Contacts of the strand formed by residues 53 - 58 (chain E) in PDB entry 2IFG


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 PHE 53 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21E  TRP*     3.4     8.2    -      -       -      -
     22E  VAL*     2.7    48.2    +      -       +      +
     25E  LYS*     3.6    39.9    -      -       +      -
     38E  VAL*     3.9    13.7    -      -       +      -
     51E  GLN*     3.8    24.0    -      -       +      -
     52E  TYR*     1.3    83.9    -      -       -      +
     54E  PHE*     1.3    62.6    +      -       -      +
     55E  GLU*     3.5    19.7    +      -       +      +
     87E  VAL*     4.8    11.9    -      -       +      -
     88E  LYS      4.2     8.1    -      -       -      -
     89E  ALA*     3.6    22.4    -      -       +      -
    102E  ILE*     3.6    20.4    -      -       +      -
    104E  ILE*     4.8     6.3    -      -       +      -
    101F  PHE*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 54 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350A  GLN*     5.1    10.5    -      -       +      -
    351A  PRO      5.5     0.9    -      -       -      -
    352A  THR*     3.9    11.0    -      -       +      -
    379A  MET*     3.5    36.8    -      -       +      -
     19E  SER*     3.9    11.4    -      -       -      -
     20E  VAL      3.8     5.2    -      -       -      -
     21E  TRP*     3.8    33.5    -      +       +      -
     53E  PHE*     1.3    70.8    -      -       -      +
     55E  GLU*     1.3    63.3    +      -       -      +
     56E  THR*     4.0    16.1    +      -       -      -
    104E  ILE*     4.9     6.1    -      -       -      +
    105E  ASP      4.0     5.4    -      -       -      +
    106E  THR*     5.5     0.2    -      -       -      -
     84F  HIS      4.7     3.8    -      -       -      -
     85F  THR*     3.6    23.0    +      -       -      -
     86F  PHE*     3.4    59.5    +      +       +      +
    101F  PHE*     5.0     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 55 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18E  VAL      3.8     0.7    -      -       -      +
     19E  SER*     3.1     3.9    -      -       -      -
     20E  VAL*     2.8    44.5    +      -       +      +
     22E  VAL*     3.4    32.6    -      -       +      +
     25E  LYS*     3.6    19.2    +      -       -      -
     53E  PHE*     3.8     9.8    -      -       -      +
     54E  PHE*     1.3    77.3    -      -       -      +
     56E  THR*     1.3    64.4    +      -       -      +
     57E  LYS*     4.3     5.5    +      -       -      +
    104E  ILE*     2.8    39.5    -      -       -      +
    105E  ASP*     3.5    28.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 56 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350A  GLN*     5.2     7.9    +      -       -      +
     17E  SER*     3.8    25.1    -      -       -      +
     18E  VAL      3.3     8.5    -      -       -      +
     19E  SER*     3.1    26.6    +      -       -      +
     54E  PHE*     4.0    12.1    -      -       -      -
     55E  GLU*     1.3    75.0    -      -       -      +
     57E  LYS*     1.3    63.5    +      -       -      +
    105E  ASP*     3.3     8.9    +      -       -      +
    106E  THR*     3.1    30.5    +      -       -      +
    107E  ALA*     3.0    24.3    +      -       -      +
     84F  HIS      5.3     1.0    +      -       -      -
     85F  THR*     5.4     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 57 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  SER*     3.2     5.5    -      -       -      -
     18E  VAL*     3.0    38.6    +      -       +      +
     20E  VAL*     4.5    20.2    -      -       -      +
     22E  VAL*     6.0     1.4    -      -       -      +
     55E  GLU*     4.3     6.1    +      -       -      +
     56E  THR*     1.3    74.2    -      -       -      +
     58E  CYS*     1.3    76.4    +      -       -      +
     82E  THR*     3.6    19.3    -      -       +      +
    105E  ASP*     3.8    20.3    +      -       -      +
    107E  ALA      4.2     0.4    -      -       -      -
    108E  CYS*     4.1     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 58 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ASP      4.2     0.2    -      -       -      +
     18E  VAL*     4.2     0.3    -      -       -      +
     57E  LYS*     1.3    89.6    -      -       -      +
     59E  ARG*     1.3    66.1    +      -       -      +
     60E  ASP      3.6     2.3    +      -       -      -
     80E  CYS*     4.1     5.2    -      -       +      -
     81E  THR*     3.1    35.4    -      -       -      -
     82E  THR*     3.1    14.5    +      -       -      +
    108E  CYS*     2.0    48.9    -      -       -      -
----------------------------------------------------------
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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