Contacts of the strand formed by residues 332 - 341 (chain C) in PDB entry 5FFO


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 LEU 332 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  PRO*     3.7    32.1    -      -       +      +
    330C  GLN      4.4     2.9    -      -       -      +
    331C  ALA*     1.3    82.7    -      -       -      +
    333C  GLU*     1.3    68.0    +      -       -      +
    334C  PRO*     4.4     2.3    -      -       -      +
    352C  ASN*     3.4    50.6    +      -       +      +
    353C  MET      4.5     2.5    -      -       -      +
    354C  ILE      3.1     8.5    -      -       -      +
    355C  VAL*     4.1    21.8    -      -       +      -
     16D  ARG*     5.5     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 333 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331C  ALA*     5.6     0.7    -      -       +      -
    332C  LEU*     1.3    79.4    -      -       -      +
    334C  PRO*     1.3    74.4    -      -       +      +
    352C  ASN*     4.2     1.8    -      -       -      -
    353C  MET      2.8     7.4    +      -       -      -
    354C  ILE*     2.7    55.2    +      -       +      +
    356C  ARG*     2.7    54.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 334 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  LEU      4.4     2.9    -      -       -      +
    333C  GLU*     1.3    93.0    -      -       +      +
    335C  LEU*     1.3    57.6    +      -       -      +
    336C  PRO*     4.1     5.5    -      -       -      +
    349C  GLN*     3.4    26.4    +      -       +      +
    350C  LEU      3.1    20.0    -      -       -      +
    351C  SER*     4.2     3.1    -      -       -      -
    352C  ASN      3.8    11.4    -      -       -      +
    353C  MET      4.4     0.4    -      -       -      +
    354C  ILE*     3.5     8.1    -      -       -      +
     58D  ARG*     4.1    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 335 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273C  PHE*     5.0     3.6    -      -       +      -
    285C  PRO*     4.1    17.7    -      -       +      -
    288C  TYR*     3.6    51.6    -      -       +      -
    334C  PRO*     1.3    74.0    -      -       -      +
    336C  PRO*     1.3    81.6    -      -       +      +
    337C  ILE*     3.7    16.0    +      -       +      +
    349C  GLN*     3.8     3.4    -      -       -      -
    350C  LEU*     2.8    37.2    +      -       +      +
    353C  MET*     4.1    17.6    -      -       +      +
    354C  ILE*     3.7    13.7    -      -       +      -
     24D  ILE*     6.1     1.6    -      -       +      -
     52D  TYR*     5.1     1.8    -      -       -      +
     56D  ARG*     6.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 336 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285C  PRO*     3.4    12.6    -      -       -      +
    334C  PRO      4.1     5.4    -      -       -      +
    335C  LEU*     1.3    92.0    -      -       +      +
    337C  ILE*     1.3    60.7    +      -       -      +
    347C  VAL*     5.6     3.8    -      -       +      -
    348C  GLU      3.5     7.4    -      -       -      +
    349C  GLN*     3.9    17.0    -      -       +      +
     52D  TYR*     3.1    34.9    +      -       +      -
     55D  THR*     3.6    32.3    -      -       +      +
     56D  ARG*     3.7    21.3    -      -       +      +
     79D  VAL*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273C  PHE*     5.4     3.4    -      -       +      -
    282C  ILE*     4.6    19.1    -      -       +      -
    284C  GLU      3.3     7.2    -      -       -      +
    285C  PRO*     4.4     6.1    -      -       +      -
    335C  LEU*     4.1    24.7    -      -       +      +
    336C  PRO*     1.3    78.8    -      -       -      +
    338C  VAL*     1.3    69.3    +      -       -      +
    339C  TYR*     4.0    24.0    -      -       +      -
    347C  VAL*     3.5     2.8    -      -       -      +
    348C  GLU*     2.6    47.1    +      -       +      +
    350C  LEU*     4.2    22.0    -      -       +      -
     24D  ILE*     5.0     4.5    -      -       +      -
     28D  LEU*     4.1    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282C  ILE*     3.7     4.1    -      -       -      +
    283C  HIS*     3.0    38.6    +      -       +      +
    284C  GLU*     2.7    25.7    +      -       +      +
    337C  ILE*     1.3    80.7    -      -       -      +
    339C  TYR*     1.3    67.8    +      -       -      +
    340C  TYR*     5.1     8.5    -      -       +      -
    345C  PRO*     5.5     4.0    -      -       +      -
    346C  LYS      3.9     4.0    -      -       -      +
    347C  VAL*     3.8    31.6    -      -       +      -
     44D  LEU*     5.9     3.4    -      -       +      -
     48D  VAL*     5.2    12.6    -      -       +      +
     49D  LEU*     6.6     0.2    -      -       +      -
     52D  TYR*     4.0    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281C  TRP*     3.7    42.6    -      +       +      +
    282C  ILE*     4.6     3.4    -      -       +      -
    283C  HIS*     4.6     0.4    -      -       -      -
    337C  ILE*     4.0    18.4    -      -       +      -
    338C  VAL*     1.3    75.2    -      -       -      +
    340C  TYR*     1.3    73.8    +      -       -      +
    341C  VAL*     3.5    21.7    -      -       +      +
    345C  PRO*     3.6     1.6    -      -       -      +
    346C  LYS*     2.7    47.9    +      -       +      +
    348C  GLU*     3.0    48.2    +      -       +      -
     28D  LEU*     4.0    22.6    +      -       +      +
     30D  LEU*     5.1     8.8    -      -       +      +
     34D  PRO*     4.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281C  TRP*     4.4     4.8    +      -       -      +
    283C  HIS*     3.3    40.6    -      +       +      -
    338C  VAL*     5.1     6.3    -      -       +      -
    339C  TYR*     1.3    92.2    -      -       -      +
    341C  VAL*     1.3    62.9    +      -       -      +
    342C  GLY      4.0     1.2    +      -       -      -
    343C  ARG      4.4     9.6    -      -       -      -
    344C  LYS      3.5     4.5    -      -       -      -
    345C  PRO*     3.4    41.6    -      -       +      +
     34D  PRO*     3.9    16.3    -      -       -      +
     35D  SER      5.5     0.5    -      -       -      +
     36D  GLN*     6.2     0.2    -      -       +      -
     39D  VAL*     3.5    39.6    -      -       +      +
     40D  PRO*     4.6    13.2    -      -       +      +
     43D  PRO      3.6    20.1    +      -       -      -
     44D  LEU*     3.7     9.7    -      -       +      +
     45D  PRO*     4.3    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  TYR*     3.5    25.4    -      -       +      +
    340C  TYR*     1.3    78.6    -      -       -      +
    342C  GLY*     1.3    59.3    +      -       -      +
    343C  ARG      2.8    10.2    +      -       -      -
    344C  LYS*     2.6    34.0    +      -       +      +
    346C  LYS*     3.5    34.1    -      -       +      -
     34D  PRO*     5.4     5.8    -      -       +      -
----------------------------------------------------------
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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