Contacts of the strand formed by residues 328 - 335 (chain P) in PDB entry 1SVC


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 ALA 328 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263P  VAL*     6.2     0.2    -      -       +      -
    287P  GLU*     4.1     6.7    -      -       -      +
    319P  TYR*     3.3    37.9    -      -       +      +
    324P  ILE*     5.7     4.9    -      -       +      -
    326P  LYS      4.0     1.3    +      -       -      +
    327P  PRO*     1.3    73.0    -      -       -      +
    329P  SER*     1.3    60.7    +      -       -      +
    330P  VAL      3.6     2.1    +      -       -      -
    349P  LEU*     3.8     2.9    -      -       -      -
    350P  TYR*     2.9    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 329 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287P  GLU*     3.6    16.0    +      -       -      +
    327P  PRO      4.3     0.6    +      -       -      -
    328P  ALA*     1.3    70.5    -      -       -      +
    330P  VAL*     1.3    62.7    +      -       -      +
    331P  PHE*     5.5     3.3    -      -       -      -
    348P  PHE      3.5     9.2    -      -       -      -
    349P  LEU*     3.3    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 330 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285P  PHE*     4.4     8.3    -      -       +      -
    286P  TYR      3.4    11.7    -      -       -      +
    287P  GLU*     3.7    24.0    -      -       +      +
    295P  TRP*     3.6    23.8    -      -       +      -
    319P  TYR*     3.9    12.1    -      -       +      -
    328P  ALA      4.4     1.3    -      -       -      +
    329P  SER*     1.3    80.4    -      -       -      +
    331P  PHE*     1.3    75.6    +      -       -      +
    347P  PRO*     4.0     1.0    -      -       -      +
    348P  PHE*     2.9    45.1    +      -       +      +
    350P  TYR*     3.4    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 331 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284P  ARG      3.4     1.4    -      -       -      +
    285P  PHE*     2.9     9.7    -      -       -      +
    286P  TYR*     2.7    76.9    +      +       +      +
    287P  GLU*     5.4     2.9    -      -       -      -
    288P  GLU*     5.8     1.8    -      -       +      -
    329P  SER      5.5     3.1    -      -       -      -
    330P  VAL*     1.3    82.5    -      -       -      +
    332P  VAL*     1.3    63.1    -      -       -      +
    345P  PRO*     3.6    22.4    -      -       +      -
    346P  LYS      3.3    16.8    -      -       -      -
    347P  PRO*     4.6    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 332 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253P  ILE*     3.7    17.4    -      -       +      +
    256P  MET*     4.1    24.0    -      -       +      -
    271P  LEU*     4.5     1.1    -      -       +      -
    283P  ILE*     4.0    21.1    -      -       +      -
    284P  ARG      3.3     4.0    -      -       -      +
    285P  PHE*     3.2    39.3    -      -       +      -
    314P  PHE*     5.2     0.4    -      -       +      -
    331P  PHE*     1.3    73.8    -      -       -      +
    333P  GLN*     1.3    66.2    +      -       -      +
    345P  PRO*     3.5     0.3    -      -       -      +
    346P  LYS*     2.7    42.2    +      -       +      +
    348P  PHE*     3.7    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 333 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253P  ILE*     3.6    11.2    -      -       -      -
    283P  ILE*     3.5     2.8    -      -       -      -
    284P  ARG*     2.7    71.1    +      -       +      +
    286P  TYR*     3.4    28.7    +      -       +      -
    332P  VAL*     1.3    80.3    -      -       -      +
    334P  LEU*     1.3    62.1    +      -       -      +
    342P  THR*     3.3    30.6    +      -       -      +
    343P  SER*     3.3    26.7    +      -       -      +
    345P  PRO*     4.1    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 334 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251P  LEU*     4.5     7.9    -      -       +      -
    252P  LYS      3.6    40.6    -      -       -      +
    253P  ILE*     3.6    10.8    -      -       +      -
    271P  LEU*     4.1    21.5    -      -       +      -
    273P  CYS*     3.7    14.4    -      -       +      -
    274P  ASP      5.1     0.4    -      -       -      +
    276P  VAL*     4.7     8.7    -      -       +      -
    281P  ILE*     4.1    16.6    -      -       +      -
    282P  GLN      3.3    11.7    -      -       -      +
    283P  ILE*     4.2    15.3    -      -       +      -
    312P  ILE*     4.5     7.2    -      -       +      -
    333P  GLN*     1.3    75.6    -      -       -      +
    335P  ARG*     1.3    61.0    +      -       -      +
    342P  THR*     3.4     6.8    -      -       -      +
    343P  SER*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 335 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251P  LEU*     4.4     2.0    -      -       -      -
    281P  ILE*     3.6     3.7    -      -       -      -
    282P  GLN*     2.8    72.6    +      -       +      +
    284P  ARG*     3.5    41.9    -      -       +      +
    296P  GLU*     3.6    12.3    +      -       -      -
    298P  PHE*     3.8    13.5    -      -       -      -
    334P  LEU*     1.3    75.5    -      -       -      +
    336P  ARG*     1.3    64.5    +      -       -      +
    337P  LYS      3.6     0.5    +      -       -      -
    340P  LEU*     3.3    38.8    -      -       +      +
    341P  GLU      3.4     3.8    -      -       -      -
    342P  THR*     3.5    21.8    -      -       +      -
----------------------------------------------------------
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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