Contacts of the strand formed by residues 303 - 307 (chain A) in PDB entry 5EPG


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 GLY 303 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  ALA*     2.8    38.2    +      -       -      +
    302A  ASN*     1.3    88.2    -      -       -      +
    304A  LEU*     1.3    54.8    +      -       -      +
    334A  TYR*     3.8     0.2    -      -       -      -
    416A  ILE      3.8     4.7    -      -       -      -
    418A  TYR*     3.1    34.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  VAL*     5.7     0.2    -      -       +      -
    298A  ASN      3.1    19.1    -      -       -      +
    299A  HIS*     4.3    13.7    -      -       +      +
    300A  ALA      4.3     0.7    -      -       -      +
    302A  ASN*     5.2     0.4    -      -       -      +
    303A  GLY*     1.3    73.1    -      -       -      +
    305A  THR*     1.3    64.8    +      -       -      +
    306A  LEU*     4.4    21.5    -      -       +      -
    318A  ILE*     4.5     1.1    -      -       +      -
    319A  LEU*     4.4    11.2    -      -       +      -
    322A  VAL*     4.2    25.4    -      -       +      -
    334A  TYR*     3.3    36.3    -      -       +      +
    414A  VAL      3.8     0.9    -      -       -      +
    415A  ASN*     3.5     1.7    -      -       -      +
    416A  ILE*     3.0    50.0    +      -       +      +
    418A  TYR*     5.0     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  VAL*     3.7    12.4    -      -       -      +
    297A  VAL*     3.8     1.0    -      -       -      -
    298A  ASN*     3.1    51.6    +      -       -      +
    300A  ALA*     4.9     7.0    -      -       +      -
    302A  ASN*     5.8     3.4    -      -       -      +
    304A  LEU*     1.3    78.4    -      -       -      +
    306A  LEU*     1.3    60.8    +      -       -      +
    380A  ASN*     4.7     6.7    -      -       -      +
    413A  SER*     4.9     4.9    -      -       -      -
    414A  VAL      3.3     7.0    -      -       -      -
    415A  ASN*     2.6    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  VAL      3.6     0.7    -      -       -      +
    297A  VAL*     4.3    12.8    -      -       +      -
    304A  LEU*     4.4    13.7    -      -       +      -
    305A  THR*     1.3    79.1    -      -       -      +
    307A  GLY*     1.3    64.5    +      -       -      +
    310A  LEU*     3.8    18.8    -      -       +      -
    315A  VAL*     4.3    17.7    -      -       +      -
    318A  ILE*     4.1    24.2    -      -       +      -
    319A  LEU*     4.0    23.1    -      -       +      -
    337A  LEU*     6.3     0.2    -      -       +      -
    355A  LEU*     4.1    11.4    -      -       +      -
    413A  SER*     3.1     3.8    -      -       -      -
    414A  VAL*     2.9    37.6    +      -       +      +
    416A  ILE*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  LEU      3.2    16.4    -      -       -      -
    296A  VAL*     2.8    29.1    +      -       -      -
    306A  LEU*     1.3    71.8    -      -       -      +
    308A  ALA*     1.3    63.8    +      -       -      -
    310A  LEU*     3.2    25.4    +      -       -      +
    355A  LEU*     3.9     8.2    -      -       -      +
    412A  VAL      3.7     7.0    -      -       -      -
    413A  SER*     3.9     3.6    -      -       -      -
----------------------------------------------------------
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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