Contacts of the helix formed by residues 35 - 50 (chain B) in PDB entry 2PI8


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 ASN 35 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  PRO*     4.2     4.4    -      -       -      +
     34B  ILE*     1.3    81.1    +      -       -      +
     36B  ALA*     1.3    58.9    +      -       -      +
     37B  GLY      3.3     2.9    -      -       -      +
     38B  ASP*     3.7    19.5    -      -       +      +
     39B  PHE*     2.8    25.6    +      -       -      +
     68B  LEU*     5.5     0.2    -      -       -      -
    255B  ARG      3.6    17.4    +      -       -      -
    256B  ALA*     4.1     7.1    -      -       -      +
    291B  ARG*     3.5    28.9    -      -       -      +
    292B  LEU*     2.7    52.8    +      -       -      +
     38D  ASP*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  PRO*     4.0     3.4    +      -       -      +
     34B  ILE      3.6     3.2    +      -       -      -
     35B  ASN*     1.3    75.9    -      -       -      +
     37B  GLY*     1.3    58.0    +      -       -      +
     39B  PHE*     4.0     1.2    -      -       -      +
     40B  ALA*     3.1    30.3    +      -       -      +
     65B  GLN*     4.7     0.5    +      -       -      -
     68B  LEU*     3.9    27.9    -      -       +      +
     34D  ILE*     4.0    35.2    -      -       +      +
     35D  ASN*     6.2     0.4    -      -       +      -
     38D  ASP*     4.2     4.1    +      -       -      +
    291D  ARG*     5.8     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASN      3.3     0.2    -      -       -      -
     36B  ALA*     1.3    77.7    -      -       -      +
     38B  ASP*     1.3    65.7    +      -       -      +
     40B  ALA*     4.0     5.0    -      -       -      +
     41B  GLU*     3.2    25.6    +      -       -      +
     38D  ASP*     3.8    16.1    +      -       -      -
    255D  ARG*     6.0     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  ILE      5.2     0.7    -      -       -      +
     35B  ASN*     3.3    27.6    +      -       +      +
     37B  GLY*     1.3    77.1    -      -       -      +
     39B  PHE*     1.3    59.8    +      -       -      +
     41B  GLU*     3.5     9.9    +      -       -      +
     42B  GLN*     3.0    26.9    +      -       -      +
    253B  VAL*     3.8    13.5    -      -       +      +
    254B  GLY      4.2    12.2    -      -       -      +
    256B  ALA*     3.7    19.0    -      -       +      +
    291B  ARG*     4.2     5.5    +      -       -      -
     38D  ASP*     4.8     5.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASN      2.8    18.0    +      -       -      +
     36B  ALA      4.0     2.9    -      -       -      +
     38B  ASP*     1.3    74.3    -      -       -      +
     40B  ALA*     1.3    63.2    +      -       -      +
     42B  GLN*     3.0     7.1    +      -       +      +
     43B  ILE*     2.9    46.3    +      -       +      +
     64B  VAL*     3.3    30.3    -      -       +      -
     65B  GLN*     3.0    22.0    -      -       -      -
     68B  LEU*     4.1     3.4    -      -       +      -
    256B  ALA*     4.3     5.3    -      -       -      +
    270B  THR*     3.6    30.5    -      -       +      -
    292B  LEU*     3.6    47.6    -      -       +      +
    293B  MSE      4.4     0.9    -      -       -      -
    294B  VAL*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  ALA      3.1    16.6    +      -       -      +
     37B  GLY*     4.0     6.5    -      -       -      +
     39B  PHE*     1.3    75.4    -      -       -      +
     41B  GLU*     1.3    61.7    +      -       -      +
     43B  ILE*     3.3     5.6    +      -       -      +
     44B  ASN*     3.1    34.1    +      -       -      +
     65B  GLN*     3.3    34.7    +      -       -      +
     69B  ARG*     6.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLY      3.2    18.2    +      -       -      +
     38B  ASP*     3.5    10.6    -      -       -      +
     40B  ALA*     1.3    76.6    -      -       -      +
     42B  GLN*     1.3    64.7    +      -       -      +
     44B  ASN*     3.2    11.3    +      -       +      +
     45B  HIS*     3.0    51.7    +      -       +      +
    253B  VAL*     3.7    21.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ASP      3.0    15.6    +      -       -      +
     39B  PHE*     3.3    12.1    -      -       +      +
     41B  GLU*     1.3    76.8    -      -       -      +
     43B  ILE*     1.3    61.1    +      -       -      +
     45B  HIS*     3.2     6.4    +      -       -      +
     46B  ILE*     3.1    18.8    +      -       +      +
    250B  VAL*     4.0     1.8    -      -       -      +
    251B  PRO      3.2    20.9    +      -       -      +
    252B  LEU*     4.1     0.2    -      -       -      -
