Contacts of the strand formed by residues 246 - 252 (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 SER 246 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  ARG*     3.9    28.8    +      -       -      -
    215A  CYS      3.4     7.6    -      -       -      -
    216A  GLN*     3.6    20.3    +      -       -      +
    242A  GLY*     3.4     4.7    -      -       -      -
    243A  GLY      3.3    23.7    +      -       -      -
    244A  LEU      3.2     0.2    -      -       -      -
    245A  PRO*     1.3    89.9    +      -       -      +
    247A  LEU*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  ARG*     3.3     4.4    -      -       -      -
    215A  CYS*     2.8    39.3    +      -       +      +
    217A  VAL*     4.7     9.2    -      -       +      -
    225A  ALA*     3.7    16.4    -      -       +      -
    226A  GLY*     3.7    34.3    -      -       -      +
    227A  TRP*     2.7    51.5    -      -       +      +
    242A  GLY*     4.3     5.2    -      -       -      +
    243A  GLY      3.9    16.2    -      -       -      +
    244A  LEU      4.1    11.4    -      -       -      +
    246A  SER*     1.3    79.7    -      -       -      +
    248A  GLY*     1.3    57.5    +      -       -      +
    265A  CYS*     5.3     0.9    -      -       +      -
    266A  TRP      5.7     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  LEU      3.7     4.9    -      -       -      -
    214A  ARG*     3.0    25.0    -      -       -      +
    227A  TRP*     3.6     6.1    +      -       -      -
    239A  MET*     3.5    19.8    -      -       -      +
    240A  LYS      3.9     0.7    +      -       -      -
    241A  SER*     3.6    24.3    +      -       -      -
    242A  GLY      3.8     8.1    -      -       -      +
    247A  LEU*     1.3    71.6    -      -       -      +
    249A  LEU*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  LEU*     2.7    59.0    +      -       +      +
    227A  TRP*     3.5    37.5    -      -       +      -
    229A  LEU*     5.2     8.7    -      -       +      -
    232A  LEU*     6.0     0.4    -      -       +      -
    237A  THR*     4.6     8.7    -      -       -      -
    238A  VAL      3.9    11.0    -      -       -      +
    239A  MET*     3.7    28.3    -      -       +      +
    248A  GLY*     1.3    75.3    -      -       -      +
    250A  THR*     1.3    75.8    +      -       -      +
    251A  LEU*     3.9    17.9    -      -       +      -
    263A  VAL*     4.9     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ASP*     4.7     9.9    -      -       +      -
    211A  VAL      3.4    14.6    -      -       -      +
    212A  LEU*     3.2    26.0    -      -       +      +
    236A  ALA      3.8     1.6    -      -       -      +
    237A  THR*     3.5     2.9    -      -       -      -
    238A  VAL*     3.0    42.8    +      -       +      +
    241A  SER*     5.6     3.1    +      -       -      -
    248A  GLY      5.4     0.2    -      -       -      -
    249A  LEU*     1.3    76.6    +      -       -      +
    251A  LEU*     1.3    71.4    +      -       -      +
    252A  ALA*     4.0     5.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ASP*     3.4     0.3    -      -       -      -
    211A  VAL*     2.9    40.4    +      -       +      +
    213A  LEU*     5.2     4.9    -      -       +      -
    232A  LEU*     3.7    16.4    -      -       +      -
    235A  SER*     3.7    13.2    -      -       -      +
    236A  ALA      3.8     2.5    -      -       -      -
    237A  THR*     3.3    32.3    -      -       +      -
    249A  LEU*     3.9    20.9    -      -       +      -
    250A  THR*     1.3    72.2    -      -       -      +
    252A  ALA*     1.3    61.4    +      -       -      +
    254A  VAL*     3.1    16.2    -      -       +      +
    258A  LEU*     3.4    34.5    -      -       +      -
    263A  VAL*     4.9     6.5    -      -       +      -
    280A  VAL*     4.1    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ASP*     3.3    17.0    -      -       +      +
    235A  SER*     3.4     2.0    +      -       -      -
    236A  ALA*     2.9    40.7    +      -       +      +
    238A  VAL*     5.6     5.4    -      -       +      -
    250A  THR*     4.0     7.2    +      -       +      +
    251A  LEU*     1.3    72.1    -      -       -      +
    253A  ASN*     1.3    79.5    +      -       -      +
    254A  VAL      3.3     2.6    +      -       -      -
----------------------------------------------------------
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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