Contacts of the strand formed by residues 237 - 250 (chain A) in PDB entry 4SBV


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 VAL 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ALA*     2.6    31.8    -      -       -      +
     80A  VAL*     3.0    37.5    +      -       +      +
    127A  THR*     4.5    15.9    -      -       +      -
    232A  SER*     5.9     5.6    -      -       -      +
    233A  SER*     4.8    11.0    -      -       -      +
    235A  THR*     3.9    13.7    -      -       -      +
    236A  ALA*     1.3    73.4    -      -       -      +
    238A  ASN*     1.3    71.5    +      -       -      +
    239A  THR      3.2     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  GLU*     5.5     6.2    -      -       -      +
     78A  LEU      3.6     7.6    -      -       -      +
     79A  ALA*     3.7    12.1    -      -       -      +
    122A  SER*     4.8     3.4    +      -       -      -
    123A  CYS*     4.9     5.4    +      -       -      +
    127A  THR*     5.2     1.0    -      -       -      +
    236A  ALA*     3.8    11.3    +      -       -      +
    237A  VAL*     1.3    85.5    -      -       -      +
    239A  THR*     1.3    59.7    +      -       -      +
    240A  GLY      3.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU      2.8    14.0    +      -       -      +
     79A  ALA*     4.2     1.3    -      -       -      +
     80A  VAL*     4.3     6.7    -      -       -      +
    119A  TYR*     3.1    17.8    +      -       +      +
    122A  SER*     3.0    24.7    +      -       -      -
    123A  CYS*     3.0    24.2    -      -       -      -
    127A  THR*     4.4     2.0    -      -       -      +
    161A  VAL*     2.8    33.0    -      -       +      +
    228A  MET*     3.3    34.5    -      -       +      -
    237A  VAL      3.2     6.3    +      -       -      -
    238A  ASN*     1.3    73.3    -      -       -      +
    240A  GLY*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  GLU*     3.8     1.4    -      -       -      +
     78A  LEU      2.9    25.0    +      -       -      +
    119A  TYR*     3.9    10.1    -      -       -      -
    120A  LEU      3.2    13.5    -      -       -      -
    122A  SER*     3.2    13.5    +      -       -      -
    239A  THR*     1.3    83.3    -      -       -      +
    241A  ARG*     1.3    71.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     3.6    23.7    -      -       +      +
     76A  THR      3.5     5.2    -      -       -      +
     77A  GLU*     2.9    34.3    +      -       +      +
     78A  LEU*     4.0     7.0    -      -       -      -
    119A  TYR*     3.1     4.8    -      -       -      -
    120A  LEU      2.8    33.7    +      -       -      +
    122A  SER*     5.1    14.3    -      -       -      -
    240A  GLY*     1.3    84.4    -      -       -      +
    242A  LEU*     1.3    62.5    +      -       -      +
    243A  TYR*     3.6    29.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     3.7     4.5    -      -       -      +
     75A  SER*     2.8    30.8    +      -       -      -
     76A  THR*     2.7    39.5    +      -       +      +
     78A  LEU*     4.1     7.8    -      -       +      +
     89A  GLU*     6.1     2.0    -      -       +      -
    117A  TYR*     3.8    31.4    -      -       +      -
    118A  THR      3.2    17.0    -      -       -      +
    119A  TYR*     3.8     9.0    -      -       +      -
    131A  ILE*     4.5     5.4    -      -       +      -
    133A  MET*     3.2    33.0    -      -       +      -
    224A  LEU*     3.9    15.5    -      -       +      -
    226A  THR*     4.9     6.5    -      -       +      -
    241A  ARG*     1.3    74.8    -      -       -      +
    243A  TYR*     1.3    56.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  CYS*     5.0     2.7    -      -       -      -
     73A  GLU*     3.1    21.3    -      -       -      +
     74A  LEU*     3.8    20.4    -      -       +      -
    116A  ARG      3.2     1.9    -      -       -      +
    117A  TYR*     3.2     6.7    -      -       -      -
    118A  THR*     2.5    43.1    +      -       -      +
    120A  LEU*     3.7    41.2    -      -       +      +
    171A  VAL*     4.5    31.2    -      -       +      -
    241A  ARG*     3.6    44.1    +      -       +      -
    242A  LEU*     1.3    73.4    -      -       -      +
    244A  ALA*     1.3    60.3    -      -       -      +
    245A  SER*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  CYS*     3.2     5.0    -      -       -      -
     73A  GLU*     2.7    42.4    +      -       +      +
     75A  SER*     4.2     7.1    -      -       -      +
