Contacts of the strand formed by residues 279 - 288 (chain L) in PDB entry 1S9C


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 ILE 279 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247L  ALA*     3.1    21.1    -      -       +      +
    248L  LYS*     3.2    19.7    +      -       -      +
    270L  GLN*     3.2    30.5    -      -       +      +
    271L  THR      3.5     4.9    -      -       -      +
    272L  LYS*     3.9    22.7    -      -       +      -
    277L  GLY      3.6     3.3    +      -       -      +
    278L  ASP*     1.3    72.7    -      -       -      +
    280L  VAL*     1.3    60.0    +      -       -      +
    281L  ILE      3.6    25.1    -      -       -      +
    282L  SER*     4.0    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 280 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219L  THR*     3.9     9.6    -      -       +      -
    246L  PHE*     3.8     4.5    -      -       -      +
    247L  ALA*     2.9    22.9    +      -       -      -
    248L  LYS*     3.3    23.2    -      -       +      +
    249L  PRO      3.6     5.2    -      -       -      +
    250L  VAL*     3.2    34.3    -      -       +      -
    256L  LEU*     4.7     0.7    -      -       +      -
    271L  THR*     2.8    41.9    +      -       +      +
    272L  LYS*     4.2     3.4    -      -       -      +
    273L  VAL*     3.5    18.6    -      -       +      -
    278L  ASP*     4.2     4.7    -      -       +      +
    279L  ILE*     1.3    76.0    -      -       -      +
    281L  ILE*     1.3    61.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 281 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219L  THR*     3.7    17.3    -      -       +      +
    220L  PHE*     3.6    39.0    -      -       +      +
    223L  SER*     4.7     1.1    -      -       -      +
    244L  ALA*     3.8    21.8    -      -       +      -
    245L  ARG      3.3    10.1    -      -       -      +
    246L  PHE*     4.2    13.7    -      -       +      -
    269L  PHE*     4.0    19.5    -      -       +      -
    270L  GLN*     3.5     8.1    -      -       -      +
    271L  THR*     2.9    39.3    +      -       -      +
    279L  ILE*     3.6     3.0    -      -       -      +
    280L  VAL*     1.3    94.2    -      -       +      +
    282L  SER*     1.3    63.0    +      -       -      +
    284L  ALA*     4.0     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 282 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245L  ARG*     2.9    43.9    +      -       -      +
    247L  ALA*     4.8     8.4    -      -       -      +
    269L  PHE      4.6     0.2    -      -       -      -
    270L  GLN*     4.4     9.9    -      -       -      +
    279L  ILE*     4.0    15.3    -      -       -      -
    280L  VAL      4.4     0.2    -      -       -      -
    281L  ILE*     1.3    74.0    -      -       -      +
    283L  ASN*     1.3    89.3    +      -       -      +
    284L  ALA*     2.9     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 283 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164L  ALA*     3.6    16.8    -      -       +      +
    165L  VAL      2.8    45.5    +      -       -      +
    166L  ALA*     3.4    22.5    -      -       -      +
    167L  ILE*     4.4    13.8    +      -       -      +
    243L  LYS*     4.3     1.9    -      -       -      +
    244L  ALA*     4.8     0.9    -      -       -      -
    245L  ARG*     3.6    22.5    -      -       +      +
    269L  PHE      4.4     2.4    +      -       -      -
    270L  GLN*     5.0     0.4    -      -       -      +
    282L  SER*     1.3    95.8    +      -       -      +
    284L  ALA*     1.3    57.5    +      -       -      +
    285L  TYR*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 284 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165L  VAL      4.4     3.1    -      -       -      +
    167L  ILE*     5.1     0.9    -      -       -      +
    243L  LYS      3.0    16.2    -      -       -      +
    244L  ALA*     3.6    12.6    -      -       +      -
    268L  HIS*     3.5     5.5    +      -       -      +
    269L  PHE*     3.0    60.0    +      -       +      +
    281L  ILE*     4.0     4.0    -      -       +      -
    282L  SER      3.0     4.0    -      -       -      +
    283L  ASN*     1.3    80.0    -      -       -      +
    285L  TYR*     1.3    68.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 285 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93L  TYR*     3.8    20.6    -      +       -      -
    162L  LYS*     5.7     1.2    -      -       -      +
    163L  VAL      4.1     5.9    +      -       -      -
    165L  VAL*     3.5    38.1    -      -       +      -
    241L  ALA      4.8     3.8    -      -       -      -
    242L  VAL*     3.2     5.7    -      -       -      +
    243L  LYS*     2.9    58.4    +      -       +      +
    266L  ARG*     3.2    40.4    +      -       +      -
    267L  ILE      3.2    13.5    -      -       -      +
    268L  HIS*     4.1     6.3    -      -       -      +
    269L  PHE*     3.7     6.1    -      -       -      -
    284L  ALA*     1.3    78.2    -      -       -      +
    286L  VAL*     1.3    68.0    +      -       -      +
    287L  ASP*     3.2    26.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 286 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224L  ALA*     6.0     1.3    -      -       -      -
    227L  VAL*     3.1    38.4    -      -       +      -
    239L  PHE*     3.7    28.3    -      -       +      -
    241L  ALA      3.0    14.1    -      -       -      +
    242L  VAL*     4.1     8.5    -      -       +      -
    265L  ASN      3.8     0.2    -      -       -      +
    266L  ARG*     3.7     0.5    -      -       -      -
    267L  ILE*     3.0    36.6    +      -       +      +
    269L  PHE*     4.2     5.4    -      -       +      -
    285L  TYR*     1.3    80.1    -      -       -      +
    287L  ASP*     1.3    66.6    +      -       -      +
    288L  LEU*     3.8    19.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 287 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93L  TYR*     6.0     0.2    -      -       -      -
    240L  LYS*     2.9    34.6    +      -       +      +
    241L  ALA*     2.7    24.6    +      -       +      +
    265L  ASN*     3.6     4.1    -      -       +      +
    266L  ARG*     2.7    53.8    +      -       -      +
    285L  TYR*     3.2    12.2    +      -       -      -
    286L  VAL*     1.3    73.6    -      -       -      +
    288L  LEU*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 288 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227L  VAL*     5.2     4.0    -      -       +      -
    228L  LEU*     5.7     0.7    -      -       -      -
    231L  PHE*     3.2    34.1    -      -       +      +
    232L  ALA*     3.9    16.4    -      -       +      -
    238L  ARG*     3.1    32.3    -      -       +      +
    239L  PHE*     4.2     8.3    -      -       +      -
    240L  LYS*     4.4     9.3    +      -       -      +
    265L  ASN*     2.8    36.5    +      -       +      +
    267L  ILE*     3.7    28.5    -      -       +      -
    286L  VAL*     3.9    22.2    -      -       +      +
    287L  ASP*     1.3    77.9    -      -       -      +
    289L  ALA*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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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