Contacts of the strand formed by residues 21 - 30 (chain E) in PDB entry 5MEP


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 21 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  SER*     3.6    13.6    -      -       -      -
     12E  ARG*     3.5     2.9    +      -       -      +
     13E  HIS*     2.8    58.9    +      -       -      +
     14E  PRO      3.9     8.1    +      -       -      -
     15E  ALA*     4.0     9.7    -      -       -      +
     16E  GLU      5.2     0.2    -      -       -      +
     19E  LYS      4.0     6.0    +      -       -      +
     20E  SER*     1.3    77.8    +      -       -      +
     22E  PHE*     1.3    89.3    +      -       -      +
     69E  GLU*     3.5     7.4    -      -       -      +
     70E  PHE*     2.7    38.9    +      -       +      +
     72E  PRO*     4.4     3.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 22 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  SER*     3.2     6.2    -      -       -      -
     12E  ARG*     2.9    81.3    +      -       +      +
     13E  HIS*     5.4     3.6    -      +       -      -
     20E  SER*     5.8     1.1    -      -       -      -
     21E  ASN*     1.3    89.4    +      -       -      +
     23E  LEU*     1.3    59.1    +      -       -      +
     24E  ASN*     4.4     8.1    -      -       -      +
     67E  TYR*     4.3    16.4    -      +       -      -
     68E  THR      3.4    19.3    -      -       -      +
     69E  GLU*     3.7    23.8    -      -       +      -
     70E  PHE*     3.4     6.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 23 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  VAL*     4.2    19.7    -      -       +      -
     10E  TYR      3.8     7.9    -      -       -      +
     22E  PHE*     1.3    73.7    -      -       -      +
     24E  ASN*     1.3    66.8    -      -       -      +
     39E  LEU*     4.1    28.7    -      -       +      +
     40E  LEU      4.8     0.7    -      -       -      +
     46E  ILE*     5.1     1.1    -      -       +      -
     67E  TYR*     3.2     5.5    -      -       -      -
     68E  THR*     2.9    38.4    +      -       +      +
     70E  PHE*     3.5    30.6    -      -       +      -
     78E  TYR*     3.8    32.8    -      -       +      -
     79E  ALA      4.8     5.6    -      -       -      +
     95E  TRP*     4.2    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 24 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235D  PRO      3.9     1.4    +      -       -      -
    236D  ALA*     3.0    28.7    +      -       -      +
    237D  GLY*     5.6     0.2    -      -       -      -
      8E  GLN      4.3     0.2    -      -       -      -
      9E  VAL*     3.3     9.9    -      -       -      +
     10E  TYR*     2.8    70.0    +      -       +      +
     12E  ARG*     4.1    10.7    +      -       -      +
     22E  PHE*     4.4     8.8    -      -       -      +
     23E  LEU*     1.3    77.6    -      -       -      +
     25E  CYS*     1.3    60.2    +      -       -      +
     26E  TYR      4.1     0.2    -      -       -      -
     39E  LEU*     5.2     1.6    -      -       -      -
     65E  LEU*     3.9    11.9    -      -       +      +
     66E  TYR      3.4     3.6    -      -       -      -
     67E  TYR*     3.2    22.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 25 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ILE*     3.8    19.7    -      -       -      -
      8E  GLN      3.3     3.6    -      -       -      -
      9E  VAL*     5.4     0.2    -      -       +      -
     24E  ASN*     1.3    75.5    -      -       -      +
     26E  TYR*     1.3    60.4    +      -       -      +
     27E  VAL*     3.7    15.1    +      -       -      +
     37E  VAL*     4.2     0.7    -      -       -      -
     39E  LEU*     3.6    16.6    -      -       +      +
     64E  LEU      3.7     2.4    -      -       -      +
     65E  LEU*     4.1     1.6    -      -       -      -
     66E  TYR*     2.8    36.9    +      -       +      +
     80E  CYS*     2.0    50.7    -      -       +      -
