Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 1M27


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 VAL 40 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ASP*     4.1     1.4    -      -       -      +
     34A  SER*     3.0    35.2    +      -       -      +
     37A  VAL*     3.4    35.6    -      -       +      +
     38A  PRO      3.2     2.7    -      -       -      +
     39A  GLY*     1.3    84.9    +      -       -      +
     41A  TYR*     1.3    75.7    +      -       -      +
     55A  ARG*     4.4    25.8    -      -       +      -
     56A  VAL      3.7     8.7    -      -       -      +
     57A  SER*     4.4    11.2    -      -       -      -
    300A  FLC      5.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ASP*     4.1    14.7    +      -       -      +
      7A  TYR*     4.0    19.5    +      +       -      -
     31A  LEU*     4.5    14.1    -      -       +      -
     32A  ARG      3.5    10.1    -      -       -      +
     33A  ASP*     3.3    30.5    -      -       -      -
     39A  GLY*     3.7    25.0    -      -       -      -
     40A  VAL*     1.3    79.8    -      -       -      +
     42A  CYS*     1.3    65.3    +      -       -      +
     43A  LEU      4.2     0.2    -      -       -      -
     55A  ARG*     3.4     5.0    -      -       -      -
     56A  VAL*     2.7    50.1    +      -       +      +
     58A  GLN*     5.7     0.4    -      -       -      -
     64A  TRP*     3.5    41.4    -      +       -      -
     80A  ILE*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LEU      3.8     0.2    -      -       -      +
     31A  LEU*     3.5     6.4    -      -       -      -
     32A  ARG*     2.9    51.2    +      -       -      +
     34A  SER*     4.2     7.9    -      -       -      -
     41A  TYR*     1.3    78.5    -      -       -      +
     43A  LEU*     1.3    61.2    -      -       -      +
     44A  CYS*     3.6     4.9    +      -       -      -
     53A  THR*     3.5    21.1    -      -       +      -
     54A  TYR      3.4     3.4    -      -       -      -
     55A  ARG*     4.7     8.1    -      -       -      -
    300A  FLC      3.5    44.0    -      -       -      -
    281B  TYR*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  TYR*     4.3    13.9    -      -       +      -
     30A  LEU      3.7    13.0    -      -       -      +
     31A  LEU*     3.7    21.2    -      -       +      +
     41A  TYR      4.2     0.2    -      -       -      -
     42A  CYS*     1.3    71.2    -      -       -      +
     44A  CYS*     1.3    58.5    +      -       -      +
     45A  VAL*     4.5     6.7    -      -       +      -
     52A  TYR      3.3     4.5    -      -       -      +
     53A  THR*     3.4     0.5    -      -       -      -
     54A  TYR*     2.8    56.8    +      -       +      +
     56A  VAL*     4.4     8.0    -      -       +      +
     83A  LEU*     4.7    18.8    -      -       +      -
     84A  ILE*     5.0     7.6    -      -       +      -
     87A  PHE*     5.1     7.9    -      -       +      -
     94A  ILE*     5.7     3.6    -      -       +      -
     98A  LEU*     4.0    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLY*     5.8     2.5    -      -       -      +
     20A  LEU*     3.6    11.3    -      -       +      +
     29A  TYR*     3.0    27.0    -      -       -      +
     30A  LEU*     2.9    26.0    +      -       +      +
     32A  ARG*     3.9    24.7    -      -       -      -
     42A  CYS*     3.8    11.9    -      -       -      -
     43A  LEU*     1.3    74.6    -      -       -      +
     45A  VAL*     1.3    63.3    +      -       -      +
     51A  ILE*     3.6    19.7    -      -       +      -
     52A  TYR      3.3     3.1    -      -       -      -
     53A  THR*     4.1    21.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LEU*     4.3     3.8    -      -       -      -
     27A  GLY*     4.0    10.8    -      -       -      -
     28A  SER      3.4     9.9    -      -       -      +
     29A  TYR*     4.3     0.2    -      -       +      -
     43A  LEU*     4.5     7.0    -      -       +      -
     44A  CYS*     1.3    79.6    -      -       -      +
     46A  LEU*     1.3    64.2    +      -       -      +
     47A  TYR      3.7     0.5    +      -       -      -
     50A  TYR      3.6     0.3    -      -       -      +
     51A  ILE*     3.5     0.6    -      -       -      -
     52A  TYR*     2.8    46.4    +      -       +      +
     54A  TYR*     4.4    15.9    -      -       +      -
     94A  ILE*     5.1     2.5    -      -       +      -
     95A  VAL*     4.9     4.5    -      -       +      -
     96A  ILE*     3.9    30.3    -      -       +      +
     98A  LEU*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LEU*     3.4    31.5    -      -       +      +
     21A  LEU*     4.0    27.1    -      -       +      -
     24A  GLY*     4.5     4.3    -      -       -      -
     25A  LEU      3.5    27.8    -      -       -      +
     26A  ASP*     3.3     7.7    -      -       -      +
     27A  GLY*     2.8    29.8    +      -       -      -
     28A  SER*     3.1    21.9    +      -       -      +
     45A  VAL*     1.3    72.9    -      -       -      +
     47A  TYR*     1.3    63.5    +      -       -      +
     49A  GLY*     4.1     6.7    -      -       -      +
     50A  TYR      3.4    28.9    -      -       -      +
     51A  ILE*     4.1     8.5    -      -       +      +
     96A  ILE*     4.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ASP*     3.8     6.7    -      -       -      -
     45A  VAL      3.7     0.6    +      -       -      -
     46A  LEU*     1.3    75.7    -      -       -      +
     48A  HIS*     1.3   105.7    +      +       +      +
     49A  GLY      3.3     1.1    -      -       -      -
     50A  TYR*     2.9    19.5    +      -       -      +
     52A  TYR*     3.4    36.6    +      +       +      -
     95A  VAL*     4.0    36.8    +      -       +      -
     96A  ILE*     3.9    35.9    -      -       +      -
----------------------------------------------------------
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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