +
    248E  LEU*     3.8     9.7    -      -       +      +
    286E  ILE*     3.4     2.8    -      -       -      -
    287E  ALA      3.0    29.6    +      -       -      -
    288E  ASP      2.5    26.4    +      -       -      -
    289E  GLY*     3.4     9.2    -      -       -      -
    291E  ILE*     4.4     8.3    +      -       +      +
    291G  ILE*     4.2    15.7    -      -       +      -
    292G  LEU*     3.7    28.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 242 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240E  VAL*     4.0     2.6    +      -       -      +
    241E  THR*     1.3    68.5    -      -       -      +
    243E  GLN*     1.3    54.9    +      -       -      +
    244E  THR*     3.4    10.9    +      -       -      -
    245E  LYS*     2.8    47.1    +      -       +      +
    246E  HIS      2.8    30.3    +      -       -      -
    247E  GLU      2.9    20.5    +      -       -      +
    249E  GLU*     3.3    34.0    +      -       +      +
    280E  ASN*     4.5     0.2    -      -       -      +
    284E  GLU*     2.9    30.0    +      -       -      +
    285E  TYR      3.6     6.7    -      -       -      -
    286E  ILE*     4.3    10.9    -      -       +      +
----------------------------------------------------------
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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