Contacts of the strand formed by residues 217 - 223 (chain B) in PDB entry 1AHF


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 TRP 217 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  LEU*     3.3    55.0    -      -       +      -
    178B  ASN*     4.9     1.3    -      -       -      -
    180B  ALA*     3.2    24.9    +      -       +      +
    181B  GLN      3.2    19.4    +      -       -      -
    184B  ASP*     3.4    10.3    -      -       +      +
    186B  VAL*     3.4    27.6    -      -       +      -
    188B  PHE*     5.2     2.9    -      +       -      -
    208B  LEU*     5.0     4.0    -      -       +      -
    211B  LEU*     4.2    18.2    -      -       +      -
    212B  SER*     3.0    50.2    +      -       -      +
    215B  LYS*     3.3    33.1    -      -       +      +
    216B  GLY*     1.3    79.3    -      -       -      +
    218B  LEU*     1.3    59.3    +      -       -      +
    219B  PRO*     3.2    13.2    -      -       -      +
    247B  HIS*     4.2     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     4.4    23.1    -      -       +      -
      6A  PHE*     3.8    18.4    -      -       +      -
    119B  LEU*     3.8    13.5    -      -       +      -
    125B  VAL*     5.1     0.2    -      -       +      -
    183B  GLY*     5.0     0.8    -      -       -      -
    184B  ASP      2.9     9.8    +      -       -      +
    185B  VAL*     3.2    24.4    -      -       +      +
    186B  VAL      2.8    25.9    +      -       -      -
    216B  GLY      4.2     0.8    +      -       -      -
    217B  TRP*     1.3    72.1    -      -       -      +
    219B  PRO*     1.4    73.8    -      -       +      +
    249B  GLU*     3.9    33.4    -      -       +      +
    250B  LEU*     4.1     5.4    -      -       -      -
    251B  ILE*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  VAL*     3.5     6.5    -      -       +      +
    188B  PHE*     4.1     9.0    -      -       +      -
    212B  SER*     4.7     2.0    -      -       -      +
    217B  TRP      3.2     9.0    -      -       -      +
    218B  LEU*     1.4    84.3    -      -       +      +
    220B  LEU*     1.3    58.2    +      -       -      +
    221B  PHE*     4.1    10.3    -      -       +      -
    243B  PHE*     3.6    29.2    -      -       +      -
    247B  HIS*     3.4    28.7    -      -       +      +
    249B  GLU      3.6    18.8    -      -       -      +
    250B  LEU*     3.5    12.6    -      -       +      +
    251B  ILE*     2.9    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  LEU*     4.8     7.0    -      -       +      -
    115B  ALA*     4.4    15.9    -      -       +      -
    119B  LEU*     4.8     9.9    -      -       +      -
    133B  VAL*     6.0     0.2    -      -       +      -
    147B  PHE*     4.2    27.6    -      -       +      -
    185B  VAL*     3.7    24.5    -      -       +      -
    186B  VAL      3.0     6.9    +      -       -      +
    187B  LEU*     2.9    17.5    -      -       +      +
    188B  PHE      2.9    24.8    +      -       -      -
    218B  LEU      3.7     0.6    +      -       -      -
    219B  PRO*     1.3    71.4    -      -       -      +
    221B  PHE*     1.3    69.2    +      -       -      +
    251B  ILE*     3.1    37.7    -      -       +      +
    252B  VAL*     4.2     1.1    -      -       -      +
    253B  ALA*     4.5     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  LEU*     4.3     0.9    -      -       -      -
    188B  PHE*     3.2    14.4    -      +       +      -
    190B  GLY*     4.1    21.3    -      -       -      -
    205B  TRP*     4.1    22.4    -      +       -      -
    219B  PRO*     4.2    11.7    -      -       +      -
    220B  LEU*     1.3    77.9    -      -       -      +
    222B  ASP*     1.3    58.6    +      -       -      +
    223B  PHE*     4.9     2.7    -      +       +      +
    239B  GLY      3.9     0.4    -      -       -      -
    240B  LEU*     3.8    41.5    -      -       +      -
    243B  PHE*     3.7    51.6    -      +       +      -
    250B  LEU*     5.1     3.8    -      -       +      -
    251B  ILE      2.7    16.2    +      -       -      +
    252B  VAL*     3.7    18.9    -      -       +      +
    253B  ALA*     2.6    36.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  GLY*     5.7     0.3    -      -       -      +
    112B  LEU*     3.6    11.4    -      -       +      +
    143B  HIS*     2.4    35.0    +      -       +      +
    187B  LEU*     3.8    15.1    -      -       +      +
    188B  PHE      2.7    12.7    +      -       -      +
    189B  HIS*     3.3     8.1    +      -       +      +
    190B  GLY      2.7    28.7    +      -       -      -
    191B  CYS      5.5     0.3    -      -       -      +
    221B  PHE*     1.3    72.4    -      -       -      +
    223B  PHE*     1.3    54.9    +      -       -      +
    224B  ALA*     3.9     7.8    +      -       -      +
    253B  ALA*     3.5     9.2    -      -       -      +
    412B  PLP      2.8    37.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  LEU*     3.9    23.6    -      -       +      -
    190B  GLY*     3.6    20.0    -      -       -      +
    191B  CYS*     3.7    23.8    -      -       -      -
    221B  PHE*     3.7     2.4    +      +       +      -
    222B  ASP*     1.3    70.1    +      -       -      +
    224B  ALA*     1.3    59.5    +      -       -      +
    225B  TYR      3.5     0.4    -      -       -      -
    226B  GLN*     3.5    42.1    +      -       +      +
    236B  ASP      3.1    33.7    -      -       -      -
    237B  ALA*     4.1     9.9    -      -       +      -
    240B  LEU*     4.6    15.9    -      -       +      -
    252B  VAL*     4.4     9.2    -      -       +      -
    253B  ALA      2.8    14.1    +      -       -      +
    254B  SER*     3.3     9.4    -      -       -      -
    255B  SER      3.1    20.8    +      -       -      +
----------------------------------------------------------
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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