Contacts of the strand formed by residues 24 - 32 (chain q) 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 24 (chain q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1364    G      4.7     7.4    -      -       -      +
     16q  THR*     4.0    16.3    -      -       +      +
     17q  ILE      3.4     4.0    -      -       -      +
     18q  GLU*     3.9    34.7    +      -       +      +
     22q  GLY      4.1     6.8    +      -       -      +
     23q  THR*     1.3    77.1    -      -       -      +
     25q  VAL*     1.3    61.7    +      -       -      +
     26q  HIS      4.2     0.2    -      -       -      -
     44q  LYS      3.6     2.5    -      -       -      +
     45q  MET*     3.4     2.8    -      -       -      -
     46q  THR*     2.8    45.7    +      -       -      +
     94r  ARG*     4.8     7.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 25 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15q  VAL      3.9     0.3    -      -       -      +
     16q  THR*     3.1     5.9    -      -       -      +
     17q  ILE*     2.7    47.1    +      -       +      +
     19q  LEU*     4.5     7.4    -      -       +      -
     23q  THR*     4.3     7.6    -      -       +      -
     24q  GLN*     1.3    79.6    -      -       -      +
     26q  HIS*     1.3    66.5    +      -       -      +
     27q  GLY      4.6     0.2    -      -       -      +
     40q  LEU*     3.5    32.1    -      -       +      -
     43q  VAL*     4.0    10.3    -      -       +      -
     44q  LYS      3.7     3.1    -      -       -      -
     45q  MET*     4.0    14.4    -      -       +      -
     58q  LEU*     3.7    25.8    -      -       +      -
     60q  ILE*     4.1     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 26 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14q  THR*     3.3    29.9    -      -       +      +
     15q  VAL      3.4     7.9    +      -       -      -
     16q  THR*     3.1    24.9    +      -       +      +
     25q  VAL*     1.3    76.2    -      -       -      +
     27q  GLY*     1.3    63.8    +      -       -      +
     42q  ALA      4.8     4.9    -      -       -      -
     43q  VAL*     3.2     4.2    -      -       -      +
     44q  LYS*     2.8    59.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 27 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14q  THR*     3.3     5.4    -      -       -      +
     15q  VAL*     2.8    36.7    +      -       -      +
     25q  VAL      4.2     0.6    +      -       -      -
     26q  HIS*     1.3    81.4    -      -       -      +
     28q  THR*     1.3    65.2    +      -       -      -
     40q  LEU*     3.8    13.9    -      -       -      +
     41q  LYS      3.8     1.8    -      -       -      -
     42q  ALA      3.5    12.8    -      -       -      -
     43q  VAL*     4.3     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 28 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12q  HIS*     3.6    33.0    -      -       -      +
     13q  GLU      3.5     4.9    -      -       -      +
     14q  THR*     2.7    19.0    +      -       -      +
     27q  GLY*     1.3    73.8    -      -       -      -
     29q  ILE*     1.3    67.5    +      -       -      +
     30q  THR      3.3     0.9    +      -       -      -
     40q  LEU*     3.2     4.0    -      -       -      +
     41q  LYS*     2.8    68.2    +      -       -      +
     42q  ALA*     4.4     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 29 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10q  LEU*     3.4    40.4    -      -       +      +
     11q  SER*     3.5     1.5    -      -       -      -
     12q  HIS*     2.7    32.7    +      -       -      -
     13q  GLU      2.8    10.5    +      -       -      +
     15q  VAL*     3.8    40.2    -      -       +      -
     28q  THR*     1.3    70.4    -      -       -      +
     30q  THR*     1.3    59.7    -      -       -      +
     31q  GLY*     3.5    16.2    -      -       -      +
     32q  VAL*     3.9    21.5    -      -       +      +
     38q  THR*     4.6     4.9    -      -       +      -
     39q  HIS      3.5     7.0    -      -       -      +
     40q  LEU*     3.8     8.7    -      -       +      -
     68q  PHE*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 30 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8p  LYS*     3.3    32.3    +      -       -      +
     11q  SER*     3.9    15.1    +      -       -      -
     12q  HIS*     5.0     5.8    -      -       -      +
     28q  THR      3.9     1.6    -      -       -      +
     29q  ILE*     1.3    74.4    -      -       -      +
     31q  GLY*     1.3    61.3    +      -       -      +
     39q  HIS*     2.9    25.5    +      -       -      +
     40q  LEU      4.0     2.4    +      -       -      +
     41q  LYS*     3.7    45.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 31 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8p  LYS*     4.3     8.0    -      -       -      +
      8q  MET      5.9     0.4    -      -       -      -
     11q  SER*     5.1     4.3    -      -       -      -
     29q  ILE*     3.5     5.1    -      -       -      +
     30q  THR*     1.3    87.5    +      -       -      +
     32q  VAL*     1.3    65.6    +      -       -      +
     38q  THR*     3.5     0.9    -      -       -      -
     39q  HIS*     2.7    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 32 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4q  VAL*     4.8     1.3    -      -       +      -
      7q  LEU*     3.7    46.7    -      -       +      +
      8q  MET*     3.4    25.8    +      -       +      +
     29q  ILE*     3.9    13.4    -      -       +      +
     31q  GLY*     1.3    79.2    -      -       -      +
     33q  ASP*     1.3    73.3    +      -       -      +
     36q  MET*     4.2     8.3    -      -       -      -
     37q  ASN      3.3     9.9    -      -       -      +
     38q  THR*     3.7    26.0    -      -       +      +
     39q  HIS*     5.4     0.9    -      -       -      -
     68q  PHE*     4.5     6.1    -      -       +      -
----------------------------------------------------------
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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