Contacts of the strand formed by residues 256 - 264 (chain C) in PDB entry 3FTN


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 VAL 256 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228C  MET*     5.7     0.6    -      -       -      +
    235C  GLY*     5.1     0.4    -      -       -      -
    236C  VAL*     3.3    12.3    -      -       -      +
    237C  ASP      4.0     8.1    -      -       -      +
    238C  ARG      4.1     0.4    -      -       -      -
    239C  VAL*     3.3    30.1    -      -       +      +
    252C  ALA      3.1    16.9    +      -       -      +
    253C  VAL      3.6     9.0    -      -       -      +
    254C  LYS      4.5     1.6    -      -       -      +
    255C  MET*     1.3    80.2    -      -       -      +
    257C  LYS*     1.3    63.6    +      -       -      +
    258C  PRO*     4.2     0.9    -      -       -      +
    260C  GLY*     4.8     1.6    -      -       -      -
    261C  ILE      3.9    20.6    -      -       -      +
    262C  ILE*     3.9    16.6    -      -       +      -
    288C  LYS*     3.1    44.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ARG*     3.8    28.0    -      -       -      +
    169C  SER*     4.8     1.8    +      -       -      -
    234C  LYS*     3.2    29.3    -      -       -      +
    235C  GLY      3.4    20.9    -      -       -      -
    236C  VAL*     2.9    19.6    +      -       -      +
    237C  ASP*     3.1    34.5    +      -       -      +
    255C  MET      3.8     0.2    +      -       -      -
    256C  VAL*     1.3    76.7    -      -       -      +
    258C  PRO*     1.3    81.7    -      -       +      +
    259C  GLY      3.3     0.3    +      -       -      -
    260C  GLY*     2.9    18.0    +      -       -      +
    288C  LYS*     3.7     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  GLU*     6.0     1.8    -      -       +      +
     97A  ARG*     2.9    32.2    +      -       -      +
     99A  TYR*     4.8     2.3    -      -       -      +
    102A  HIS*     3.6    32.5    -      -       +      +
    105A  GLY*     4.7     1.8    -      -       -      -
    106A  MET*     3.9    36.8    -      -       +      +
    234C  LYS      5.7     1.1    -      -       -      +
    256C  VAL      4.2     2.7    -      -       -      +
    257C  LYS*     1.3    86.0    -      -       +      +
    259C  GLY*     1.3    56.7    +      -       -      +
    286C  ALA      3.3    10.8    -      -       -      +
    288C  LYS*     3.7    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ARG*     4.3     4.5    +      -       -      -
     99A  TYR*     3.4    40.7    +      -       -      -
    238C  ARG*     4.5     5.7    +      -       -      -
    257C  LYS      3.3     0.2    +      -       -      -
    258C  PRO*     1.3    71.4    -      -       -      +
    260C  GLY*     1.3    64.3    +      -       -      +
    261C  ILE*     4.7     2.9    -      -       -      +
    286C  ALA      3.0    12.5    +      -       -      -
    287C  HIS*     3.1    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ARG*     4.5     3.3    -      -       -      +
    237C  ASP      3.3    16.8    -      -       -      -
    238C  ARG*     3.9     4.9    -      -       -      -
    256C  VAL*     4.7     6.1    -      -       -      -
    257C  LYS*     2.9    19.2    +      -       -      -
    258C  PRO      3.2     1.2    +      -       -      -
    259C  GLY*     1.3    82.9    -      -       -      +
    261C  ILE*     1.3    64.9    +      -       -      +
    287C  HIS      3.3     1.8    +      -       -      +
    288C  LYS*     3.7     3.0    -      -       -      -
    289C  THR*     3.2    22.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 261 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  TYR*     6.1     0.4    -      -       -      +
    161C  LEU      3.9    17.3    -      -       -      +
    162C  ALA*     3.5    21.3    -      -       -      +
    163C  ASP*     3.6    22.4    -      -       +      +
    237C  ASP      3.4     6.3    +      -       -      -
    238C  ARG*     3.3    29.4    -      -       -      +
    239C  VAL      3.1    22.5    +      -       -      +
    256C  VAL*     3.9     2.3    -      -       -      +
    259C  GLY      4.7     2.9    -      -       -      +
    260C  GLY*     1.3    79.9    -      -       -      +
    262C  ILE*     1.3    73.8    +      -       -      +
    289C  THR*     3.6    17.9    -      -       +      +
    291C  LYS*     4.3    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239C  VAL*     3.3     7.4    -      -       +      +
    241C  MET*     3.6    31.0    -      -       +      -
    249C  LEU*     4.3     6.7    -      -       +      -
    252C  ALA*     3.7    13.5    -      -       +      -
    253C  VAL*     3.6    47.1    -      -       +      +
    256C  VAL*     3.9    20.9    -      -       +      -
    261C  ILE*     1.3    76.4    -      -       -      +
    263C  SER*     1.3    60.8    +      -       -      +
    264C  ASN      4.9     0.4    -      -       -      +
    288C  LYS*     4.9     5.2    -      -       +      -
    289C  THR      2.8    15.2    +      -       -      +
    290C  ILE*     4.2    17.0    -      -       +      -
    291C  LYS*     2.8    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158C  GLY*     2.7    35.1    +      -       -      -
    161C  LEU*     3.3    20.0    -      -       -      +
    162C  ALA*     3.9    20.0    -      -       -      -
    239C  VAL      2.7    13.4    +      -       -      -
    240C  ILE*     3.2     9.1    -      -       -      +
    241C  MET*     2.7    30.1    +      -       -      -
    261C  ILE*     4.1     0.8    -      -       -      -
    262C  ILE*     1.3    73.6    -      -       -      +
    264C  ASN*     1.3    54.3    +      -       -      +
    291C  LYS*     3.8     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 264 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  TRP*     4.5     9.6    -      -       +      -
    284A  GLY*     2.8    33.4    +      -       -      -
    161C  LEU*     4.6     1.0    -      -       -      +
    241C  MET*     3.5    25.1    -      -       +      +
    262C  ILE*     4.0     1.0    -      -       +      +
    263C  SER*     1.3    71.2    +      -       -      +
    265C  ILE*     1.3    63.5    +      -       -      +
    266C  ASN*     3.1    31.5    +      -       -      +
    268C  HIS*     2.8    25.8    +      -       -      -
    290C  ILE*     5.8     0.7    -      -       +      -
    291C  LYS      2.7    19.3    +      -       -      +
    292C  GLY*     3.0    21.2    -      -       -      -
    293C  GLY      3.2     6.9    +      -       -      -
----------------------------------------------------------
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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