Contacts of the strand formed by residues 296 - 305 (chain B) in PDB entry 2G4C


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 296 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292B  ASN*     4.0     6.6    +      -       -      -
    293B  PHE*     2.5    30.4    +      -       -      +
    294B  PRO      3.7     0.6    -      -       -      -
    295B  TRP*     1.3    80.1    -      -       -      +
    297B  LYS*     1.3    70.5    +      -       -      +
    298B  GLU*     3.5     9.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 297 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274B  SER*     4.1    22.4    +      -       -      +
    290B  TYR*     4.2    25.9    -      -       +      -
    291B  TYR      3.6     8.3    -      -       -      -
    292B  ASN*     3.8    31.2    +      -       +      +
    296B  GLY*     1.3    76.3    -      -       -      +
    298B  GLU*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LEU*     3.6    30.8    -      -       +      +
    290B  TYR*     3.5     5.5    -      -       -      -
    291B  TYR*     2.9    27.8    +      -       -      +
    293B  PHE*     3.3    27.6    -      -       +      -
    295B  TRP*     3.5    21.3    +      -       -      -
    296B  GLY      3.7     0.7    -      -       -      +
    297B  LYS*     1.3    82.1    -      -       -      +
    299B  LEU*     1.3    66.8    +      -       -      +
    300B  ILE*     4.0     2.8    -      -       -      +
    344B  ARG*     3.9    16.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  LYS*     3.9    26.5    -      -       +      -
    289B  LEU      3.0    22.4    -      -       -      +
    290B  TYR*     3.8    22.0    -      -       +      +
    298B  GLU*     1.3    75.4    -      -       -      +
    300B  ILE*     1.3    64.6    +      -       -      +
    301B  GLU      3.5    18.2    -      -       -      +
    302B  THR*     3.4    22.9    -      -       +      -
    341B  ASP*     5.2     0.7    -      -       -      +
    344B  ARG*     3.0    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  TRP*     3.6    33.0    -      -       +      +
    273B  PHE*     3.4    38.8    -      -       +      -
    289B  LEU*     3.0    23.9    +      -       +      +
    290B  TYR      4.4     2.9    -      -       -      +
    291B  TYR*     4.2    13.9    -      -       +      -
    293B  PHE*     5.2     1.1    -      -       +      -
    298B  GLU      4.0     7.9    -      -       -      +
    299B  LEU*     1.3    81.7    -      -       -      +
    301B  GLU*     1.3    62.8    +      -       -      +
    302B  THR*     5.5     0.2    -      -       -      -
    339B  ASN      4.1     0.2    -      -       -      +
    340B  GLY*     3.3     1.2    -      -       -      -
    341B  ASP*     2.6    41.8    +      -       -      +
    344B  ARG*     4.0    27.8    -      -       +      +
    345B  GLY*     4.7     1.8    -      -       -      +
    348B  ALA*     4.9     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  TRP*     4.2     4.7    +      -       -      -
    237B  ALA      5.0     0.2    -      -       -      +
    259B  ARG*     2.6    51.8    +      -       -      +
    263B  TRP*     2.7    28.6    +      -       +      +
    288B  LYS*     3.5     1.2    -      -       -      -
    289B  LEU*     2.6    50.5    +      -       +      +
    299B  LEU*     3.5     2.7    -      -       -      +
    300B  ILE*     1.3    85.0    -      -       -      +
    302B  THR*     1.3    67.9    +      -       -      +
    303B  LEU*     4.7     0.9    -      -       +      -
    338B  VAL*     3.4    13.8    -      -       +      +
    339B  ASN      3.1    18.2    -      -       -      +
    340B  GLY*     3.7    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287B  ASN      3.7     7.6    -      -       -      -
    288B  LYS*     4.4     9.2    -      -       +      -
    299B  LEU*     3.4    32.1    -      -       +      -
    300B  ILE      5.5     0.2    -      -       -      -
    301B  GLU*     1.3    80.2    -      -       -      +
    303B  LEU*     1.3    65.6    +      -       -      +
    304B  TRP*     4.4    18.7    -      -       -      -
    337B  SER      3.7     2.3    +      -       -      +
    339B  ASN*     2.8    47.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  LEU*     4.0    17.5    -      -       +      -
    255B  TRP*     3.8    17.9    -      -       +      +
    256B  LEU*     3.6    41.3    -      -       +      +
    259B  ARG*     4.3     4.3    -      -       +      -
    286B  GLY*     4.2     0.4    -      -       -      -
    287B  ASN*     3.0    34.2    +      -       -      +
    289B  LEU*     3.2    35.2    -      -       +      -
    301B  GLU*     4.6     3.8    -      -       +      +
    302B  THR*     1.3    78.7    -      -       -      +
    304B  TRP*     1.3    78.3    +      -       -      +
    337B  SER      3.4     6.1    -      -       -      +
    338B  VAL*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  LEU*     4.3     7.2    -      -       -      +
    278B  CYS*     3.7    17.5    -      -       +      -
    279B  GLN*     3.7    22.0    -      -       -      -
    280B  ASP      4.0     5.8    -      -       -      -
    281B  GLU*     3.6    54.8    +      -       +      -
    282B  GLU      6.3     0.2    -      -       -      -
    283B  GLY      4.8     5.2    -      -       -      -
    284B  ARG      5.3     0.2    -      -       -      -
    285B  LYS      3.4    22.9    -      -       -      -
    286B  GLY*     3.5    18.2    -      -       -      -
    287B  ASN      5.4     0.4    -      -       -      -
    288B  LYS*     3.8    23.0    -      -       -      +
    302B  THR*     4.4    19.7    +      -       -      -
    303B  LEU*     1.3    88.2    +      -       -      +
    305B  ASN*     1.3    60.9    +      -       -      +
    306B  LEU*     3.7    18.6    +      -       +      -
    336B  LEU*     3.3     4.9    -      -       -      +
    337B  SER*     2.7    44.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  SER*     2.5    45.9    +      -       -      -
    249B  ASN*     3.6    10.7    -      -       -      +
    252B  LEU*     4.6    12.2    -      -       +      +
    283B  GLY*     4.2     1.0    -      -       -      -
    284B  ARG      3.8    26.8    +      -       -      +
    285B  LYS*     3.1    21.5    +      -       +      +
    304B  TRP*     1.3    72.2    -      -       -      +
    306B  LEU*     1.3    61.6    +      -       -      +
    307B  GLY*     3.3    17.3    +      -       -      -
    334B  CYS*     4.1     4.1    -      -       -      +
    335B  VAL      4.1     2.9    -      -       -      +
    336B  LEU*     4.3     9.9    -      -       +      +
----------------------------------------------------------
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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