Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 1ASC


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 LEU 250 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     4.4     2.5    -      -       +      -
    219A  LEU*     4.0     3.8    -      -       -      +
    220A  PRO*     3.5    21.8    -      -       +      +
    222A  PHE*     5.6     2.5    -      -       +      -
    240A  LEU*     4.1    12.1    -      -       +      -
    243A  PHE*     4.1     9.9    -      -       +      -
    244A  ALA*     3.6    39.9    -      -       +      +
    247A  HIS*     4.1     7.6    -      -       +      -
    249A  GLU*     1.3    76.5    -      -       -      +
    251A  ILE*     1.3    67.3    +      -       -      +
    252A  VAL*     3.7    28.3    -      -       +      -
    272A  LEU      3.6     0.2    -      -       -      -
    273A  VAL*     2.8    55.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ALA*     3.9    16.4    -      -       +      -
    125A  PHE*     5.1     1.8    -      -       +      -
    126A  LEU*     3.8    28.0    -      -       +      -
    219A  LEU*     3.5    33.0    -      -       +      -
    220A  PRO      3.0     8.5    +      -       -      +
    221A  LEU*     3.3    23.2    -      -       +      -
    222A  PHE*     2.8    25.6    +      -       -      +
    250A  LEU*     1.3    80.5    -      -       -      +
    252A  VAL*     1.3    63.9    +      -       -      +
    270A  CYS*     4.0    13.2    -      -       -      -
    271A  THR      3.2    11.9    -      -       -      +
    272A  LEU*     3.9    22.2    -      -       +      -
    287A  MET*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  LEU*     4.0    27.8    -      -       +      -
     95A  PHE*     4.2    10.5    -      -       +      -
    222A  PHE*     3.5     8.5    -      -       +      +
    224A  PHE*     4.1    16.6    -      -       +      -
    240A  LEU*     3.7    30.7    -      -       +      -
    250A  LEU*     3.7    11.9    -      -       +      -
    251A  ILE*     1.3    77.4    -      -       -      +
    253A  ALA*     1.3    69.9    +      -       -      +
    254A  SER      4.0     0.9    -      -       -      +
    269A  ALA      3.6     0.9    -      -       -      +
    270A  CYS*     3.4     6.6    -      -       -      -
    271A  THR*     2.8    44.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  GLY*     4.1     4.0    -      -       -      +
    118A  ALA*     3.9    14.8    -      -       +      +
    119A  LEU*     3.6    35.0    -      -       +      +
    122A  ALA*     5.9     0.4    -      -       +      -
    221A  LEU*     4.8     2.7    -      -       +      -
    222A  PHE      2.7    15.3    +      -       -      +
    223A  ALA*     3.5     2.4    -      -       -      -
    224A  PHE*     2.7    29.1    +      -       -      +
    252A  VAL*     1.3    75.0    -      -       -      +
    254A  SER*     1.3    57.6    +      -       -      +
    269A  ALA      3.4     6.5    -      -       -      -
    270A  CYS*     5.5     0.9    -      -       -      -
    409A  NPL      4.5     3.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  THR*     3.8    10.7    -      -       -      +
     94A  LEU*     4.1    25.9    -      -       -      +
    115A  GLY*     3.3     9.3    -      -       -      -
    224A  PHE*     3.0    12.3    -      -       -      -
    227A  GLN*     5.6     1.8    -      -       -      -
    252A  VAL      4.0     0.4    -      -       -      -
    253A  ALA*     1.3    75.3    -      -       -      +
    255A  SER*     1.3    65.9    +      -       -      +
    256A  TYR*     4.9     6.5    -      -       -      -
    268A  GLY*     3.2     3.3    -      -       -      -
    269A  ALA*     2.9    48.8    +      -       -      +
    271A  THR*     5.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  GLY*     3.6    11.9    +      -       -      -
    224A  PHE      3.1     9.2    +      -       -      +
    225A  ALA*     4.0    29.9    +      -       -      +
    227A  GLN*     5.7     1.2    +      -       -      +
    254A  SER*     1.3    81.0    -      -       -      +
    256A  TYR*     1.3    69.0    +      -       -      +
    257A  SER*     3.2    14.0    +      -       -      -
    258A  LYS*     4.9     0.3    -      -       -      -
    259A  ASN*     4.0     9.7    +      -       -      +
    267A  VAL      3.8     4.9    +      -       -      -
    268A  GLY*     4.1     0.4    -      -       -      -
    409A  NPL      2.3    31.2    +      -       -      -
----------------------------------------------------------
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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