Contacts of the strand formed by residues 273 - 280 (chain A) in PDB entry 1II7


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 PHE 273 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLN*     3.4    24.2    -      -       -      -
     16A  PHE*     3.8    24.2    -      +       -      -
     21A  ARG*     3.5    21.8    -      -       -      -
    228A  ARG*     3.7    33.9    -      -       +      +
    230A  ASP      3.4    31.4    -      -       -      -
    231A  PHE*     4.1    17.3    -      +       +      -
    234A  TYR*     3.7    10.7    -      -       -      -
    235A  GLU*     2.9    29.0    +      -       -      +
    236A  VAL      3.6     1.7    +      -       -      -
    271A  ARG*     3.7    11.6    +      -       -      -
    272A  PRO*     1.3    82.1    -      -       -      +
    274A  ILE*     1.3    62.1    +      -       -      +
    275A  ASP      4.1     0.2    -      -       -      -
    301A  TYR*     3.3    24.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     4.0     4.1    -      -       -      -
    235A  GLU*     4.9     2.5    -      -       +      +
    236A  VAL*     3.5    24.5    -      -       +      +
    238A  TYR*     3.5    36.3    -      -       +      +
    272A  PRO*     4.4    13.5    -      -       +      -
    273A  PHE*     1.3    81.3    -      -       -      +
    275A  ASP*     1.3    60.0    +      -       -      +
    276A  VAL*     4.1    11.0    -      -       +      -
    295A  LEU      5.4     1.3    -      -       -      +
    296A  ILE*     4.6    10.3    -      -       +      -
    297A  PRO*     4.8    13.2    -      -       +      -
    300A  ALA*     3.9    23.3    -      -       +      -
    301A  TYR      2.8     8.6    +      -       -      +
    302A  VAL*     3.4    11.1    -      -       +      +
    303A  ARG      3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     4.0    15.5    -      -       +      +
    234A  TYR*     4.0    13.8    -      -       +      +
    236A  VAL      3.0     8.2    +      -       -      +
    237A  ARG*     2.5    42.6    +      -       +      -
    238A  TYR*     2.7    32.2    +      -       -      +
    274A  ILE*     1.3    71.3    -      -       -      +
    276A  VAL*     1.3    60.6    +      -       -      +
    303A  ARG*     2.8    45.4    +      -       -      +
    305A  ASN*     3.1    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ARG*     5.7     0.4    -      -       -      -
    238A  TYR*     3.3    10.8    -      -       +      +
    245A  PHE*     4.0     9.0    -      -       +      -
    274A  ILE*     4.1    13.0    -      -       +      -
    275A  ASP*     1.3    83.9    +      -       -      +
    277A  LYS*     1.3    63.6    +      -       -      +
    278A  ILE*     3.7    30.1    -      -       +      -
    292A  LEU*     4.0    24.9    -      -       +      -
    296A  ILE*     5.3     0.2    -      -       +      -
    302A  VAL*     4.1     9.6    -      -       +      -
    303A  ARG      2.8    16.6    +      -       -      +
    304A  LEU*     3.6    17.7    -      -       +      -
    305A  ASN*     2.8    37.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ARG*     5.2    17.9    -      -       +      +
    238A  TYR      2.7    14.4    +      -       -      +
    239A  GLU*     3.4    37.4    +      -       +      +
    240A  TRP      3.0    26.5    +      -       -      -
    245A  PHE*     4.2     0.3    -      -       -      -
    276A  VAL*     1.3    73.7    -      -       -      +
    278A  ILE*     1.3    66.7    +      -       -      +
    279A  LYS*     5.6     6.3    -      -       -      +
    305A  ASN*     3.7    20.6    -      -       +      +
    331A  TRP*     4.5    23.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  TRP*     4.1    10.5    -      -       +      -
    245A  PHE*     3.8    20.4    -      -       +      -
    276A  VAL*     3.7    22.9    -      -       +      -
    277A  LYS*     1.3    82.7    -      -       -      +
    279A  LYS*     1.3    67.2    +      -       -      +
    285A  ILE*     4.1    26.2    -      -       +      -
    288A  ALA*     3.7    24.2    -      -       +      -
    289A  ILE*     3.9    29.4    -      -       +      -
    292A  LEU*     4.9     0.2    -      -       +      -
    304A  LEU*     5.3     2.5    -      -       +      -
    305A  ASN      3.2    11.6    +      -       -      +
    306A  ILE*     3.4    10.6    -      -       +      +
    307A  GLY      3.0    21.7    +      -       -      +
    331A  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  TRP*     4.3     9.1    +      -       -      +
    277A  LYS*     5.6     7.0    -      -       -      +
    278A  ILE*     1.3    80.6    -      -       -      +
    280A  GLY*     1.3    57.4    +      -       -      +
    284A  GLU*     4.2    12.8    -      -       -      +
    285A  ILE*     4.6     4.9    -      -       -      -
    307A  GLY*     3.4     7.9    -      -       -      +
    331A  TRP*     3.5    25.4    -      -       +      -
    333A  ILE*     3.2    49.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  LYS*     1.3    79.6    -      -       -      +
    281A  SER*     1.3    67.4    +      -       -      -
    284A  GLU*     4.5     7.2    -      -       -      -
    285A  ILE*     3.5     7.3    -      -       -      +
    307A  GLY      3.0    17.4    +      -       -      +
    308A  TRP      4.1     0.2    -      -       -      -
    309A  ARG*     3.6    14.7    +      -       -      -
    333A  ILE*     3.6     9.1    -      -       -      +
----------------------------------------------------------
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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