Contacts of the strand formed by residues 79 - 87 (chain L) in PDB entry 3SHD


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 79 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  PRO*     4.9     0.9    -      -       -      -
      5L  HIS*     3.6    22.0    -      +       +      -
      7L  THR*     3.3    39.7    -      -       +      +
     37L  HIS*     4.1    13.2    -      +       -      -
     70L  GLN*     3.2     6.4    -      -       -      +
     71L  TRP*     2.7    66.4    +      +       +      +
     72L  ILE      3.9     4.0    -      -       -      -
     73L  ALA*     4.5     6.3    -      -       +      -
     75L  ASP*     5.3     0.4    -      -       -      -
     77L  THR*     3.4    35.0    -      -       +      -
     78L  PRO*     1.3    76.8    -      -       -      +
     80L  LEU*     1.3    66.0    +      -       -      +
     81L  ARG*     3.9     1.6    -      -       +      +
    158L  SO4      4.4    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 80 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  VAL*     3.8    27.6    -      -       +      -
     38B  LEU*     4.8     4.0    -      -       +      -
     44B  LEU*     5.1     4.0    -      -       +      -
     80B  LEU*     5.3     1.6    -      -       +      -
     82B  PHE*     4.7     9.4    -      -       +      -
      4L  PRO*     3.8    28.5    -      -       +      +
      5L  HIS      3.1     9.8    +      -       -      +
      6L  VAL*     3.5    15.4    -      -       +      +
      7L  THR*     3.1    22.7    +      -       -      +
     68L  MET*     3.7    22.7    -      -       +      -
     69L  HIS      3.5     3.4    -      -       -      -
     70L  GLN*     3.5    42.0    -      -       +      +
     79L  PHE*     1.3    73.5    -      -       -      +
     81L  ARG*     1.3    59.5    +      -       -      +
     82L  PHE*     3.8     3.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 81 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7L  THR*     3.3    23.8    -      -       -      +
      9L  ALA*     3.4    26.5    -      -       +      +
     32L  ASN*     4.1    11.5    +      -       -      -
     33L  GLN*     2.8    27.3    +      -       -      +
     35L  ALA*     4.7     0.8    -      -       -      +
     68L  MET*     3.2     6.8    -      -       -      +
     69L  HIS*     2.7    49.7    +      -       +      +
     71L  TRP*     5.3     1.3    -      -       +      +
     79L  PHE*     5.0     5.6    -      -       +      -
     80L  LEU*     1.3    69.6    -      -       -      +
     82L  PHE*     1.3    67.4    +      -       -      +
     83L  LEU*     3.6     6.0    +      -       +      +
    120L  SER*     5.4     1.8    -      -       -      -
    122L  LEU*     3.3    44.3    +      -       +      +
    123L  VAL*     5.4     0.2    -      -       -      +
    126L  SER*     2.8    24.8    +      -       -      -
    158L  SO4      3.2    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  MET*     3.9     9.9    -      -       -      -
     80B  LEU*     4.2     7.9    -      -       +      -
     82B  PHE*     3.8    17.5    -      +       -      -
    141B  ILE*     5.5     0.4    -      -       +      -
      6L  VAL*     3.9    28.0    -      -       +      -
      7L  THR      2.9     9.1    +      -       -      +
      8L  VAL*     3.4     5.2    -      -       +      -
      9L  ALA*     2.9    26.7    +      -       -      +
     44L  LEU*     3.6    32.1    -      -       +      -
     65L  PHE*     3.6    20.2    -      +       +      -
     67L  ARG      4.0     2.0    -      -       -      -
     68L  MET*     3.7    32.1    -      -       +      -
     80L  LEU*     4.0     7.4    -      -       +      -
     81L  ARG*     1.3    72.1    -      -       -      +
     83L  LEU*     1.3    59.1    +      -       -      +
     84L  PHE*     3.9    20.8    -      -       +      -
    141L  ILE*     3.8    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 83 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  ALA*     3.5    23.6    -      -       +      +
