Contacts of the strand formed by residues 90 - 101 (chain d) in PDB entry 4PJO


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 90 (chain d).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75d  THR*     3.3     5.5    +      -       -      -
     76d  GLU*     2.8    56.9    +      -       +      +
     77d  VAL      3.7    17.9    -      -       -      +
     88d  LYS      3.3     4.1    +      -       -      +
     89d  PRO*     1.3    71.5    -      -       -      +
     91d  ASN*     1.3    77.1    +      -       -      +
     92d  LYS*     4.4    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 91 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74d  TRP      3.8     6.6    -      -       -      +
     75d  THR*     3.8    11.6    +      -       -      -
     89d  PRO      4.1     4.1    +      -       -      +
     90d  VAL*     1.3    84.3    -      -       -      +
     92d  LYS*     1.3    70.5    -      -       -      +
     93d  ASP*     6.1     0.4    -      -       -      +
     44k  TYR*     5.5     2.7    +      -       -      -
     46k  ARG*     5.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 92 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73d  MET*     3.3     3.6    -      -       -      +
     74d  TRP*     3.0    59.9    +      -       +      +
     76d  GLU*     3.6    44.5    +      -       +      +
     90d  VAL*     4.4    14.6    -      -       +      +
     91d  ASN*     1.3    84.8    -      -       -      +
     93d  ASP*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 93 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71d  LYS*     4.1    30.8    +      -       -      -
     72d  GLU      3.1    13.5    -      -       -      +
     73d  MET*     4.2     4.3    -      -       +      -
     74d  TRP*     3.8     6.4    -      -       -      -
     91d  ASN*     6.1     0.3    -      -       -      +
     92d  LYS*     1.3    80.3    -      -       -      +
     94d  ARG*     1.3    66.7    +      -       -      +
     95d  TYR*     4.7    11.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 94 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1362    G      5.6     0.2    -      -       -      +
     16c  THR*     6.2     0.2    -      -       -      +
     18c  GLU*     2.7    30.9    +      -       -      -
     24c  GLN*     4.9     7.4    +      -       -      +
     67c  TYR*     3.3    11.9    +      -       -      -
     69c  ILE*     3.8    18.2    -      -       -      +
     50d  LYS*     5.3     2.2    -      -       -      +
     71d  LYS*     3.4     3.4    -      -       -      -
     72d  GLU*     2.6    60.6    +      -       +      +
     74d  TRP*     4.1    11.6    -      -       +      -
     93d  ASP*     1.3    81.2    -      -       -      +
     95d  TYR*     1.3    66.8    +      -       -      +
     96d  ILE*     3.7    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69d  ASN      6.0     0.9    -      -       -      -
     70d  VAL      3.5    10.8    -      -       -      +
     71d  LYS*     3.8    39.5    +      -       +      -
     93d  ASP*     4.7     9.8    +      -       -      -
     94d  ARG*     1.3    79.5    -      -       -      +
     96d  ILE*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 96 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67c  TYR*     4.6     0.7    -      -       +      -
     69c  ILE*     3.8    35.7    -      -       +      -
     69d  ASN*     3.8     0.3    -      -       -      -
     70d  VAL*     2.8    40.2    +      -       +      +
     72d  GLU*     4.2    13.2    -      -       +      +
     94d  ARG*     3.7    42.4    -      -       +      +
     95d  TYR*     1.3    77.3    -      -       -      +
     97d  SER*     1.3    62.5    +      -       -      +
     98d  LYS      4.2     4.9    -      -       -      +
     99d  MET*     4.0    39.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 97 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69c  ILE*     5.9     0.2    -      -       -      +
     72c  ASP*     3.0    40.2    +      -       -      -
     67d  LEU      5.2     0.2    -      -       -      -
     68d  GLU*     3.2     7.0    -      -       -      +
     69d  ASN*     3.0    33.8    +      -       -      +
     96d  ILE*     1.3    75.6    -      -       -      +
     98d  LYS*     1.3    73.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 98 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69c  ILE*     3.8     1.2    -      -       -      +
     70c  LEU*     2.8    48.8    +      -       +      +
     71c  PRO      3.8     6.5    -      -       -      +
     72c  ASP      2.9    26.3    +      -       -      +
     73c  SER*     3.6     3.8    +      -       -      +
     74c  LEU*     2.7    30.5    +      -       +      +
     75c  PRO*     5.0     0.6    -      -       -      +
     76c  LEU*     3.7    32.3    -      -       +      +
     67d  LEU      3.4     6.1    -      -       -      +
     68d  GLU*     4.0    14.8    -      -       +      -
     96d  ILE*     4.2     4.2    -      -       -      +
     97d  SER*     1.3    94.4    +      -       -      +
     99d  MET*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 99 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67c  TYR*     3.4    54.5    -      -       +      -
     68c  PHE      3.3    11.9    -      -       -      +
     69c  ILE*     4.5     0.4    -      -       +      -
     70c  LEU*     4.0     5.9    -      -       -      +
     52d  LEU*     4.4     9.6    -      -       +      -
     66d  VAL*     3.4     9.4    -      -       -      +
     67d  LEU*     2.8    57.5    +      -       +      +
     70d  VAL*     3.8    32.3    -      -       +      +
     96d  ILE*     4.0    22.4    -      -       +      -
     97d  SER      4.4     0.2    -      -       -      -
     98d  LYS*     1.3    74.9    -      -       -      +
    100d  PHE*     1.3    62.9    +      -       -      +
    101d  LEU*     5.3     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 100 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1312    U      5.4     0.2    -      -       -      -
      3c  LEU*     3.7    38.1    -      -       +      -
      4c  VAL      4.8     0.7    -      -       -      -
      6c  PHE*     4.2     3.4    -      +       -      -
      7c  LEU*     3.7    41.1    -      -       +      -
     36c  MET*     4.0    14.8    -      -       +      -
     67c  TYR*     3.1     6.0    -      -       -      +
     68c  PHE*     2.9    46.6    +      +       +      -
     70c  LEU*     4.1     7.4    -      -       +      +
     64d  ASN*     3.7    28.7    -      -       +      -
     65d  MET      3.3     5.4    -      -       -      -
     66d  VAL*     3.8    17.9    -      -       +      +
     99d  MET*     1.3    74.2    -      -       -      +
    101d  LEU*     1.3    75.1    +      -       -      +
    102d  ARG*     4.0     2.5    -      -       -      -
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Residues in contact with LEU 101 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66c  ARG      3.4    13.0    -      -       -      +
     67c  TYR*     4.0    17.9    -      -       +      -
     44d  ILE*     4.3    17.0    -      -       +      -
     46d  CYS*     4.3    17.9    -      -       -      -
     52d  LEU*     3.9    23.1    -      -       +      -
     63d  CYS      5.1     1.1    -      -       -      +
     64d  ASN*     3.3     3.3    -      -       -      -
     65d  MET*     2.8    37.1    +      -       +      +
     67d  LEU*     4.5    12.3    -      -       +      -
     99d  MET*     4.1     3.0    -      -       +      +
    100d  PHE*     1.3    76.6    -      -       -      +
    102d  ARG*     1.3    83.6    +      -       -      +
    105d  SER*     4.3     4.3    -      -       -      -
    106d  VAL*     4.1    22.2    -      -       +      -
----------------------------------------------------------
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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