Contacts of the strand formed by residues 331 - 341 (chain B) in PDB entry 4F4W


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 ILE 331 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  MET*     3.1    23.4    -      -       +      +
    255B  ASN*     3.2     6.9    -      -       -      -
    256B  SER      2.9    36.2    +      -       -      +
    262B  ILE*     4.2     6.5    -      -       +      -
    289B  ALA*     4.0    21.8    -      -       +      -
    290B  VAL      3.8     4.0    -      -       -      +
    291B  THR*     4.2     4.9    -      -       +      +
    320B  LEU*     3.9    21.3    -      -       +      -
    323B  ILE*     4.4     8.7    -      -       +      -
    324B  LEU*     3.7    25.4    -      -       +      -
    329B  ARG      4.4     8.1    -      -       -      +
    330B  LYS*     1.3    76.9    -      -       -      +
    332B  ARG*     1.3    57.8    -      -       -      +
    333B  ARG      3.1    28.3    -      -       -      +
    334B  ILE*     4.5     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  ARG*     3.3    42.8    +      -       -      +
     40B  SER*     4.6     4.0    -      -       -      -
    251B  THR*     3.8     4.9    -      -       +      +
    252B  MET*     3.0    32.6    +      -       -      +
    255B  ASN*     3.3    23.1    +      -       -      +
    290B  VAL*     2.7    15.7    +      -       -      +
    291B  THR      4.1    10.8    -      -       -      +
    292B  GLU*     4.2     8.2    +      -       -      +
    294B  LEU*     4.0    24.6    -      -       -      +
    330B  LYS      4.0     1.4    +      -       -      -
    331B  ILE*     1.3    73.3    -      -       -      +
    333B  ARG*     1.3    67.1    +      -       +      +
      4F    C      3.7    20.4    +      -       -      -
      5F    G      3.0    40.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  ILE*     4.1    11.0    -      -       +      -
    250B  VAL      3.1    12.6    -      -       -      +
    251B  THR*     3.2    24.1    +      -       -      +
    252B  MET*     5.0     0.4    -      -       -      -
    289B  ALA*     3.4     1.4    -      -       -      -
    290B  VAL*     2.9    65.6    +      -       +      +
    294B  LEU*     4.6    12.5    -      -       -      +
    296B  ILE*     6.1     1.4    -      -       -      +
    331B  ILE*     3.1    12.5    -      -       -      +
    332B  ARG*     1.3    84.4    -      -       +      +
    334B  ILE*     1.3    59.5    +      -       -      +
      4F    C      4.2    11.9    +      -       -      +
      5F    G      2.7    66.4    +      -       -      +
      6F    G      3.7    15.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 334 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  ILE*     3.7     4.0    -      -       -      -
    250B  VAL*     3.0    30.0    +      -       +      +
    252B  MET*     4.2     8.5    -      -       +      -
    262B  ILE*     3.7    24.0    -      -       +      -
    265B  TYR*     3.5    31.2    -      -       +      -
    266B  LEU*     4.1    21.3    -      -       +      +
    269B  ALA*     4.8     1.7    -      -       -      +
    287B  VAL*     3.9    18.8    -      -       +      -
    288B  VAL      3.5    15.7    -      -       -      +
    289B  ALA*     4.1    13.0    -      -       +      -
    320B  LEU*     4.1    18.6    -      -       +      -
    331B  ILE*     4.5     6.3    -      -       +      -
    333B  ARG*     1.3    74.9    -      -       -      +
    335B  GLY*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ARG      3.1    13.5    -      -       -      -
    249B  ILE*     3.8     7.4    -      -       -      +
    266B  LEU*     3.9     2.3    -      -       -      +
    269B  ALA*     4.5     6.5    -      -       -      -
    287B  VAL*     3.5     7.4    -      -       -      +
    288B  VAL*     2.9    33.8    +      -       -      -
    334B  ILE*     1.3    79.1    -      -       -      +
    336B  VAL*     1.3    70.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 336 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  GLY*     3.1     3.0    -      -       -      -
    248B  ARG      2.9    34.5    +      -       -      +
    249B  ILE*     4.9     0.8    -      -       -      +
    266B  LEU*     3.2    31.4    -      -       +      -
    269B  ALA*     3.9    19.5    -      -       +      +
    270B  ILE*     3.8    15.0    -      -       +      -
    273B  SER*     3.7    12.8    -      -       -      +
    285B  ILE*     4.8     4.7    -      -       +      -
