Contacts of the strand formed by residues 257 - 265 (chain B) in PDB entry 1FIC


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 THR 257 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  GLU*     5.3    13.9    -      -       +      +
    250B  LEU      3.1     8.3    -      -       -      +
    251B  GLU*     3.7    28.0    -      -       +      +
    255B  GLY      4.0     4.4    +      -       -      +
    256B  ARG*     1.3    78.8    -      -       -      +
    258B  SER*     1.3    65.7    +      -       -      +
    259B  THR*     6.4     0.2    -      -       -      -
    285B  ASP*     4.1     7.8    -      -       -      +
    372B  TRP*     4.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  VAL      3.8     0.3    -      -       -      +
    249B  GLU*     3.5     2.8    -      -       -      +
    250B  LEU*     2.8    33.6    +      -       -      +
    257B  THR*     1.3    77.7    -      -       -      +
    259B  THR*     1.3    66.0    +      -       -      +
    285B  ASP*     3.5    17.3    -      -       -      -
    286B  ALA*     3.3    16.8    -      -       -      +
    372B  TRP*     3.2    45.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  ARG*     3.8    38.4    +      -       -      +
    248B  VAL      3.2     9.4    -      -       -      +
    249B  GLU*     4.2    14.1    -      -       +      -
    257B  THR*     6.4     0.4    -      -       -      -
    258B  SER*     1.3    78.7    -      -       -      +
    260B  ALA*     1.3    61.5    +      -       -      +
    261B  ASP*     4.6     2.6    +      -       -      -
    284B  GLY*     3.2    15.1    -      -       -      -
    285B  ASP*     3.0    11.7    +      -       -      -
    286B  ALA*     2.9    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  LEU      3.7     0.9    -      -       -      +
    247B  ARG*     3.6     0.5    -      -       -      -
    248B  VAL*     2.9    33.2    +      -       +      +
    259B  THR*     1.3    80.3    -      -       -      +
    261B  ASP*     1.3    62.9    +      -       -      +
    262B  TYR*     3.9     6.7    -      -       +      -
    281B  PHE*     4.0     7.9    -      -       +      -
    283B  GLY      3.6     6.9    +      -       -      -
    286B  ALA*     4.1     4.0    -      -       +      -
    287B  GLY      3.6    24.0    -      -       -      +
    369B  TRP*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  LEU      3.2     7.0    -      -       -      +
    247B  ARG*     2.9    48.0    +      -       -      +
    259B  THR*     4.6     2.3    -      -       -      -
    260B  ALA*     1.3    79.6    +      -       -      +
    262B  TYR*     1.3    59.2    +      -       -      +
    281B  PHE*     3.3    12.5    -      -       -      -
    282B  ALA*     2.7    47.4    +      -       +      +
    283B  GLY      2.8    18.5    +      -       -      +
    284B  GLY*     5.8     0.2    -      -       -      -
    392B  LEU*     4.4    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  ALA*     3.4     3.8    -      -       -      -
    246B  LEU*     2.9    50.9    +      -       +      +
    248B  VAL*     4.7     1.6    -      -       +      -
    260B  ALA*     3.9    25.8    -      -       +      -
    261B  ASP*     1.3    76.4    -      -       -      +
    263B  ALA*     1.3    63.1    +      -       -      +
    265B  PHE*     4.2     3.4    -      -       +      +
    278B  TYR*     3.4    48.9    -      +       +      -
    280B  TYR      3.4     2.2    -      -       -      -
    281B  PHE*     3.6    15.7    -      +       +      -
    282B  ALA*     4.7     0.9    -      -       -      -
    288B  ASP*     2.6    44.8    +      -       -      -
    289B  ALA      3.6     1.0    +      -       -      -
    290B  PHE*     3.4    30.7    +      +       +      +
    369B  TRP*     3.6    10.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  TYR      4.4     0.9    -      -       -      -
    245B  ALA*     4.5     1.1    -      -       -      +
    261B  ASP      4.2     0.4    -      -       -      -
    262B  TYR*     1.3    71.6    -      -       -      +
    264B  MET*     1.3    65.6    +      -       +      +
    278B  TYR*     3.7     1.2    -      -       -      +
    279B  ALA      2.8    24.9    +      -       -      -
    280B  TYR*     2.8    48.0    +      -       +      +
    282B  ALA*     4.3     5.2    -      -       +      +
    389B  PHE*     3.5    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  PRO*     4.0    23.8    -      -       +      -
    244B  TYR      3.0    14.4    +      -       -      -
    263B  ALA*     1.3    76.6    -      -       +      +
    265B  PHE*     1.3    62.3    +      -       -      +
    266B  LYS*     3.9     9.5    +      -       -      +
    277B  THR      3.5     1.6    -      -       -      +
    278B  TYR*     3.1    16.3    +      -       -      -
    279B  ALA*     3.5    17.4    +      -       +      +
    280B  TYR*     3.4    40.2    -      -       +      +
    389B  PHE*     3.9    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  PHE*     3.8    23.6    -      +       -      -
    233B  ILE*     4.2     6.3    -      -       +      -
    237B  SER*     4.0    19.7    -      -       -      +
    244B  TYR*     2.9    21.2    +      -       +      +
    245B  ALA      4.5     0.2    -      -       -      -
    246B  LEU*     3.8    42.6    -      -       +      +
    262B  TYR*     4.2     3.6    -      -       +      +
    263B  ALA      3.5     0.2    -      -       -      -
    264B  MET*     1.3    75.7    -      -       -      +
    266B  LYS*     1.3    69.0    +      -       -      +
    267B  VAL*     3.5    27.4    -      -       +      -
    276B  LEU*     3.2    34.1    -      -       +      -
    277B  THR      3.3     7.0    -      -       -      -
    278B  TYR*     4.3     7.0    -      +       +      +
    335B  TRP*     5.0     4.7    -      +       -      -
    384B  MET*     5.5     0.2    -      -       +      -
    386B  ILE*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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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