Contacts of the strand formed by residues 277 - 284 (chain C) in PDB entry 4X4R


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 ALA 277 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276C  THR*     1.3    70.8    -      -       -      +
    278C  VAL*     1.3    60.8    +      -       -      +
    279C  PHE*     4.0     7.2    -      -       +      -
    331C  PHE      3.5     2.1    -      -       -      +
    332C  GLU*     3.3     3.8    -      -       -      -
    333C  CYS*     2.8    38.3    +      -       +      +
    335C  ILE      4.1     5.4    -      -       -      +
    336C  LYS*     3.7    27.9    -      -       +      +
    385C  PRO*     4.1    14.1    -      -       +      -
    386C  GLU*     4.1    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 278 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271C  VAL*     3.8    32.2    -      -       +      +
    276C  THR*     3.6    21.0    +      -       -      +
    277C  ALA*     1.3    73.3    -      -       -      +
    279C  PHE*     1.3    65.0    +      -       -      +
    331C  PHE      3.4     9.2    -      -       -      +
    332C  GLU*     3.9    11.0    -      -       +      -
    386C  GLU*     5.0     1.4    +      -       -      -
    416C  SER*     3.6    14.2    +      -       -      -
    417C  GLY      4.4     2.3    +      -       -      -
    420C  LEU*     3.7    18.9    -      -       +      +
    421C  PHE*     5.5     3.6    -      -       +      -
    429C  LEU*     3.7    31.6    -      -       +      -
    432C  MET*     4.6     4.0    -      -       +      -
    433C  MET*     4.4     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 279 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277C  ALA      4.0    10.3    -      -       -      -
    278C  VAL*     1.3    76.6    -      -       -      +
    280C  ALA*     1.3    66.5    +      -       -      +
    281C  VAL*     5.0     0.2    -      -       +      -
    308C  LEU*     4.2     4.7    -      -       +      -
    329C  LEU      3.9     0.2    -      -       -      +
    330C  LEU*     3.7     1.4    -      -       -      +
    331C  PHE*     3.0    62.1    +      +       +      +
    333C  CYS*     4.1    10.1    -      -       -      -
    385C  PRO*     3.5    28.5    -      -       +      -
    386C  GLU*     3.7    31.6    -      -       +      +
    389C  VAL*     3.6    40.4    -      -       +      -
    414C  ILE*     3.9    16.2    -      -       +      -
    415C  ILE      3.4    12.6    -      -       -      +
    416C  SER*     4.2     3.4    -      -       -      -
    420C  LEU*     4.1     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 280 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279C  PHE*     1.3    76.9    -      -       -      +
    281C  VAL*     1.3    65.5    +      -       -      +
    282C  LYS      4.0     0.6    +      -       -      +
    328C  TYR*     4.6    13.2    -      -       +      -
    329C  LEU      3.1     6.3    -      -       -      +
    330C  LEU*     3.5    21.8    -      -       +      -
    414C  ILE*     3.4     8.5    -      -       -      +
    415C  ILE*     3.0    33.0    +      -       +      +
    420C  LEU*     3.5    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 281 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279C  PHE*     5.0     1.1    -      -       +      -
    280C  ALA*     1.3    74.7    -      -       -      +
    282C  LYS*     1.3    60.3    +      -       -      +
    283C  PHE*     3.8    19.7    -      -       +      -
    304C  ILE*     4.3     7.0    -      -       +      -
    327C  CYS      3.4     6.9    -      -       -      +
    328C  TYR*     3.4     2.0    -      -       -      -
    329C  LEU*     3.0    36.6    +      -       +      -
    331C  PHE*     4.0    17.7    -      -       +      -
    389C  VAL*     3.7    28.9    -      -       +      -
    393C  ALA*     5.3     3.6    -      -       +      -
    408C  ILE*     4.8     7.4    -      -       +      -
    412C  PHE*     4.0    26.0    -      -       +      -
    413C  GLU      3.9     1.8    -      -       -      -
    414C  ILE*     3.8     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 282 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280C  ALA      4.0     0.4    +      -       -      -
    281C  VAL*     1.3    73.0    -      -       -      +
    283C  PHE*     1.3    62.3    +      -       -      +
    326C  PHE*     3.5    46.7    -      -       +      -
    327C  CYS      3.5     4.9    -      -       -      +
    328C  TYR*     3.5    28.1    +      -       +      -
    411C  TYR*     5.1     1.2    -      -       -      -
    412C  PHE*     3.2     7.3    -      -       -      +
    413C  GLU*     3.0    57.9    +      -       +      +
    415C  ILE*     4.2    15.3    -      -       +      -
    423C  GLU*     2.9    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 283 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281C  VAL*     3.8    19.3    -      -       +      -
    282C  LYS*     1.3    80.2    -      -       -      +
    284C  ARG*     1.3    74.8    +      -       -      +
    286C  PRO*     4.4     3.1    -      -       +      -
    297C  LEU*     4.0     9.9    -      -       +      -
    326C  PHE*     3.3    12.1    -      -       -      -
    327C  CYS*     2.8    57.7    +      -       +      -
    329C  LEU*     4.0    17.3    -      -       +      -
    404C  VAL*     3.6    35.4    -      -       +      -
    407C  SER*     3.6    15.3    -      -       -      +
    408C  ILE*     3.8    20.2    -      -       +      -
    411C  TYR*     3.7    22.4    -      -       -      +
    412C  PHE*     4.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 284 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283C  PHE*     1.3    76.8    -      -       -      +
    285C  LYS*     1.3    69.9    +      -       -      +
    286C  PRO*     3.2     5.7    -      -       -      +
    325C  GLU*     2.7    51.6    +      -       -      +
    326C  PHE*     4.0    13.0    -      -       +      -
    407C  SER*     2.7    28.8    +      -       -      +
    411C  TYR*     4.9     7.8    +      -       +      +
----------------------------------------------------------
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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