Contacts of the strand formed by residues 343 - 349 (chain B) in PDB entry 6CIM


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 PHE 343 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549A  PRO*     5.4     5.8    -      -       +      -
     12B  ILE*     4.1    17.9    -      -       +      +
     15B  ILE      4.2    21.3    -      -       -      -
     16B  GLN*     5.7     0.2    -      -       +      -
     17B  PRO*     4.2    17.3    -      -       +      -
    316B  ILE*     5.2     3.4    -      -       +      -
    318B  PHE*     3.3    35.9    -      +       -      -
    331B  ILE      3.5    13.9    -      -       -      +
    332B  PRO*     3.8    21.3    -      -       +      -
    333B  GLY      4.9     0.2    -      -       -      +
    341B  GLU*     3.3    15.9    +      -       -      +
    342B  ALA*     1.3    93.2    -      -       +      +
    344B  TYR*     1.3    64.4    +      -       -      +
    345B  PHE*     3.6    24.8    +      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 344 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     4.8    16.2    -      -       +      -
    310B  ASP*     6.1     4.5    -      -       +      -
    330B  GLY*     3.3     1.7    -      -       -      -
    331B  ILE*     2.9    53.1    +      -       +      +
    332B  PRO      4.8     1.1    -      -       -      -
    333B  GLY*     4.0    26.2    -      -       -      -
    340B  SER*     3.2    25.0    +      -       -      -
    341B  GLU*     3.7    26.3    +      -       +      -
    343B  PHE*     1.3    77.2    -      -       -      +
    345B  PHE*     1.3    62.0    +      -       -      +
    346B  TYR*     4.0    16.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 345 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     3.8     4.8    -      -       -      +
      6B  VAL*     2.9    38.0    +      -       +      +
      8B  VAL*     3.7    20.2    -      -       +      -
     12B  ILE*     3.9    19.1    -      -       +      -
     15B  ILE*     3.4    46.2    -      -       +      -
    318B  PHE*     3.8    20.6    -      +       -      -
    328B  PHE*     3.4    30.3    -      +       +      -
    329B  LEU      3.1    17.7    -      -       -      +
    330B  GLY*     3.5     7.6    -      -       -      -
    343B  PHE*     3.6    28.9    -      +       +      -
    344B  TYR*     1.3    72.5    -      -       -      +
    346B  TYR*     1.3    69.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 346 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LEU*     3.5    34.5    -      -       +      -
      4B  GLN      3.1     9.4    -      -       -      +
      5B  MET*     3.3    46.3    -      -       +      +
      6B  VAL*     4.0     1.1    -      -       -      -
    308B  THR*     3.8    15.2    +      -       +      +
    310B  ASP*     3.7    21.7    +      -       -      +
    311B  ILE*     3.5    32.1    -      -       +      +
    328B  PHE*     3.5     6.2    -      -       -      -
    329B  LEU*     2.8    43.6    +      -       +      +
    330B  GLY*     5.6     0.2    -      -       -      -
    331B  ILE*     4.7     6.7    -      -       +      -
    344B  TYR*     4.0    26.4    -      -       +      +
    345B  PHE*     1.3    78.6    -      -       -      +
    347B  THR*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 347 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  SER      3.4     5.4    -      -       -      +
      3B  LEU*     4.4     2.0    -      -       -      -
      4B  GLN*     2.8    46.4    +      -       -      +
      6B  VAL*     3.5    21.3    -      -       +      +
     50B  ILE*     3.6    26.9    -      -       +      +
     53B  ASN*     5.2     1.6    +      -       -      -
    322B  MET*     4.4     7.6    -      -       -      -
    326B  THR*     5.7     2.5    -      -       -      -
    327B  ILE      3.2     9.2    -      -       -      +
    328B  PHE*     4.0     8.3    -      -       +      -
    346B  TYR*     1.3    75.6    -      -       -      +
    348B  LEU*     1.3    60.7    +      -       -      +
    349B  ARG*     4.0    15.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 348 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.8    27.1    -      -       +      -
      2B  SER      3.7    13.5    -      -       -      +
      3B  LEU*     4.3    16.2    -      -       +      +
    274B  VAL*     4.1    31.4    -      -       +      -
    305B  PRO*     4.2    17.7    -      -       +      -
    307B  TRP*     4.0    24.9    -      -       +      -
    325B  GLY      4.0     0.9    -      -       -      +
    326B  THR*     3.3     3.3    -      -       -      -
    327B  ILE*     2.9    43.6    +      -       +      +
    329B  LEU*     4.7     8.5    -      -       +      +
    346B  TYR      4.2     0.4    -      -       -      -
    347B  THR*     1.3    71.7    -      -       -      +
    349B  ARG*     1.3    63.0    +      -       -      +
    350B  CYS*     4.5     5.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 349 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.0    30.4    -      -       -      +
      2B  SER*     3.2    28.5    +      -       -      +
      4B  GLN*     5.5     6.9    -      -       -      +
     53B  ASN*     4.5    14.5    +      -       -      -
    326B  THR*     3.6    25.0    -      -       +      +
    347B  THR*     4.7    16.0    +      -       -      +
    348B  LEU*     1.3    74.1    -      -       -      +
    350B  CYS*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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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