     82E  VAL*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 26 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232D  GLU*     3.9    30.9    +      -       -      +
    233D  THR      4.2    10.4    +      -       -      -
    234D  ARG*     4.2     9.0    -      -       +      -
    235D  PRO*     3.8    35.9    -      -       +      -
      6E  LYS      3.9     0.5    -      -       -      +
      7E  ILE*     3.4     4.3    -      -       -      +
      8E  GLN*     2.8    40.8    +      -       +      +
     10E  TYR*     3.5    23.7    -      -       +      +
     24E  ASN      4.1     1.0    -      -       -      -
     25E  CYS*     1.3    71.4    -      -       -      +
     27E  VAL*     1.3    61.8    +      -       -      +
     28E  SER*     4.3     6.6    +      -       -      -
     63E  TYR*     3.6    48.3    -      +       +      +
     64E  LEU      3.5    18.2    -      -       -      -
     65E  LEU*     4.2     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 27 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  PRO*     3.5    29.8    -      -       +      -
      6E  LYS      3.4     5.6    -      -       -      +
      7E  ILE*     4.5     4.3    -      -       +      +
     25E  CYS*     3.9    27.8    -      -       -      +
     26E  TYR*     1.3    75.8    -      -       -      +
     28E  SER*     1.3    61.4    +      -       -      +
     30E  PHE*     3.7     6.3    -      -       +      -
     35E  ILE*     3.6    19.5    -      -       +      -
     37E  VAL*     4.0    20.6    -      -       +      -
     63E  TYR*     3.1     3.1    -      -       -      +
     64E  LEU*     2.8    38.1    +      -       +      +
     66E  TYR*     4.5     3.6    -      -       +      -
     82E  VAL*     4.5     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 28 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232D  GLU*     3.1    33.4    +      -       -      -
      5E  PRO*     3.4     1.9    -      -       -      +
      6E  LYS*     2.8    41.9    +      -       -      +
     26E  TYR*     4.3    10.5    +      -       -      -
     27E  VAL*     1.3    77.7    -      -       -      +
     29E  GLY*     1.3    65.0    +      -       -      +
     30E  PHE*     3.2     5.1    +      -       -      -
     57E  SER*     6.1     0.4    -      -       -      -
     62E  PHE      3.2     8.1    -      -       -      -
     63E  TYR*     3.7    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 29 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  ARG*     3.2    21.1    -      -       -      +
      4E  THR      3.5     9.1    -      -       -      +
      6E  LYS*     4.3    17.4    +      -       -      +
     28E  SER*     1.3    77.4    -      -       -      +
     30E  PHE*     1.3    57.9    +      -       -      +
     57E  SER*     5.8     1.2    +      -       -      -
     59E  ASP*     5.5     0.9    -      -       -      -
     61E  SER*     3.5    24.1    +      -       -      -
     62E  PHE      3.0     6.5    +      -       -      -
     63E  TYR*     5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 30 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  ARG*     3.2    12.3    -      -       -      +
      5E  PRO*     3.6    27.8    -      -       +      -
     27E  VAL*     3.7    17.0    -      -       +      -
     28E  SER*     3.8    12.3    -      -       -      -
     29E  GLY*     1.3    78.6    -      -       -      +
     31E  HIS*     1.3    63.8    +      -       -      +
     32E  PRO      3.4    14.6    -      -       -      -
     33E  SER*     3.5    23.6    -      -       -      -
     35E  ILE*     3.8    28.7    -      -       +      -
     54E  LEU*     4.8     0.9    -      -       +      -
     61E  SER*     3.5     1.5    -      -       -      -
     62E  PHE*     2.8    73.4    +      -       +      -
     63E  TYR*     4.0     2.7    -      -       -      -
     64E  LEU*     4.4    13.5    -      -       +      -
     84E  HIS*     4.0     7.9    -      +       -      +
----------------------------------------------------------
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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