Contacts of the helix formed by residues 321 - 336 (chain B) in PDB entry 2Y4T


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 LYS 321 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  THR*     5.9     4.0    -      -       +      -
    316B  PHE*     2.8    40.4    +      -       +      +
    317B  SER*     5.5     0.4    -      -       -      -
    319B  ASP*     3.4    35.8    +      -       +      +
    320B  GLU*     1.3    77.5    +      -       -      +
    322B  PRO*     1.3    62.1    -      -       +      +
    323B  VAL      3.4     2.2    +      -       -      -
    324B  GLU*     3.2    20.5    +      -       -      +
    325B  ALA*     2.9    29.7    +      -       -      +
    352B  ILE*     5.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320B  GLU      3.2    13.0    -      -       -      +
    321B  LYS*     1.3    84.5    -      -       +      +
    323B  VAL*     1.3    66.6    +      -       +      +
    324B  GLU*     4.5     2.0    -      -       -      +
    326B  ILE*     3.2    32.5    +      -       -      +
    349B  ALA*     3.5    20.7    -      -       +      +
    352B  ILE*     4.1    22.0    -      -       +      -
    353B  GLU*     3.4    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321B  LYS      3.4     0.4    -      -       -      -
    322B  PRO*     1.3    80.6    -      -       +      +
    324B  GLU*     1.3    62.6    +      -       -      +
    326B  ILE*     3.2    11.1    +      -       +      +
    327B  ARG*     2.8    41.3    +      -       +      +
    353B  GLU*     4.8     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316B  PHE*     3.4    40.4    -      -       +      -
    321B  LYS*     3.2    29.2    -      -       -      +
    322B  PRO*     4.5     1.4    -      -       -      +
    323B  VAL*     1.3    83.1    +      -       +      +
    325B  ALA*     1.3    57.4    +      -       -      +
    327B  ARG*     3.3    18.4    +      -       -      +
    328B  VAL*     2.9    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313B  CYS      4.5     0.2    -      -       -      -
    316B  PHE*     3.6     9.1    -      -       -      +
    317B  SER*     3.7    27.8    -      -       -      +
    321B  LYS      2.9    17.6    +      -       -      +
    324B  GLU*     1.3    75.8    -      -       -      +
    326B  ILE*     1.3    55.6    +      -       -      +
    328B  VAL*     5.1     0.2    -      -       -      -
    329B  CYS*     2.7    45.8    +      -       -      -
    345B  ASP      4.7     0.2    -      -       -      +
    346B  ARG*     5.0     0.4    -      -       -      -
    349B  ALA*     3.6    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  PRO      3.2    22.7    +      -       -      +
    323B  VAL*     3.6     7.2    -      -       +      +
    325B  ALA*     1.3    77.0    -      -       -      +
    327B  ARG*     1.3    59.6    +      -       -      +
    330B  SER*     2.7    42.4    +      -       -      +
    346B  ARG*     4.0    17.5    -      -       +      -
    349B  ALA*     3.9    15.0    -      -       +      +
    350B  TYR*     4.0    36.3    -      -       +      +
    353B  GLU*     4.4    15.7    -      -       +      -
    355B  MET*     5.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316B  PHE*     4.4    12.3    -      -       -      -
    323B  VAL*     2.8    26.7    +      -       +      +
    324B  GLU*     3.5    15.7    +      -       -      +
    325B  ALA      3.2     0.2    -      -       -      -
    326B  ILE*     1.3    76.6    -      -       -      +
    328B  VAL*     1.3    87.0    +      -       -      +
    330B  SER*     4.1     2.8    -      -       -      -
    331B  GLU*     3.6    20.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309B  LYS*     3.4    40.8    -      -       +      +
    312B  ILE*     4.1     8.5    -      -       +      -
    313B  CYS*     3.7    15.0    -      -       -      +
    316B  PHE*     3.7    15.5    -      -       +      -
    324B  GLU      2.9    22.8    +      -       -      +
    327B  ARG*     1.3    97.0    -      -       -      +
    329B  CYS*     1.3    67.1    +      -       -      +
    331B  GLU*     2.9    17.0    +      -       +      +
    332B  VAL*     3.0    11.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313B  CYS*     2.0    59.2    -      -       -      +
