Contacts of the strand formed by residues 49 - 58 (chain A) in PDB entry 4OIP


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 PRO 49 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  SER      3.2    10.3    -      -       -      +
     48A  ILE*     1.3    98.1    -      -       +      +
     50A  GLY*     1.3    58.8    +      -       -      +
    146A  ARG*     6.1     4.0    -      -       -      +
    147A  GLY      3.3    13.2    -      -       -      +
    148A  VAL*     4.2     9.2    -      -       +      -
    173A  PRO*     3.4    13.3    -      -       -      +
    205A  VAL*     4.6     6.9    -      -       -      +
    213A  GLN*     3.7    20.1    +      -       +      +
    217A  ILE*     5.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ILE      3.8     0.4    +      -       -      -
     49A  PRO*     1.3    74.7    -      -       -      +
     51A  THR*     1.3    65.3    +      -       -      -
    146A  ARG*     3.6     9.0    -      -       -      +
    147A  GLY      2.8    32.6    +      -       -      +
    171A  PHE*     3.2    19.5    +      -       -      -
    173A  PRO*     3.8     9.0    -      -       -      -
    204A  SER*     4.9     3.6    -      -       -      -
    205A  VAL*     5.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLY*     1.3    79.1    -      -       -      +
     52A  ALA*     1.3    64.8    +      -       -      +
     85A  LEU      5.0     4.6    -      -       -      +
     86A  VAL*     5.8     0.9    -      -       -      -
     87A  VAL*     2.3    39.6    +      -       -      +
     89A  PHE*     3.8    36.1    -      -       +      +
    144A  VAL*     4.2     8.5    -      -       -      -
    145A  ASP      3.6     8.1    -      -       -      +
    146A  ARG*     4.3     9.4    -      -       +      +
    170A  VAL      4.0     2.8    -      -       -      +
    171A  PHE*     3.5     9.7    +      -       -      +
    173A  PRO*     5.5     0.4    -      -       -      +
    202A  ASP*     5.1     6.1    +      -       -      +
    204A  SER*     3.5    14.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR*     1.3    78.4    -      -       -      +
     53A  VAL*     1.3    63.1    +      -       -      +
     54A  THR*     3.4     3.5    +      -       -      +
     83A  LYS      5.8     4.3    -      -       -      +
     85A  LEU      5.1     7.0    -      -       -      -
    144A  VAL*     3.2     7.4    -      -       -      +
    145A  ASP      3.1    28.9    +      -       -      +
    169A  ALA*     3.7    17.0    -      -       +      -
    170A  VAL      3.4    23.1    -      -       -      +
    171A  PHE*     3.7    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ALA*     1.3    71.7    -      -       -      +
     54A  THR*     1.3    59.8    +      -       -      +
     55A  SER      3.4    26.2    -      -       -      +
     56A  VAL*     4.2     9.9    -      -       +      -
     82A  LEU*     3.4    29.8    -      -       +      +
     83A  LYS*     5.4     4.3    +      -       -      +
     85A  LEU*     3.9    25.1    +      -       +      +
     87A  VAL*     5.4     0.2    -      -       +      -
    142A  VAL*     4.1    14.8    -      -       +      -
    143A  ARG      3.5     7.0    -      -       -      +
    144A  VAL*     3.7    17.5    -      -       +      -
    167A  VAL*     3.7    24.1    -      -       +      +
    168A  ASP      4.1     1.9    -      -       -      +
    169A  ALA*     4.0     6.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ALA      3.7     9.9    -      -       -      +
     53A  VAL*     1.3    73.3    -      -       -      +
     55A  SER*     1.3    59.1    +      -       -      -
    143A  ARG*     2.5    21.7    +      -       -      +
    145A  ASP*     2.8    37.9    +      -       +      +
    156A  HIS*     3.2    25.1    -      -       +      -
    158A  ILE*     3.7    18.2    -      -       -      +
    166A  PRO*     4.0     1.2    -      -       -      +
    167A  VAL      3.3    14.7    +      -       -      -
    169A  ALA*     4.4     3.8    -      -       +      -
    171A  PHE*     4.1     9.6    -      -       +      -
      2B  LEU*     3.6    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     3.4     5.5    +      -       -      +
     54A  THR*     1.3    82.5    -      -       -      +
     56A  VAL*     1.3    74.3    +      -       -      +
    141A  GLU      4.7     0.2    -      -       -      -
    142A  VAL*     3.4     2.4    -      -       -      -
    143A  ARG*     2.9    43.2    +      -       -      -
    158A  ILE*     3.4    24.8    +      -       -      -
    159A  LYS*     4.4     1.3    -      -       -      -
    160A  ASP*     4.5     3.6    +      -       -      +
    164A  ALA*     3.9    17.3    -      -       -      +
    165A  ILE      3.5    10.0    +      -       -      -
    167A  VAL*     4.4     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     4.2     6.5    -      -       +      -
     55A  SER*     1.3    84.5    +      -       -      +
     57A  TYR*     1.3    62.9    +      -       -      +
     58A  ILE*     3.9    26.2    -      -       +      -
     79A  ILE*     4.6    13.2    -      -       +      -
     82A  LEU*     3.6    34.5    -      -       +      -
    140A  MET*     4.6     1.3    -      -       -      -
    141A  GLU      3.7     3.6    -      -       -      -
    142A  VAL*     3.9    11.2    -      -       +      -
    165A  ILE*     2.8    46.9    +      -       +      +
    167A  VAL*     3.7    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  VAL*     1.3    74.8    -      -       -      +
     58A  ILE*     1.3    82.5    +      -       -      +
     59A  GLU*     3.8    24.3    -      -       +      +
     60A  ASP      4.5     2.9    +      -       -      -
     61A  VAL      4.6     0.2    -      -       -      -
    139A  ASN*     5.4     3.6    -      -       -      -
    140A  MET*     3.3     5.0    -      -       -      +
    141A  GLU*     2.9    57.3    +      -       +      +
    160A  ASP*     6.5     0.2    -      -       +      -
    161A  ARG*     3.2    54.6    +      -       +      +
    163A  ASN*     3.7    40.1    +      -       +      -
    164A  ALA*     4.3     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  VAL*     3.9    13.2    +      -       +      -
     57A  TYR*     1.3    94.7    -      -       -      +
     59A  GLU*     1.3    74.7    +      -       -      +
     61A  VAL*     3.2    29.1    +      -       +      +
     68A  ILE*     3.6    34.8    -      -       +      -
     75A  VAL*     4.3    22.4    -      -       +      -
     78A  ILE*     4.6     9.9    -      -       +      -
    138A  LEU*     3.8    11.7    -      -       +      -
    139A  ASN      3.4    13.5    -      -       -      +
    140A  MET*     3.6    26.2    -      -       +      -
    163A  ASN      5.5     0.2    +      -       -      -
    165A  ILE*     5.8     3.4    -      -       +      +
----------------------------------------------------------
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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