Contacts of the strand formed by residues 342 - 348 (chain A) 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 ARG 342 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  PHE*     4.4     0.8    -      -       -      -
    304A  SER*     3.3     5.4    -      -       -      -
    305A  VAL*     2.9    44.6    +      -       +      +
    310A  ALA*     5.8     8.5    -      -       +      -
    332A  PHE*     2.9    58.1    -      -       +      +
    333A  LEU      3.0    21.2    +      -       -      -
    334A  GLU      4.1     0.2    +      -       -      -
    335A  PRO*     3.0    42.6    -      -       -      +
    340A  THR      3.7    10.5    -      -       -      +
    341A  VAL*     1.3    79.9    -      -       -      +
    343A  HIS*     1.3    65.5    +      -       -      +
      2G  NDG      5.9     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  PHE*     3.4     7.2    -      -       -      -
    304A  SER*     3.2    23.7    +      -       -      -
    332A  PHE*     3.6     5.9    -      -       -      +
    333A  LEU*     2.9    36.8    +      -       +      +
    336A  ALA*     6.1     2.0    -      -       +      -
    339A  GLU*     4.1     9.5    +      -       -      -
    341A  VAL*     3.6    39.9    -      -       +      +
    342A  ARG*     1.3    77.0    +      -       -      +
    344A  GLY*     1.3    59.5    +      -       -      +
      4E  HIS*     4.0     3.8    -      -       +      -
      5E  PRO*     3.4    39.5    -      -       +      +
      9E  ARG*     6.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  PRO*     3.4     5.0    -      -       -      +
    303A  PHE*     2.9    41.3    +      -       -      +
    331A  GLU      2.9    13.7    -      -       -      -
    332A  PHE*     4.0     0.7    -      -       -      -
    333A  LEU*     4.2     9.9    -      -       -      -
    343A  HIS*     1.3    75.7    -      -       -      +
    345A  CYS*     1.3    63.4    +      -       -      +
      4E  HIS*     3.8     7.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  CYS*     2.0    50.3    -      -       +      -
    301A  ILE      3.3     6.1    -      -       -      -
    302A  PRO*     4.5     0.2    -      -       -      -
    303A  PHE*     3.2     8.5    -      -       -      -
    330A  THR*     3.5     1.4    -      -       -      -
    331A  GLU*     2.7    41.3    +      -       +      +
    344A  GLY*     1.3    74.3    -      -       -      -
    346A  LEU*     1.3    62.4    +      -       -      +
    347A  ARG*     3.4    15.6    +      -       +      -
      6E  ILE*     3.5    29.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  CYS*     3.3     3.6    -      -       -      -
    301A  ILE*     2.9    54.4    +      -       +      -
    315A  TRP*     3.4    43.0    -      -       +      +
    322A  LEU*     4.0     8.7    -      -       +      -
    324A  GLU*     5.5     1.8    -      -       +      -
    328A  ILE*     3.8    17.7    -      -       +      -
    329A  PHE*     3.5    18.8    -      -       -      +
    330A  THR*     4.3     3.8    -      -       -      +
    345A  CYS*     1.3    72.1    -      -       -      +
    347A  ARG*     1.3    61.5    +      -       -      +
    348A  LEU*     3.2    19.5    -      -       +      +
    359A  TYR*     3.5    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  HIS*     4.0    11.3    -      -       -      -
    298A  HIS*     2.7    48.1    +      -       -      +
    299A  TRP      3.6     6.1    -      -       -      +
    300A  CYS*     5.0     1.3    -      -       +      -
    327A  PHE      3.2     3.0    -      -       -      +
    328A  ILE*     3.2     7.1    -      -       -      -
    329A  PHE*     2.8    57.6    +      -       +      +
    331A  GLU*     2.6    51.0    +      -       +      -
    345A  CYS*     3.4    22.6    +      -       +      -
    346A  LEU*     1.3    72.1    -      -       -      +
    348A  LEU*     1.3    60.3    +      -       -      +
     11E  GLU*     3.1    29.0    +      -       -      +
     79F  TYR*     5.4     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  HIS*     3.6     3.3    -      -       -      +
    299A  TRP*     2.8    55.4    +      -       +      +
    301A  ILE*     4.0    16.2    -      -       +      -
    327A  PHE      3.4     2.7    -      -       -      -
    328A  ILE*     3.4    42.6    -      -       +      -
    346A  LEU*     3.2    36.3    -      -       +      +
    347A  ARG*     1.3    71.4    -      -       -      +
    349A  ASN*     1.3    59.9    +      -       -      +
    350A  GLN      3.3     5.2    +      -       -      -
    351A  PRO*     3.9    15.5    -      -       +      -
    359A  TYR*     4.8     9.4    -      -       -      +
    378A  PHE*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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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