    286B  HIS      3.3     6.7    -      -       -      +
    287B  VAL*     4.2    12.8    -      -       +      -
    288B  VAL*     4.7     1.0    -      -       -      +
    316B  SER*     4.7     1.1    -      -       -      -
    335B  GLY*     1.3    71.7    -      -       -      +
    337B  ARG*     1.3    67.5    +      -       -      +
    338B  PHE*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 337 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  SER*     3.2    27.7    +      -       -      -
    246B  ILE      3.7     5.8    -      -       -      +
    247B  GLY*     4.6     5.6    -      -       -      -
    248B  ARG      5.4     0.2    -      -       -      +
    284B  ALA      4.5     0.2    -      -       -      -
    285B  ILE*     3.5     3.8    -      -       -      +
    286B  HIS*     2.9    46.5    +      -       +      +
    288B  VAL*     4.1    20.9    -      -       +      -
    336B  VAL*     1.3    79.2    -      -       -      +
    338B  PHE*     1.3    64.0    +      -       -      +
    339B  SER*     4.4     0.6    +      -       -      -
      9E    T      4.6     7.7    +      -       -      +
     10E    C      4.3     4.2    -      -       -      +
      8F    C      3.5    39.7    +      -       -      +
      9F    G      2.9    48.3    +      -       -      -
     10F    A      5.2     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 338 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  SER*     3.0     6.5    -      -       -      -
    246B  ILE      2.8    40.7    +      -       -      +
    270B  ILE*     4.3     9.9    -      -       +      -
    273B  SER*     3.8    21.1    -      -       -      -
    274B  TYR*     3.5    29.4    -      +       -      -
    277B  LEU*     4.3    15.3    -      -       +      -
    282B  PRO*     3.7    29.2    -      -       +      -
    284B  ALA      3.3    10.8    -      -       -      -
    285B  ILE*     3.7    32.5    -      -       +      -
    307B  ILE*     4.9     2.5    -      -       +      -
    312B  ALA*     3.9    11.2    -      -       +      -
    336B  VAL*     3.6    24.2    -      -       +      -
    337B  ARG*     1.3    74.5    -      -       -      +
    339B  SER*     1.3    62.7    +      -       -      +
    341B  PHE*     3.6     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 339 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  LYS      3.5    17.5    -      -       -      -
    245B  SER*     4.1     8.1    -      -       -      -
    282B  PRO*     3.6     2.8    -      -       -      +
    283B  LYS      3.2     3.8    +      -       -      -
    284B  ALA*     3.1    36.5    +      -       -      +
    286B  HIS*     4.8     7.8    +      -       -      -
    337B  ARG*     5.3     1.1    +      -       -      -
    338B  PHE*     1.3    75.4    -      -       -      +
    340B  LYS*     1.3    80.4    +      -       -      +
    341B  PHE*     3.5     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 340 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  LYS      4.1     5.1    +      -       -      -
    283B  LYS*     2.9    46.9    +      -       +      +
    284B  ALA*     3.9    10.8    -      -       +      -
    286B  HIS*     6.1     1.8    -      -       -      -
    302B  THR*     2.8    36.6    +      -       +      +
    339B  SER*     1.3    81.3    -      -       -      +
    341B  PHE*     1.3    62.5    +      -       -      +
      6E    T      3.1    41.1    +      -       -      +
      7E    G      3.8    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 341 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  ARG*     3.5    26.2    -      -       +      -
    244B  LYS*     3.8    11.4    -      -       -      -
    245B  SER*     3.8    14.8    -      -       -      -
    246B  ILE*     3.9     6.3    -      -       +      -
    277B  LEU*     3.4    30.1    -      -       +      -
    280B  ARG*     3.9    31.0    -      -       +      -
    281B  ILE      3.3     5.4    -      -       -      +
    282B  PRO*     3.9    17.0    -      -       +      -
    283B  LYS*     4.1     4.0    +      -       -      -
    338B  PHE      3.6    26.9    -      -       -      -
    339B  SER*     3.8     6.5    -      -       -      -
    340B  LYS*     1.3    77.5    -      -       -      +
    342B  ILE*     1.3    69.4    +      -       -      +
----------------------------------------------------------
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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