Contacts of the strand formed by residues 337 - 348 (chain A) in PDB entry 3L2V


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 TRP 337 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     3.0    36.6    +      -       -      +
    102A  THR      4.3     1.3    -      -       -      -
    103A  ASN      3.1    27.5    +      -       -      -
    104A  ALA*     3.9     9.4    -      -       +      +
    105A  SER*     4.6    12.3    -      -       -      -
    324A  GLN*     3.6    21.3    -      -       -      +
    325A  GLU      3.6     7.0    -      -       -      -
    326A  ARG*     3.4    68.2    -      -       +      -
    327A  VAL*     3.9     8.5    -      -       -      +
    335A  PRO*     3.2     8.1    -      -       -      +
    336A  ARG*     1.3    92.6    -      -       +      +
    338A  HIS*     1.3    69.1    +      -       -      +
    368A  ASN      3.9     4.0    -      -       -      -
    369A  LEU      4.1     4.0    -      -       -      -
    370A  LYS*     3.6    42.4    -      -       +      -
    802A  GOL      5.4     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     3.7     2.4    -      -       -      +
    324A  GLN*     2.6    34.7    +      -       -      +
    325A  GLU*     2.8    43.6    +      -       +      +
    326A  ARG      3.5    14.6    +      -       -      -
    327A  VAL*     3.7    25.3    -      -       +      +
    328A  ALA*     4.3     5.4    +      -       +      +
    337A  TRP*     1.3    74.9    -      -       -      +
    339A  LYS*     1.3    61.6    +      -       -      +
    341A  SER*     6.0     0.2    -      -       -      +
    357A  HIS*     3.5    31.2    +      +       +      -
    802A  GOL      2.2    40.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLN*     4.0    16.6    -      -       -      +
    101A  ILE*     4.0     8.8    -      -       +      +
    324A  GLN*     3.8     5.0    -      -       -      +
    338A  HIS*     1.3    84.0    -      -       -      +
    340A  PRO*     1.4    81.8    -      -       +      +
    341A  SER*     3.6     7.4    +      -       -      -
    357A  HIS*     6.1     0.6    -      -       +      -
    358A  LEU*     6.0     5.2    -      -       +      -
    802A  GOL      2.5    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLN*     4.8    12.3    -      -       -      +
    100A  LEU*     4.8    13.2    -      -       +      -
    101A  ILE*     5.1     2.2    -      -       +      -
    322A  LEU*     4.3    22.0    -      -       +      -
    324A  GLN*     3.5    18.4    -      -       +      +
    339A  LYS*     1.4    92.3    -      -       +      +
    341A  SER*     1.3    62.0    +      -       -      +
    356A  ASP      5.9     0.3    -      -       -      -
    358A  LEU*     5.2     8.7    -      -       -      +
    372A  THR*     3.8    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  GLN      3.4     1.4    -      -       -      +
    322A  LEU*     3.7     4.7    -      -       -      +
    323A  VAL*     2.9    42.1    +      -       -      +
    324A  GLN*     4.4     3.3    -      -       -      -
    325A  GLU*     4.6     3.1    +      -       -      +
    338A  HIS*     6.0     0.2    -      -       -      +
    339A  LYS      3.9     6.5    +      -       -      -
    340A  PRO*     1.3    75.5    -      -       -      +
    342A  THR*     1.3    64.8    +      -       -      +
    354A  ILE*     4.0    18.9    -      -       -      +
    355A  LEU      3.1    20.6    -      -       -      -
    356A  ASP*     3.9    14.7    -      -       -      +
    357A  HIS*     6.1     0.3    -      -       -      -
    369A  LEU*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  GLY*     3.8    25.4    -      -       -      -
    321A  GLN      3.5     7.0    -      -       -      +
    322A  LEU*     4.2    10.9    -      -       +      +
    323A  VAL*     5.4     0.2    -      -       -      -
    341A  SER*     1.3    79.3    -      -       -      +
    343A  VAL*     1.3    69.9    +      -       -      +
    344A  LEU*     3.3    10.6    +      -       +      +
    354A  ILE*     3.3     6.8    -      -       -      -
    355A  LEU*     3.2    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PRO*     4.7     5.8    -      -       +      -
    318A  VAL      3.4    27.4    -      -       -      +
    319A  VAL*     3.6    10.8    -      -       -      +
    320A  GLY*     3.0    23.0    +      -       -      +
    321A  GLN*     3.2    10.6    +      -       +      +
    323A  VAL*     3.7    31.6    -      -       +      -
    342A  THR*     1.3    73.5    -      -       -      +
    344A  LEU*     1.3    63.3    +      -       -      +
    345A  LYS      3.9     4.5    -      -       -      +
    346A  VAL*     3.8    21.3    -      -       +      -
    352A  VAL*     3.9    21.1    -      -       +      -
    353A  VAL      3.8     3.8    -      -       -      -
    354A  ILE*     4.4     2.2    -      -       +      -
    369A  LEU*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  VAL*     3.4    21.0    -      -       -      +
    342A  THR*     3.3     8.9    +      -       +      +
    343A  VAL*     1.3    75.3    -      -       -      +
    345A  LYS*     1.3    59.4    +      -       +      +
    353A  VAL*     2.7    24.3    +      -       +      +
    354A  ILE      4.1     2.2    -      -       -      -
    355A  LEU*     3.6    48.7    -      -       +      +
    361A  ASN*     3.9    28.9    -      -       -      +
      1C    A      6.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  VAL*     5.1     3.1    -      -       -      -
    343A  VAL*     3.9     0.6    -      -       -      +
    344A  LEU*     1.3    80.3    -      -       +      +
    346A  VAL*     1.3    65.3    +      -       -      +
    347A  LEU*     3.8    11.7    -      -       +      -
    352A  VAL*     3.6     6.8    -      -       -      +
    353A  VAL*     3.0    36.2    +      -       +      +
      1C    A      4.7    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PRO*     3.5    34.3    -      -       +      +
    319A  VAL*     4.1    19.4    -      -       +      +
    343A  VAL*     3.8    20.0    -      -       +      -
    345A  LYS*     1.3    75.2    -      -       -      +
    347A  LEU*     1.3    64.9    +      -       -      +
    348A  ASN*     3.4    25.5    -      -       -      +
    349A  PRO*     4.6     4.9    -      -       +      -
    351A  THR      4.0     4.5    -      -       -      +
    352A  VAL*     4.6     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  LYS*     3.8     8.0    -      -       +      -
    346A  VAL*     1.3    72.9    -      -       -      +
    348A  ASN*     1.3    62.4    +      -       -      +
    351A  THR*     3.1    19.6    +      -       +      +
    352A  VAL      4.9     0.2    -      -       -      -
    353A  VAL*     3.8    21.5    -      -       +      +
    363A  THR*     3.6    31.0    -      -       +      +
      1C    A      3.8    39.7    -      -       +      +
      2C    T      3.0    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LEU*     3.5    19.4    -      -       +      +
    317A  PRO*     4.8     0.5    -      -       -      +
    346A  VAL*     3.3    14.4    -      -       -      +
    347A  LEU*     1.3    77.9    -      -       -      +
    349A  PRO*     1.4    65.5    -      -       +      +
    350A  ARG*     2.6    23.2    +      -       -      -
    351A  THR*     2.5    61.8    +      -       -      +
      2C    T      4.6     9.8    +      -       +      +
      3C    T      3.2    24.0    +      -       -      -
----------------------------------------------------------
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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