Contacts of the strand formed by residues 329 - 340 (chain E) in PDB entry 6Q2J


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 329 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283E  VAL*     4.7     4.5    -      -       +      -
    293E  VAL*     4.1    18.6    -      -       +      -
    318E  LEU*     4.0    11.5    -      -       +      +
    324E  TRP*     5.2     4.9    -      +       -      -
    325E  ALA      2.7    21.9    +      -       -      +
    326E  GLN*     4.0    14.2    -      -       -      +
    328E  THR*     1.3   102.0    -      -       -      +
    330E  ARG*     1.3    60.9    +      -       -      +
    356E  LEU*     4.5    22.0    -      -       +      -
    357E  VAL      3.5    11.0    -      -       -      -
    358E  LEU*     3.6    24.9    -      -       +      -
    359E  ASN*     5.0     3.8    +      -       -      -
    362E  LEU*     5.0     1.3    -      -       +      -
    370E  MET*     3.8    34.3    -      -       +      -
    372E  LEU*     4.4    15.3    -      -       +      -
    395E  VAL*     4.0    23.3    -      -       +      -
    397E  VAL*     5.0     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 330 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289E  GLU      4.6     2.6    +      -       -      -
    290E  ASP*     4.0    12.5    +      -       -      +
    318E  LEU*     5.0     2.0    -      -       -      -
    329E  PHE*     1.3    73.5    -      -       -      +
    331E  VAL*     1.3    66.5    +      -       -      +
    332E  GLU*     3.6    16.8    +      -       +      +
    356E  LEU*     3.6     4.4    -      -       -      +
    357E  VAL*     2.9    64.0    +      -       +      +
    358E  LEU      3.5    15.4    +      -       -      -
    359E  ASN*     3.5    29.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316E  SER*     4.4    15.8    +      -       -      +
    318E  LEU*     3.7    42.1    -      -       +      +
    330E  ARG*     1.3    76.7    -      -       -      +
    332E  GLU*     1.3    61.4    +      -       -      +
    333E  HIS      3.8     2.3    +      -       -      -
    354E  TYR*     4.5    17.5    -      -       +      -
    355E  ARG      3.4    11.9    -      -       -      +
    356E  LEU*     3.8    15.7    -      -       +      -
    374E  VAL*     3.8    30.7    -      -       +      -
    393E  PHE*     5.6     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 332 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330E  ARG*     3.6    18.9    +      -       +      +
    331E  VAL*     1.3    72.0    -      -       -      +
    333E  HIS*     1.3    62.0    +      -       -      +
    334E  TRP*     3.2    34.7    +      -       +      -
    353E  ASP      4.1     0.5    -      -       -      +
    354E  TYR*     3.7     1.3    -      -       -      -
    355E  ARG*     2.9    48.2    +      -       +      +
    357E  VAL*     3.4    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 333 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310E  LEU*     4.4     8.1    -      -       +      +
    314E  TYR*     4.2    27.9    -      -       +      +
    316E  SER*     4.1    13.7    -      -       -      +
    331E  VAL      3.8     1.2    +      -       -      +
    332E  GLU*     1.3    76.5    -      -       -      +
    334E  TRP*     1.3    83.9    +      -       -      +
    335E  PRO*     4.0    10.5    -      -       +      +
    352E  HIS*     3.6    28.4    +      +       +      -
    353E  ASP      3.4     8.1    +      -       -      -
    354E  TYR*     3.2    47.7    +      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 334 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332E  GLU*     3.2    46.0    -      -       +      -
    333E  HIS*     1.3    82.4    -      -       -      +
    335E  PRO*     1.3    80.6    -      -       +      +
    336E  ASN*     5.9     0.2    -      -       +      -
    353E  ASP*     2.9    49.2    +      -       +      +
    355E  ARG*     3.3    48.2    -      -       -      +
    702E  NAG      4.5    17.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 335 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307E  SER*     6.2     0.7    -      -       -      +
    310E  LEU*     3.6    43.3    -      -       +      -
    333E  HIS*     4.0     4.9    -      -       +      +
    334E  TRP*     1.3   100.4    -      -       +      +
    336E  ASN*     1.3    67.4    +      -       -      +
    350E  THR*     5.6     2.5    -      -       +      -
    351E  VAL      3.5     7.4    -      -       -      +
    352E  HIS*     3.5    28.0    -      -       +      +
    353E  ASP*     5.9     0.4    -      -       -      -
    702E  NAG      4.0     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 336 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294C  ARG*     4.1     6.2    +      -       -      -
    334E  TRP*     5.9     0.2    -      -       +      -
    335E  PRO*     1.3    75.3    -      -       -      +
    337E  GLU*     1.3    75.2    +      -       -      +
    338E  THR*     6.1     1.3    -      -       -      -
    350E  THR*     3.3     8.6    -      -       -      +
    351E  VAL*     2.9    36.0    +      -       +      +
    353E  ASP*     5.7     3.8    -      -       -      +
    702E  NAG      1.4    73.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 337 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294C  ARG*     3.2    31.3    +      -       +      +
    295C  THR*     4.9     2.9    -      -       -      -
    296C  ILE      5.3     1.6    -      -       -      +
    303E  VAL*     3.8    27.3    -      -       -      +
    336E  ASN*     1.3    89.6    +      -       -      +
    338E  THR*     1.3    63.2    +      -       -      +
    348E  ARG*     2.9    39.5    +      -       +      +
    349E  ALA      3.2    13.9    -      -       -      +
    350E  THR*     4.1    13.6    -      -       +      +
    351E  VAL      4.6     0.4    -      -       -      +
    702E  NAG      5.0     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 338 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297E  ARG*     6.1     0.2    -      -       -      +
    299E  PHE*     5.6     4.3    -      -       +      -
    336E  ASN*     6.1     1.1    -      -       -      -
    337E  GLU*     1.3    74.8    -      -       -      +
    339E  SER*     1.3    76.8    +      -       -      +
    340E  VAL*     6.3     0.2    -      -       +      -
    348E  ARG*     3.3    11.8    -      -       -      +
    349E  ALA*     2.9    32.6    +      -       +      +
    351E  VAL*     3.9    28.3    -      -       +      -
    702E  NAG      4.6    14.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 339 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338E  THR*     1.3    92.7    +      -       -      +
    340E  VAL*     1.3    60.6    +      -       -      +
    346E  PHE*     3.9    34.7    -      -       -      -
    347E  VAL      3.8     4.3    -      -       -      -
    348E  ARG*     4.4     7.4    -      -       -      +
    349E  ALA*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 340 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299E  PHE*     4.6    27.8    -      -       +      -
    301E  ALA*     6.6     0.2    -      -       +      -
    338E  THR*     4.3     0.6    +      -       +      -
    339E  SER*     1.3    75.2    -      -       -      +
    341E  GLN*     1.3    78.0    +      -       -      +
    346E  PHE*     3.4     4.3    -      -       -      -
    347E  VAL*     2.9    49.2    +      -       +      +
    349E  ALA*     4.7     8.5    -      -       +      +
----------------------------------------------------------
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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