     96A  VAL*     3.5    32.5    -      -       +      +
    115A  ILE*     4.9     2.9    -      -       +      -
    116A  ARG      3.2     5.4    -      -       -      +
    117A  TYR*     3.8    18.6    -      -       +      -
    243A  TYR*     1.3    73.0    -      -       -      +
    245A  SER*     1.3    62.4    +      -       -      +
    246A  TYR*     3.9     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  HIS      3.5     3.6    +      -       -      -
     72A  CYS*     2.7    31.3    -      -       -      +
    114A  ALA*     4.2     1.0    -      -       -      +
    115A  ILE*     3.1     3.8    +      -       -      -
    116A  ARG*     2.8    47.1    +      -       -      +
    118A  THR*     5.4     1.3    -      -       -      -
    170A  PHE*     3.1    22.3    +      -       -      -
    243A  TYR      5.2     0.9    -      -       -      -
    244A  ALA*     1.3    71.5    -      -       -      +
    246A  TYR*     1.3    61.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     4.5     6.3    -      -       +      -
     70A  SER*     3.3     1.0    -      -       -      -
     71A  HIS*     2.9    75.4    +      -       +      +
     73A  GLU*     2.7    33.4    +      -       +      -
     96A  VAL*     4.6     7.6    -      -       +      -
     99A  TRP*     3.3     1.6    -      +       -      -
    100A  LEU*     3.3    33.5    -      -       +      +
    112A  TRP*     3.7    22.0    -      +       +      -
    114A  ALA*     3.0    13.7    -      -       -      +
    115A  ILE*     4.0     7.2    -      -       +      -
    244A  ALA*     3.9    24.9    -      -       +      -
    245A  SER*     1.3    78.4    -      -       -      +
    247A  THR*     1.3    68.6    +      -       -      +
    248A  ILE*     4.6     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ILE*     4.1    18.2    -      -       +      -
     69A  LEU      3.5     6.1    -      -       -      +
     70A  SER*     2.4    34.2    +      -       -      +
    112A  TRP      3.8     0.2    -      -       -      -
    113A  VAL*     2.7    54.9    +      -       +      +
    114A  ALA*     2.5    25.1    +      -       -      +
    246A  TYR*     1.3    71.7    +      -       -      +
    248A  ILE*     1.3    56.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  THR      4.0     0.9    -      -       -      +
     68A  ILE*     3.6     3.8    -      -       -      +
     69A  LEU*     2.9    52.4    +      -       +      +
     93A  PRO*     3.9    16.2    -      -       +      -
    100A  LEU*     4.3    15.7    -      -       +      -
    104A  ALA*     5.2     1.1    -      -       +      -
    110A  TYR*     3.2    33.0    -      -       +      -
    111A  ALA      3.6    11.9    -      -       -      +
    112A  TRP*     3.7    26.5    -      -       +      -
    113A  VAL      4.4     0.4    -      -       -      +
    246A  TYR*     4.0     4.6    -      -       +      -
    247A  THR*     1.3    78.8    -      -       -      +
    249A  ARG*     1.3    62.9    -      -       -      +
    250A  LEU*     3.1    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  VAL*     3.1    43.1    -      -       +      +
     67A  THR      3.5     3.6    -      -       -      -
     68A  ILE*     4.3    12.6    -      -       +      -
    110A  TYR*     3.1    23.4    -      -       -      -
    111A  ALA*     3.1    20.8    +      -       -      +
    113A  VAL*     4.2    16.8    -      -       +      +
    196A  ARG*     3.6    14.0    -      -       -      +
    247A  THR      4.3     0.2    +      -       -      -
    248A  ILE*     1.3    75.4    -      -       -      +
    250A  LEU*     1.3    60.6    +      -       -      +
    251A  ILE*     3.1    17.8    -      -       -      +
    191C  GLU*     2.5    30.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  VAL*     3.9     0.9    -      -       -      +
     67A  THR*     2.9    34.4    +      -       +      +
     69A  LEU*     3.3    31.0    -      -       +      -
    100A  LEU*     5.5     0.9    -      -       +      -
    103A  VAL*     4.5     4.3    -      -       +      -
    104A  ALA*     4.6    10.1    -      -       +      -
    107A  TRP*     3.4    53.1    -      -       +      -
    109A  LYS      4.1     4.0    -      -       -      -
    110A  TYR*     4.2     4.0    -      -       +      -
    248A  ILE*     3.1    46.2    -      -       +      -
    249A  ARG*     1.3    67.9    -      -       -      +
    251A  ILE*     1.4    72.0    +      -       -      +
----------------------------------------------------------
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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