Contacts of the strand formed by residues 56 - 62 (chain u) 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 ASN 56 (chain u).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44u  GLU      5.8     1.8    -      -       -      -
     45u  CYS      3.4     5.6    -      -       -      +
     46u  VAL*     4.1    21.4    -      -       -      +
     54u  GLN*     4.7     3.4    +      -       -      +
     55u  ASN*     1.3    98.3    +      -       -      +
     57u  ILE*     1.3    63.3    +      -       -      +
     58u  GLY      3.7     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34s  TRP*     5.8     2.0    -      -       +      -
     86s  LEU*     6.4     0.2    -      -       +      -
     88s  GLN*     2.9    46.9    -      -       +      +
     89s  SER*     3.5    36.8    -      -       -      +
     90s  VAL*     5.1     5.4    -      -       +      -
     45u  CYS*     2.9    21.9    +      -       -      +
     47u  GLU*     5.4     4.0    -      -       +      +
     55u  ASN*     3.9     6.7    +      -       -      +
     56u  ASN*     1.3    77.7    -      -       -      +
     58u  GLY*     1.3    65.6    +      -       -      +
     59u  MET      3.3     9.0    +      -       -      +
     60u  VAL*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 58 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42u  ILE      3.4     3.3    -      -       -      +
     43u  ASP*     4.8     0.7    -      -       -      -
     44u  GLU*     3.4    17.5    -      -       -      -
     45u  CYS*     3.1    40.0    +      -       -      +
     56u  ASN*     3.7     2.8    -      -       -      +
     57u  ILE*     1.3    77.0    -      -       -      +
     59u  MET*     1.3    63.7    +      -       -      -
     60u  VAL*     3.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 59 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15s  VAL*     4.8    15.0    -      -       +      -
     20s  LEU*     3.6    28.5    -      -       +      -
     24s  TYR*     3.3    12.1    +      -       +      +
     89s  SER*     5.0     5.5    +      -       -      -
     32u  ARG*     4.8     5.8    -      -       +      +
     41u  VAL*     3.9    20.2    -      -       +      -
     42u  ILE      3.2     7.2    -      -       -      +
     43u  ASP*     2.9    52.0    +      -       +      +
     44u  GLU      4.0     1.4    -      -       -      +
     57u  ILE*     3.3     5.8    +      -       -      +
     58u  GLY*     1.3    70.5    -      -       -      -
     60u  VAL*     1.3    71.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 60 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20s  LEU*     3.5     8.2    -      -       -      +
     24s  TYR*     3.3     6.5    -      -       -      -
     86s  LEU*     3.8    14.1    -      -       +      -
     87s  LEU      3.1    18.4    -      -       -      +
     88s  GLN*     3.9     9.6    -      -       +      -
     41u  VAL*     3.4     6.4    -      -       -      -
     42u  ILE*     2.9    62.9    +      -       +      +
     45u  CYS*     3.6    18.4    -      -       +      -
     57u  ILE*     3.8    29.8    -      -       +      +
     58u  GLY      3.9     0.2    -      -       -      +
     59u  MET*     1.3    85.7    -      -       -      +
     61u  VAL*     1.3    54.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 61 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17s  PRO*     3.9    25.8    -      -       +      +
     20s  LEU*     3.4    30.3    -      -       +      -
     21s  ILE*     4.0    18.2    -      -       +      -
     24s  TYR*     3.8     4.6    +      -       +      -
     54s  MET*     4.6    11.7    -      -       +      -
     84s  ILE*     5.7     0.8    -      -       +      +
     86s  LEU*     3.1     4.7    -      -       -      +
     87s  LEU*     2.7    58.3    +      -       +      +
     40u  LEU      3.4     8.7    -      -       -      +
     41u  VAL*     4.8     0.2    -      -       +      -
     60u  VAL*     1.3    71.5    -      -       -      +
     62u  ILE*     1.3    72.4    +      -       -      +
     63u  ARG      4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85s  THR      3.6    13.5    -      -       -      +
     86s  LEU*     3.8    19.7    -      -       +      -
     19u  LEU*     4.1    21.8    -      -       +      -
     21u  LEU*     4.2    12.3    -      -       +      -
     27u  VAL*     4.4     9.6    -      -       +      -
     38u  MET      4.4     0.2    -      -       -      +
     39u  ASN*     3.2     5.4    -      -       -      +
     40u  LEU*     2.8    42.9    +      -       +      +
     42u  ILE*     4.0    34.3    -      -       +      -
     61u  VAL*     1.3    79.6    -      -       -      +
     63u  ARG*     1.3    67.0    +      -       -      +
     66u  SER*     5.3     0.4    -      -       -      -
     67u  ILE*     3.5    31.2    -      -       +      +
----------------------------------------------------------
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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