Contacts of the strand formed by residues 302 - 311 (chain B) in PDB entry 3GV5


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 302 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  PRO*     4.3    14.4    -      -       +      -
    301B  SER*     1.3    78.6    -      -       -      +
    303B  SER*     1.3    60.7    +      -       -      +
    328B  LEU*     3.6    16.1    -      -       +      +
    331B  ARG*     3.8    27.8    -      -       +      +
    332B  VAL*     3.7    40.8    -      -       +      -
    335B  ASP*     3.6    33.7    -      -       +      -
    337B  ARG*     3.7    20.9    -      -       -      -
    339B  PRO*     5.6     1.1    -      -       +      -
    409B  CYS*     3.3     2.9    -      -       -      -
    410B  PHE*     2.8    45.6    +      +       +      +
    413B  LEU*     3.9    21.1    -      -       +      -
    843T    C      3.5     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  SER*     6.0     0.2    -      -       -      -
    302B  PHE*     1.3    75.9    -      -       -      +
    304B  GLU*     1.3    62.0    +      -       -      +
    305B  GLU*     5.0     1.7    +      -       -      -
    328B  LEU*     3.9     1.8    -      -       -      -
    331B  ARG*     2.6    27.8    +      -       -      -
    345B  ILE*     5.3     1.1    -      -       -      -
    407B  SER*     3.9    11.7    +      -       -      -
    408B  VAL      3.1    13.7    -      -       -      -
    409B  CYS*     3.7    16.6    -      -       -      -
    842T    T      3.3    30.5    -      -       -      +
    843T    C      2.7    18.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ARG*     3.9     7.7    +      -       -      -
    303B  SER*     1.3    75.3    -      -       -      +
    305B  GLU*     1.3    60.4    +      -       -      +
    324B  LEU*     3.8    32.8    -      -       +      +
    327B  SER*     3.7    24.3    +      -       -      +
    328B  LEU*     3.6    21.8    -      -       +      +
    331B  ARG*     2.8    30.0    +      -       -      +
    407B  SER*     3.0    21.4    +      -       -      -
    408B  VAL      2.9    12.6    +      -       -      +
    422B  GOL      3.6    14.9    +      -       -      -
    842T    T      3.7    12.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  SER*     5.0     1.2    +      -       -      -
    304B  GLU*     1.3    74.1    -      -       -      +
    306B  ASP*     1.3    59.7    +      -       -      +
    324B  LEU*     3.9     3.6    -      -       -      -
    357B  ARG*     2.6    32.9    +      -       -      -
    405B  LEU*     3.5    21.5    -      -       +      +
    406B  LEU      3.3    11.9    -      -       -      +
    407B  SER*     3.3    14.8    +      -       -      +
    422B  GOL      2.6    35.9    +      -       -      -
    841T    C      3.3    49.0    +      -       +      +
    842T    T      3.0    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 306 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     3.0    23.5    +      -       -      -
     97B  GLU*     4.9     0.5    -      -       -      +
    305B  GLU*     1.3    76.6    -      -       -      +
    307B  SER*     1.3    65.4    +      -       -      +
    308B  PHE*     3.4    21.1    -      -       +      +
    320B  LYS*     5.1     7.8    +      -       +      +
    323B  GLU*     5.0     8.6    -      -       -      +
    324B  LEU*     4.3    14.1    -      -       +      +
    405B  LEU*     3.4     6.0    -      -       -      +
    406B  LEU      3.0    30.4    +      -       -      +
    422B  GOL      2.9    22.4    +      -       -      -
    841T    C      4.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 307 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     3.0    40.0    +      -       -      +
    306B  ASP*     1.3    77.6    +      -       -      +
    308B  PHE*     1.3    64.4    +      -       -      +
    347B  ARG*     3.7     6.5    -      -       -      -
    404B  THR      3.3    12.6    -      -       -      -
    405B  LEU*     4.2     6.7    -      -       -      +
    840T    T      3.2    31.3    +      -       -      -
    841T    C      2.8    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     5.2     1.8    -      -       -      +
    306B  ASP*     3.4    33.7    -      -       +      +
    307B  SER*     1.3    80.4    -      -       -      +
    309B  LYS*     1.3    66.3    +      -       -      +
    310B  LYS      4.4     3.8    -      -       -      +
    311B  CYS*     3.4    31.6    -      -       +      -
    320B  LYS*     4.2    22.9    -      -       +      +
    347B  ARG*     5.0     0.9    +      -       -      -
    403B  LEU*     3.5    19.3    -      -       +      -
    404B  THR*     3.0    25.2    +      -       -      +
    405B  LEU      3.6    11.0    -      -       -      -
    406B  LEU*     3.6    43.7    -      -       +      -
    840T    T      5.2     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  TYR*     6.1     7.5    -      -       -      -
    308B  PHE*     1.3    75.2    -      -       -      +
    310B  LYS*     1.3    54.3    +      -       +      +
    349B  TYR*     4.9     1.7    -      -       -      -
    402B  HIS*     2.8    26.9    -      -       -      -
    403B  LEU      4.3     0.2    -      -       -      -
    404B  THR*     3.6     9.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308B  PHE*     3.4     9.1    -      -       -      +
    309B  LYS*     1.3    81.5    -      -       +      +
    311B  CYS*     1.3    53.2    +      -       -      +
    312B  SER*     3.4    34.4    +      -       -      +
    316B  GLU*     4.0    12.2    +      -       -      +
    320B  LYS*     5.3     2.3    +      -       -      -
    402B  HIS*     3.5    29.6    -      -       +      +
    403B  LEU      3.5     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308B  PHE*     3.4    24.9    -      -       +      -
    310B  LYS*     1.3    66.6    -      -       -      +
    312B  SER*     1.3    61.6    +      -       -      +
    313B  SER      3.8     2.7    -      -       -      -
    316B  GLU*     3.5    37.2    +      -       -      -
    317B  ALA*     3.5    29.4    -      -       -      -
    320B  LYS*     4.7     6.7    -      -       -      +
    401B  PHE*     3.8     3.8    -      -       -      -
    402B  HIS*     3.2     3.3    +      -       -      -
    403B  LEU*     2.7    44.3    +      -       +      +
    406B  LEU*     4.7     3.4    -      -       -      -
----------------------------------------------------------
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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