Contacts of the strand formed by residues 247 - 253 (chain H) in PDB entry 1FNS


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 GLY 247 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246H  TYR*     1.3    76.3    -      -       -      +
    248H  VAL*     1.3    68.8    +      -       -      +
    264H  MET*     4.1     1.1    -      -       -      -
    265H  ILE      3.1    13.7    -      -       -      -
    266H  TRP*     4.4     0.4    -      -       -      -
    311H  ARG*     3.5     5.2    -      -       -      +
    312H  ASP*     2.8    41.4    +      -       -      +
    314H  ALA*     3.5    17.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 248 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218H  LEU*     4.4    11.2    -      -       +      -
    236H  CYS*     4.5     1.1    -      -       -      -
    238H  VAL*     4.6     0.9    -      -       +      -
    241H  PHE*     4.4    13.9    -      -       +      -
    243H  LEU*     3.5    31.4    -      -       +      -
    247H  GLY*     1.3    80.0    -      -       -      +
    249H  ASP*     1.3    74.5    +      -       -      +
    250H  TRP*     4.5     4.4    -      -       -      +
    264H  MET*     3.2     1.7    -      -       -      -
    265H  ILE*     2.9    37.0    +      -       +      +
    283H  ILE*     4.9     0.2    -      -       -      +
    292H  VAL*     4.0    28.5    -      -       +      -
    309H  CYS*     4.1    17.3    -      -       +      -
    310H  VAL      3.5     8.1    -      -       -      +
    311H  ARG*     4.6     0.4    -      -       -      -
    312H  ASP*     4.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 249 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248H  VAL*     1.3    76.5    -      -       -      +
    250H  TRP*     1.3    66.4    +      -       -      +
    251H  VAL*     4.9     0.7    -      -       +      -
    261H  TRP*     2.9    27.1    +      -       +      +
    263H  GLY      3.2     9.9    -      -       -      +
    264H  MET*     3.3    14.3    -      -       -      +
    309H  CYS*     3.2     5.9    -      -       -      -
    310H  VAL*     2.6    40.9    +      -       +      +
    312H  ASP*     2.4    35.0    -      -       -      +
    323H  LEU*     3.4    23.3    -      -       +      +
     96L  TRP*     4.5     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 250 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220H  GLU*     4.1    10.3    -      -       +      -
    234H  ILE*     3.5    44.9    -      -       +      -
    236H  CYS*     3.6    31.2    -      -       +      -
    248H  VAL*     4.5     2.3    -      -       -      +
    249H  ASP*     1.3    78.2    +      -       -      +
    251H  VAL*     1.3    59.4    +      -       -      +
    261H  TRP*     4.2     1.0    -      -       -      -
    262H  LEU*     2.9    42.7    +      -       +      +
    263H  GLY      3.0     9.7    +      -       -      +
    281H  LEU*     5.8     0.4    -      -       +      -
    283H  ILE*     3.8    30.9    -      -       +      +
    292H  VAL*     3.7    29.9    -      -       +      +
    294H  LEU*     3.5    39.9    -      -       +      +
    307H  TYR*     4.7     6.3    -      +       +      -
    308H  TYR      3.2    22.0    -      -       -      -
    309H  CYS*     3.8    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 251 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249H  ASP*     4.9     1.6    -      -       +      -
    250H  TRP*     1.3    81.5    -      -       -      +
    252H  ARG*     1.3    63.7    +      -       -      +
    259H  LEU*     4.1    24.0    -      -       +      -
    260H  GLU      3.4    12.6    -      -       -      +
    261H  TRP*     4.1    22.2    -      -       +      -
    262H  LEU*     4.3     2.6    -      -       -      +
    307H  TYR*     3.6     1.9    -      -       -      +
    308H  TYR*     2.7    37.2    +      -       +      +
    310H  VAL*     4.3     9.9    -      -       +      -
    323H  LEU*     4.4     9.0    -      -       +      -
    326H  TRP*     3.8    38.8    -      -       +      -
     98L  PHE*     4.4     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 252 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251H  VAL*     1.3    78.1    -      -       -      +
    253H  GLN*     1.3    61.9    +      -       -      +
    254H  PRO*     4.2     7.3    -      -       +      +
    258H  GLY      3.8     0.3    -      -       -      +
    259H  LEU*     3.6     3.0    -      -       -      -
    260H  GLU*     2.7    67.9    +      -       +      +
    262H  LEU*     3.7    11.6    -      -       +      +
    277H  LEU*     3.8    19.7    -      -       -      +
    280H  ARG*     4.7     1.2    -      -       -      +
    296H  MET*     3.7     9.9    -      -       -      +
    302H  ASP      4.5     7.4    +      -       -      -
    303H  ASP*     2.7    36.7    +      -       -      +
    305H  ALA*     4.0    13.7    -      -       +      +
    306H  ARG      3.1    11.2    -      -       -      +
    307H  TYR*     2.8    44.0    +      -       +      -
    308H  TYR*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 253 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252H  ARG*     1.3    75.7    -      -       -      +
    254H  PRO*     1.3    71.3    -      -       -      +
    255H  PRO*     3.5     1.1    -      -       +      +
    256H  GLY      5.7     0.4    -      -       -      +
    257H  LYS      3.0    29.3    +      -       -      +
    258H  GLY      3.2     6.9    +      -       -      +
    259H  LEU*     3.8    17.4    -      -       +      +
    305H  ALA*     3.4     2.9    -      -       -      -
    306H  ARG*     2.7    36.1    +      -       +      +
    308H  TYR*     3.1    14.4    +      -       +      -
     38L  GLN*     3.0    42.2    +      -       -      -
     87L  TYR*     3.4    13.1    +      -       -      -
----------------------------------------------------------
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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