     10L  CYS      4.8     0.2    -      -       -      -
     11L  VAL*     3.7    25.1    -      -       +      +
     33L  GLN*     5.3     0.9    -      -       +      +
     65L  PHE*     3.7     3.2    -      -       -      -
     66L  ILE*     2.8    52.5    +      -       +      +
     67L  ARG*     2.9    23.2    +      -       +      +
     69L  HIS*     4.1    21.3    -      -       +      +
     81L  ARG*     3.6     7.6    +      -       +      +
     82L  PHE*     1.3    72.4    -      -       -      +
     84L  PHE*     1.3    55.2    +      -       -      +
    126L  SER*     3.6    40.4    -      -       -      +
    129L  CYS*     4.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 84 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8L  VAL*     3.9    14.8    -      -       +      -
      9L  ALA      2.9    16.2    +      -       -      +
     10L  CYS*     3.6     6.0    -      -       -      -
     11L  VAL*     3.0    24.9    +      -       -      +
     44L  LEU*     4.0    28.3    -      -       +      -
     45L  VAL*     3.7    20.9    -      -       +      -
     48L  ALA*     3.6    25.4    -      -       +      -
     62L  PRO*     3.7    26.2    -      -       +      -
     64L  HIS      3.2    15.3    -      -       -      +
     65L  PHE*     4.2    10.5    -      +       -      -
     66L  ILE*     3.7     9.6    -      -       -      +
     82L  PHE*     3.9    17.9    -      -       +      -
     83L  LEU*     1.3    75.8    -      -       -      +
     85L  ALA*     1.3    62.9    +      -       -      +
    138L  LEU*     3.9     9.0    -      -       +      -
    141L  ILE*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11L  VAL      3.5     7.6    -      -       -      +
     62L  PRO*     4.1     0.2    -      -       -      +
     63L  GLN*     2.9    27.3    +      -       -      +
     64L  HIS*     2.8    28.6    +      -       +      +
     66L  ILE*     3.7    22.2    -      -       +      +
     84L  PHE*     1.3    75.8    -      -       -      +
     86L  ILE*     1.3    64.1    +      -       -      +
     87L  GLU*     6.0     2.2    -      -       +      -
    130L  TYR*     4.4    14.6    -      -       +      -
    135L  ARG*     5.8     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 86 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10L  CYS*     3.6    29.6    -      -       +      -
     11L  VAL      3.1     7.3    +      -       -      +
     12L  VAL*     3.4    22.3    -      -       +      +
     13L  HIS*     3.0    27.2    +      -       -      +
     52L  LEU*     4.4    12.8    -      -       +      -
     60L  ALA*     4.0    26.7    -      -       +      +
     61L  GLN      3.8     8.5    -      -       -      +
     62L  PRO*     3.7    20.4    -      -       +      -
     63L  GLN*     3.6    15.9    -      -       -      +
     85L  ALA*     1.3    78.2    -      -       -      +
     87L  GLU*     1.3    64.3    +      -       -      +
     88L  LEU*     4.2    14.4    -      -       +      -
    130L  TYR*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 87 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144H  PHE*     5.1    15.5    -      -       +      -
    145H  ASN*     5.3     2.9    -      -       -      +
     13L  HIS*     2.9    31.5    -      -       -      +
     14L  ALA*     5.1     0.3    -      -       -      -
     63L  GLN*     2.7    35.0    -      -       -      +
     85L  ALA*     6.0     2.9    -      -       +      -
     86L  ILE*     1.3    74.0    -      -       -      +
     88L  LEU*     1.3    66.4    +      -       -      +
     89L  GLU      4.3     0.5    +      -       -      -
    130L  TYR*     2.4    33.2    +      -       +      -
    135L  ARG*     4.5    18.3    +      -       -      +
----------------------------------------------------------
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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