    253B  VAL*     3.3    23.9    +      -       +      +
    256B  ALA*     3.7    15.4    -      -       +      +
    257B  SER*     3.2    25.8    -      -       -      -
    294B  VAL*     4.1    19.5    -      -       +      -
    296B  LEU*     3.2    24.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  PHE*     2.9    47.9    +      -       +      +
     40B  ALA*     3.5     9.4    -      -       -      +
     41B  GLU      3.2     0.2    -      -       -      -
     42B  GLN*     1.3    75.4    -      -       -      +
     44B  ASN*     1.3    62.0    +      -       -      +
     46B  ILE*     3.3     7.3    +      -       +      +
     47B  ARG*     2.9    27.4    +      -       -      +
     54B  TYR*     4.0    10.4    -      -       +      -
     61B  TYR*     3.6    61.5    -      -       +      +
     62B  ASN*     5.6     1.1    -      -       -      +
     65B  GLN*     4.7     9.0    -      -       +      +
    294B  VAL*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  ALA*     3.1    22.3    +      -       -      +
     41B  GLU*     3.2    12.0    +      -       +      +
     43B  ILE*     1.3    81.5    -      -       -      +
     45B  HIS*     1.3    62.2    +      -       +      +
     47B  ARG*     3.2    34.4    +      -       -      +
     48B  ASN*     2.9    34.0    +      -       -      +
    316D  GLU*     4.9    10.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  GLU*     3.0    41.2    +      -       +      +
     42B  GLN*     3.4    15.3    -      -       -      +
     43B  ILE      3.1     0.2    -      -       -      -
     44B  ASN*     1.3    76.1    -      -       +      +
     46B  ILE*     1.3    61.0    +      -       -      +
     48B  ASN*     3.4     3.5    +      -       -      +
     49B  SER*     2.8    36.1    +      -       -      -
    243B  PRO*     5.9     2.0    -      -       +      -
    250B  VAL*     3.9     2.7    -      -       +      -
    251B  PRO*     3.4    37.3    -      -       +      +
    253B  VAL*     3.5    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  GLN*     3.1    19.0    +      -       +      +
     43B  ILE*     3.7     7.0    -      -       -      +
     45B  HIS*     1.3    74.4    -      -       -      +
     47B  ARG*     1.3    59.5    +      -       -      +
     50B  SER*     2.8    51.4    +      -       -      +
     53B  LEU*     4.3    13.2    -      -       +      -
     54B  TYR*     4.0    20.6    -      -       +      +
     61B  TYR*     3.7    30.3    -      -       +      +
    250B  VAL*     3.7    20.6    -      -       +      -
    294B  VAL*     3.8    25.4    -      -       +      -
    296B  LEU*     3.9    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  ILE      2.9    15.8    +      -       -      +
     44B  ASN*     3.2    38.9    +      -       -      +
     46B  ILE*     1.3    79.9    -      -       -      +
     48B  ASN*     1.3    91.5    +      -       -      +
     51B  PRO*     4.2    17.2    -      -       -      +
     54B  TYR*     3.6    45.9    +      -       +      +
    110C  HIS*     3.9     7.3    +      -       -      +
    111C  THR*     3.7    31.6    +      -       -      +
    316D  GLU*     4.8    10.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  ASN*     2.9    23.1    +      -       -      +
     45B  HIS*     4.2     3.7    +      -       -      +
     47B  ARG*     1.3   107.0    -      -       -      +
     49B  SER*     1.3    61.0    +      -       -      +
     50B  SER      3.7     0.2    -      -       -      -
     51B  PRO*     4.8     7.2    -      -       -      +
    110C  HIS*     3.1    60.8    +      -       +      +
    147C  LEU*     5.5     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  HIS*     2.8    19.3    +      -       -      -
     48B  ASN*     1.3    79.5    -      -       -      +
     50B  SER*     1.3    60.7    +      -       -      +
     51B  PRO*     3.6     7.7    -      -       -      +
    245B  LYS*     4.8     7.2    +      -       -      -
    248B  SER      5.4     0.3    -      -       -      +
    249B  ALA*     3.8    17.7    -      -       -      +
    250B  VAL*     4.1     4.7    -      -       -      -
    251B  PRO*     3.2    30.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ILE*     2.8    22.3    +      -       -      +
     49B  SER*     1.3    80.8    -      -       -      +
     51B  PRO*     1.3    61.1    -      -       -      +
     52B  ARG      3.4     1.1    -      -       -      -
     53B  LEU*     2.9    33.7    +      -       -      +
     54B  TYR*     3.0    21.7    +      -       -      +
    248B  SER      4.8     4.9    +      -       -      -
    250B  VAL*     3.8    21.3    -      -       -      -
----------------------------------------------------------
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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