Contacts of the strand formed by residues 276 - 282 (chain C) in PDB entry 4L28


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 ARG 276 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249C  ASP      3.0    14.7    +      -       -      +
    250C  MET*     3.4    21.0    -      -       +      +
    251C  LEU      2.9    26.5    +      -       -      +
    274C  GLY      4.2     8.1    -      -       -      +
    275C  CYS*     1.3    75.9    -      -       -      +
    277C  ILE*     1.3    61.6    +      -       -      +
    278C  ILE*     3.8    12.2    +      -       +      +
    321C  ASP*     3.5    21.4    +      -       -      +
    322C  LYS*     4.1    30.5    -      -       -      +
    360C  ALA      5.6     0.2    +      -       -      -
    363C  GLU*     2.9    39.3    +      -       -      -
    364C  LEU*     6.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 277 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251C  LEU*     3.8    13.5    -      -       +      +
    261C  ILE*     3.7    33.2    -      -       +      -
    265C  ALA*     3.8    27.1    -      -       +      +
    268C  LEU*     4.2    24.2    -      -       +      -
    269C  LYS*     4.2    10.5    -      -       +      -
    275C  CYS*     4.5     4.7    -      -       -      +
    276C  ARG*     1.3    76.5    -      -       -      +
    278C  ILE*     1.3    63.5    +      -       -      +
    319C  VAL      3.5    26.9    -      -       -      +
    320C  VAL*     3.8     3.6    -      -       -      +
    321C  ASP*     3.0    31.8    +      -       -      +
    322C  LYS      3.3     9.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 278 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  MET*     3.9    41.5    -      -       +      -
    251C  LEU      2.9    12.4    +      -       -      +
    252C  VAL*     3.4    10.3    -      -       +      +
    253C  ALA*     3.0    26.0    +      -       -      +
    261C  ILE*     4.1     4.5    -      -       -      +
    276C  ARG*     4.4    15.7    -      -       +      +
    277C  ILE*     1.3    79.9    -      -       -      +
    279C  GLY*     1.3    61.3    +      -       -      +
    321C  ASP*     5.5     0.2    -      -       +      -
    322C  LYS*     3.5    22.7    -      -       +      +
    324C  PHE*     3.7    32.8    -      -       +      -
    356C  VAL*     4.1    14.8    -      -       +      -
    360C  ALA*     4.2     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 279 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253C  ALA      3.4     6.1    -      -       -      -
    255C  VAL*     4.4     0.2    -      -       -      -
    261C  ILE*     3.7    14.4    -      -       -      -
    278C  ILE*     1.3    74.4    -      -       -      +
    280C  VAL*     1.3    63.8    +      -       -      +
    320C  VAL*     3.7     9.9    -      -       -      +
    322C  LYS      2.9    11.4    +      -       -      -
    323C  TRP*     3.4    13.8    -      -       -      -
    324C  PHE*     2.9    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 280 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  VAL*     3.9    17.3    -      -       +      -
    253C  ALA      3.0    11.9    +      -       -      +
    254C  SER*     3.6    12.7    -      -       -      -
    255C  VAL*     3.1    27.4    +      -       -      +
    278C  ILE*     5.1     0.2    -      -       +      -
    279C  GLY*     1.3    77.6    -      -       -      +
    281C  ASP*     1.3    62.6    +      -       -      +
    282C  PRO*     4.3     1.9    -      -       -      +
    306C  ILE*     5.0     1.6    -      -       +      +
    323C  TRP*     4.6     1.6    -      -       -      -
    324C  PHE      3.5     2.5    -      -       -      +
    326C  SER*     3.8    20.6    -      -       -      +
    352C  SER*     4.1    14.4    -      -       -      +
    353C  THR*     4.4     5.4    -      -       -      -
    356C  VAL*     3.6    44.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 281 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255C  VAL      4.4     0.9    -      -       -      +
    279C  GLY      4.2     0.2    +      -       -      -
    280C  VAL*     1.3    75.4    -      -       -      +
    282C  PRO*     1.3    74.7    -      -       -      +
    285C  SER*     2.8    28.2    +      -       -      -
    287C  LEU*     3.3    34.3    +      -       -      +
    288C  ALA*     3.3    20.3    +      -       +      -
    307C  GLY*     3.8     0.3    +      -       -      -
    323C  TRP*     4.1     8.5    -      -       +      -
    324C  PHE      2.9     7.9    +      -       -      +
    325C  LYS*     2.9    30.2    +      -       -      +
    326C  SER*     2.9    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 282 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280C  VAL      4.3     1.1    -      -       -      +
    281C  ASP*     1.3    99.4    -      -       -      +
    283C  GLU*     1.3    66.6    +      -       -      +
    285C  SER*     3.2    17.5    +      -       -      -
    301C  TYR*     3.6    30.5    -      -       +      +
    303C  VAL*     5.7     2.2    -      -       +      -
    306C  ILE*     3.8    27.4    -      -       +      +
    307C  GLY*     3.6    26.0    -      -       -      +
    325C  LYS*     3.3     6.2    +      -       -      -
    326C  SER*     3.3    14.3    -      -       -      +
    327C  ASN*     6.1     0.4    -      -       -      -
    328C  ASP*     6.0     1.1    -      -       -      +
----------------------------------------------------------
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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