Contacts of the strand formed by residues 58 - 66 (chain C) in PDB entry 5EWL


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 ILE 58 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  PRO*     3.6     0.2    -      -       -      +
     25C  LYS*     3.6    12.1    -      -       +      +
     27C  VAL*     3.7    18.6    -      -       +      -
     54C  PHE      3.3    17.4    -      -       -      +
     55C  THR*     3.2    11.9    -      -       -      +
     56C  ARG      3.3     2.6    +      -       -      +
     57C  LYS*     1.3    84.8    -      -       +      +
     59C  GLN*     1.4    62.1    +      -       -      +
    313C  ILE*     3.7    19.7    -      -       +      +
    314C  HIS*     3.7    38.2    +      -       +      +
    317C  PHE*     3.6    46.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  PRO*     3.9    21.5    -      -       +      +
     25C  LYS      2.9    12.8    +      -       -      +
     26C  ILE*     3.3    26.1    -      -       +      +
     27C  VAL*     2.9    27.2    +      -       -      -
     50C  ASN*     3.5    16.8    -      -       -      +
     55C  THR*     3.4    30.5    -      -       +      +
     58C  ILE*     1.4    74.9    -      -       -      +
     60C  LEU*     1.3    72.6    +      -       -      +
     61C  GLN*     5.6     1.8    +      -       -      -
    314C  HIS*     5.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  VAL*     3.2    27.4    -      -       +      +
     29C  ILE*     3.5    30.7    -      -       +      -
     46C  VAL*     4.0    16.2    -      -       +      +
     49C  ALA*     4.0    15.0    -      -       +      -
     50C  ASN*     3.0    27.4    +      -       -      +
     58C  ILE*     5.2     1.6    -      -       +      -
     59C  GLN*     1.3    86.1    +      -       -      +
     61C  GLN*     1.3    62.4    +      -       -      +
    306C  VAL*     5.6     1.1    -      -       +      -
    310C  ALA*     3.7    31.6    -      -       +      -
    313C  ILE*     4.1    18.2    -      -       +      -
    314C  HIS*     4.8    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  ILE*     3.5    35.2    -      -       +      +
     27C  VAL      3.1     5.7    +      -       -      -
     28C  ASN*     3.2    30.7    +      -       -      +
     29C  ILE*     2.9    24.9    +      -       -      -
     46C  VAL*     4.1     3.8    -      -       -      -
     59C  GLN*     5.6     2.2    +      -       -      +
     60C  LEU*     1.3    75.7    -      -       -      +
     62C  ALA*     1.3    70.3    +      -       -      +
     63C  THR*     3.7     0.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ILE      3.6     5.2    -      -       -      -
     42C  PHE*     3.6    23.1    -      -       +      -
     43C  ARG*     4.1    22.4    -      -       +      +
     46C  VAL*     3.6    28.2    -      -       +      +
     61C  GLN*     1.3    82.2    -      -       -      +
     63C  THR*     1.3    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  ASN*     3.4    31.7    +      -       -      +
     29C  ILE      2.9     9.1    +      -       -      -
     30C  GLY*     3.1     4.0    -      -       -      -
     31C  ALA      3.0    20.6    +      -       -      -
     42C  PHE*     3.2     4.4    -      -       -      -
     61C  GLN*     4.9     0.3    +      -       -      +
     62C  ALA*     1.3    72.5    +      -       -      +
     64C  SER*     1.3    63.6    +      -       -      +
     81C  ASP      3.4    26.0    -      -       -      +
     82C  LEU*     3.8    10.3    -      -       +      -
     85C  SER*     3.7    17.6    -      -       -      +
     87C  VAL*     4.2     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  ALA*     3.2    15.7    -      -       -      -
     33C  LEU*     4.8     1.3    -      -       -      -
     39C  GLU*     2.7    44.2    +      -       -      +
     42C  PHE*     3.8    21.4    -      -       -      -
     43C  ARG*     5.7     2.1    +      -       -      +
     62C  ALA      4.4     0.2    -      -       -      -
     63C  THR*     1.3    79.9    -      -       -      +
     65C  VAL*     1.3    72.6    +      -       -      +
     82C  LEU*     4.0     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 65 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  ALA      3.0    12.2    +      -       -      +
     32C  VAL*     3.3    12.0    -      -       +      -
     33C  LEU*     2.9    23.9    +      -       -      +
     39C  GLU*     3.4    12.1    -      -       -      +
     64C  SER*     1.3    78.8    -      -       -      +
     66C  THR*     1.3    68.5    +      -       -      +
     68C  ARG*     4.2     8.1    -      -       -      +
     74C  MET*     4.0    14.6    -      -       +      -
     77C  SER*     3.7    16.6    -      -       -      +
     81C  ASP*     3.4    39.5    -      -       +      +
     82C  LEU*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  VAL*     4.3     3.0    -      -       -      +
     33C  LEU      3.0    15.9    -      -       -      +
     34C  SER      3.5    16.8    -      -       -      +
     35C  THR*     3.6    18.6    -      -       -      +
     36C  LYS*     4.0     2.5    -      -       +      +
     39C  GLU*     3.6    21.8    +      -       -      +
     65C  VAL*     1.3    82.0    -      -       -      +
     67C  HIS*     1.3    67.2    +      -       -      +
     68C  ARG*     3.3    32.8    +      -       -      +
     74C  MET*     4.4     0.2    -      -       -      +
----------------------------------------------------------
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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