Contacts of the strand formed by residues 39 - 42 (chain E) in PDB entry 3CME


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 ASP 39 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ASP*     4.4     6.0    -      -       -      +
     38E  ILE*     1.3    80.4    +      -       -      +
     40E  VAL*     1.3    62.1    +      -       -      +
     41E  SER*     4.2     3.6    -      -       -      +
     48E  VAL      3.4     1.7    -      -       -      +
     49E  ILE*     3.4     4.9    -      -       -      -
     50E  GLU*     2.9    55.2    +      -       +      +
     51E  SER*     4.8     3.5    -      -       -      -
     52E  ASP*     5.5     2.1    -      -       -      +
    124J  LEU*     5.7     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15E  GLN*     4.0    17.2    +      -       -      +
     17E  HIS      4.9     1.7    -      -       -      +
     20E  ILE*     3.2    34.8    -      -       +      -
     33E  LEU*     4.2    15.0    -      -       +      +
     38E  ILE*     4.0     5.5    +      -       +      +
     39E  ASP*     1.3    77.6    -      -       -      +
     41E  SER*     1.3    65.3    +      -       -      +
     47E  VAL*     4.1     4.5    -      -       +      -
     48E  VAL      3.1     8.7    -      -       -      +
     49E  ILE*     4.1    13.2    -      -       +      -
     65E  PHE*     4.0    27.6    -      -       +      -
     69E  ILE*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 41 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15E  GLN*     4.1    10.3    -      -       -      -
     39E  ASP*     5.1     4.1    +      -       -      +
     40E  VAL*     1.3    79.0    +      -       -      +
     42E  VAL*     1.3    66.5    +      -       -      +
     43E  ASP*     3.8     0.9    +      -       -      +
     47E  VAL*     3.3     7.2    -      -       -      +
     48E  VAL*     2.7    47.4    +      -       -      +
     50E  GLU*     4.7     7.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 42 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ILE*     5.4     3.4    -      -       +      -
     13E  ALA*     3.3    30.7    -      -       +      +
     14E  GLU*     4.2     2.9    -      -       -      -
     15E  GLN*     3.8    30.4    +      -       +      +
     20E  ILE*     5.8     1.6    -      -       +      -
     41E  SER*     1.3    78.2    -      -       -      +
     43E  ASP*     1.3    60.5    +      -       -      +
     44E  GLY*     3.3    23.0    +      -       -      +
     46E  THR      3.4    10.3    -      -       -      +
     47E  VAL*     4.5    11.2    -      -       +      +
----------------------------------------------------------
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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