Contacts of the strand formed by residues 41 - 46 (chain r) 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 GLN 41 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47n  GLU*     3.3    24.1    +      -       -      +
     48n  PHE*     2.5    54.1    +      -       +      +
     40r  THR*     1.3    85.3    +      -       -      +
     42r  VAL*     1.3    64.9    +      -       -      +
     53r  LEU*     3.5    28.9    +      -       +      +
     54r  GLY*     3.3    12.2    -      -       -      +
     55r  ARG*     3.5    21.6    -      -       +      +
     69r  ASN      5.6     2.2    +      -       -      -
    112r  ASN*     3.4    25.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47n  GLU*     4.5     0.9    +      -       -      -
     32r  LEU*     5.3     1.3    -      -       +      -
     35r  SER*     3.8    19.1    -      -       -      +
     40r  THR      4.3     0.7    -      -       -      +
     41r  GLN*     1.3    81.8    -      -       -      +
     43r  LEU*     1.3    59.2    +      -       -      +
     44r  ILE*     4.1    22.9    -      -       +      -
     52r  LEU      3.5     0.9    -      -       -      +
     53r  LEU*     3.1     6.2    -      -       -      +
     54r  GLY      2.9    38.3    +      -       -      +
     56r  VAL*     3.7    26.0    -      -       +      -
     65r  MET*     5.4     0.2    -      -       -      -
     67r  LEU*     5.0     1.8    -      -       +      -
    109r  VAL*     3.5    26.2    -      -       +      -
    110r  LEU      3.4    15.5    -      -       -      +
    111r  ARG*     4.1     2.7    -      -       +      +
    112r  ASN      4.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41n  ILE*     3.9    47.2    -      -       +      +
     44n  TYR*     4.1    16.8    -      -       +      +
     45n  ILE*     4.9     1.1    -      -       +      -
     47n  GLU*     4.7     9.9    -      -       -      +
     42r  VAL*     1.3    75.8    -      -       -      +
     44r  ILE*     1.3    61.6    +      -       -      +
     51r  LYS*     4.2    10.5    -      -       +      -
     52r  LEU      3.4     6.3    -      -       -      +
     53r  LEU*     3.9    28.3    -      -       +      -
     73r  MET*     4.0    16.2    -      -       +      -
    108r  VAL      3.8     1.2    -      -       -      +
    109r  VAL*     3.6     1.0    -      -       -      -
    110r  LEU*     2.9    50.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 44 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42r  VAL*     4.1    18.6    -      -       +      -
     43r  LEU*     1.3    79.4    -      -       -      +
     45r  ASN*     1.3    71.8    +      -       -      +
     46r  CYS*     3.7     3.8    +      -       +      +
     51r  LYS*     3.2     7.4    -      -       -      -
     52r  LEU*     2.7    47.0    +      -       +      +
     65r  MET*     3.5    31.9    -      -       +      -
     67r  LEU*     4.0    22.9    -      -       +      -
    101r  LEU*     4.3    10.1    -      -       +      -
    106r  VAL*     4.0    24.5    -      -       +      -
    108r  VAL      3.4    10.8    -      -       -      +
    109r  VAL*     4.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 45 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38n  TYR*     6.0     0.2    -      -       -      +
     39n  CYS      3.2    21.8    +      -       -      +
     40n  GLY*     4.2     6.1    -      -       -      -
     41n  ILE*     3.5    21.8    -      -       +      +
     43r  LEU      4.1     0.4    +      -       -      -
     44r  ILE*     1.3    74.4    -      -       -      +
     46r  CYS*     1.3    67.3    +      -       -      +
     49r  ASN*     4.2     1.8    +      -       -      +
     50r  LYS      3.8     1.5    -      -       -      +
     51r  LYS*     3.1    27.8    +      -       -      +
    107r  ILE*     3.0    52.3    +      -       +      +
    108r  VAL*     3.0    19.6    +      -       +      +
     27t  MET*     4.2    10.7    -      -       -      -
     29t  TYR*     4.4     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 46 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66q  ARG*     4.0    19.3    -      -       -      -
     67q  TYR*     5.2     0.7    -      -       -      -
     44r  ILE*     4.4     6.3    -      -       +      +
     45r  ASN*     1.3    76.2    +      -       -      +
     47r  ARG*     1.3    62.9    +      -       -      +
     48r  ASN*     3.2    18.4    -      -       -      +
     49r  ASN*     2.7    23.2    +      -       -      -
     50r  LYS      3.0    19.4    +      -       -      +
     52r  LEU*     4.5    17.7    -      -       +      -
    101r  LEU*     4.3    15.9    -      -       -      -
    105r  SER*     3.4    15.3    -      -       -      -
    106r  VAL*     4.9     0.9    -      -       -      +
    107r  ILE*     3.7     9.6    -      -       -      +
----------------------------------------------------------
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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