    325B  ALA*     2.7    33.1    +      -       -      +
    328B  VAL*     1.3    70.5    -      -       -      +
    330B  SER*     1.3    60.0    +      -       -      +
    332B  VAL*     3.2     5.5    +      -       -      +
    333B  LEU*     3.0    30.3    +      -       +      +
    342B  ALA*     4.0     4.0    -      -       -      +
    345B  ASP*     4.1     2.2    -      -       -      -
    346B  ARG*     3.7    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  ILE*     2.7    31.2    +      -       -      +
    327B  ARG*     4.1     4.5    -      -       -      -
    329B  CYS*     1.3    76.0    -      -       -      +
    331B  GLU*     1.3    56.7    +      -       -      +
    333B  LEU*     3.3     3.6    +      -       -      +
    334B  GLN*     2.9    33.3    +      -       -      +
    346B  ARG*     3.1    31.3    +      -       -      +
    350B  TYR*     5.1     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309B  LYS*     2.6    38.3    +      -       +      +
    327B  ARG*     3.6    13.6    +      -       -      +
    328B  VAL*     2.9    10.8    +      -       -      +
    330B  SER*     1.3    75.3    -      -       -      +
    332B  VAL*     1.3    66.8    +      -       +      +
    334B  GLN*     3.2    27.6    +      -       +      +
    335B  MET*     3.3    20.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306B  VAL*     4.6    10.5    -      -       +      +
    309B  LYS*     3.6    20.0    -      -       +      +
    310B  GLU*     3.6    35.2    -      -       +      +
    313B  CYS*     4.2     1.3    -      -       +      -
    328B  VAL      3.0    16.2    +      -       -      +
    329B  CYS*     3.4    11.4    -      -       -      +
    331B  GLU*     1.3    75.4    -      -       -      +
    333B  LEU*     1.3    50.4    +      -       -      +
    335B  MET*     3.0    15.7    +      -       -      +
    336B  GLU*     2.7    30.5    +      -       -      +
    339B  ASN*     3.8    26.2    -      -       -      +
    342B  ALA*     3.9    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329B  CYS      3.0    20.9    +      -       -      +
    330B  SER*     3.7     4.0    -      -       -      +
    332B  VAL*     1.3    72.0    -      -       -      +
    334B  GLN*     1.3    64.8    +      -       -      +
    336B  GLU      3.3    17.9    -      -       -      +
    337B  PRO*     3.0    35.3    -      -       +      +
    339B  ASN*     3.7    13.5    -      -       +      +
    342B  ALA*     3.6    23.3    -      -       +      -
    343B  LEU*     3.7    32.8    -      -       +      +
    346B  ARG*     3.4    37.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 334 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  SER*     2.9    22.8    +      -       -      +
    331B  GLU*     3.2    20.6    -      -       +      +
    333B  LEU*     1.3    76.8    -      -       -      +
    335B  MET*     1.3    62.0    +      -       +      +
    337B  PRO*     4.5     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305B  THR*     5.8     2.5    -      -       -      -
    306B  VAL*     3.9    46.4    -      -       +      -
    309B  LYS*     4.3    19.7    -      -       +      -
    331B  GLU*     3.3    29.4    +      -       +      +
    332B  VAL*     3.0    17.5    +      -       +      +
    334B  GLN*     1.3    81.2    -      -       +      +
    336B  GLU*     1.3    64.5    +      -       +      +
    337B  PRO*     3.8     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 336 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  GLU*     4.6     4.7    -      -       -      +
    306B  VAL*     3.4    16.8    -      -       +      +
    307B  ARG*     2.8    36.3    +      -       -      -
    332B  VAL      2.7    12.9    +      -       -      +
    333B  LEU*     3.3    12.1    -      -       -      +
    335B  MET*     1.3    80.0    -      -       -      +
    337B  PRO*     1.4    68.1    -      -       -      +
    338B  ASP*     3.2    12.8    -      -       -      +
    339B  ASN*     2.8    46.2    +      -       +      +
----------------------------------------------------------
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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