Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 4S0H


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 LYS 99 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  LYS      4.6     4.3    -      -       -      +
     98A  THR*     1.3    86.7    -      -       -      +
    100A  TYR*     1.3    60.7    -      -       -      +
    142A  PRO*     4.1    34.7    +      -       +      +
    143A  ALA*     3.5    11.7    -      -       -      +
    144A  THR*     4.5    15.3    -      -       +      +
    187A  LYS*     3.7     1.2    -      -       -      +
    188A  ALA*     3.0    37.0    +      -       +      -
    158B  LYS*     5.5     3.2    -      -       -      +
    129E  PRO*     6.0     1.2    -      -       -      +
    130E  ALA*     4.9    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ILE*     4.9     8.2    -      -       +      +
     94A  LEU*     3.6    22.3    -      -       +      +
     95A  ASN*     3.3    29.6    +      -       -      +
     98A  THR*     3.4    44.6    +      -       +      +
     99A  LYS*     1.3    78.0    -      -       -      +
    101A  ILE*     1.3    67.6    +      -       -      +
    102A  LEU*     4.3     4.7    -      -       +      -
    142A  PRO*     3.2     5.6    -      -       -      +
    143A  ALA      2.9    29.3    +      -       -      -
    145A  GLY*     3.8    12.8    -      -       -      -
    148A  TRP*     3.3    20.4    +      +       +      +
    185A  ILE*     3.6    25.6    -      -       +      -
    186A  VAL      3.3    11.0    -      -       -      +
    187A  LYS*     4.0    20.8    -      -       +      -
    188A  ALA      4.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  TYR*     1.3    76.5    -      -       -      +
    102A  LEU*     1.3    65.6    +      -       -      +
    103A  LEU*     3.6    24.9    -      -       +      -
    137A  VAL*     3.9     7.2    -      -       +      -
    141A  SER*     3.5    21.8    -      -       -      +
    142A  PRO*     4.3     9.0    -      -       +      -
    184A  HIS      3.6     1.0    -      -       -      +
    185A  ILE*     3.6     2.8    -      -       -      -
    186A  VAL*     2.6    47.5    +      -       +      +
    187A  LYS      4.6     0.2    -      -       -      +
    188A  ALA*     4.0    19.7    -      -       +      +
    105E  ASP*     4.2     7.9    -      -       -      +
    107E  VAL*     4.9     3.8    -      -       +      -
    133E  GLY*     5.7     5.2    -      -       -      +
    135E  LEU*     6.3     1.3    -      -       +      -
    182E  ARG*     3.8    25.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  VAL*     5.6     0.2    -      -       +      -
     91A  VAL*     4.5     9.4    -      -       +      -
     94A  LEU*     5.3     1.6    -      -       +      -
    100A  TYR*     4.3     5.4    -      -       +      -
    101A  ILE*     1.3    79.5    -      -       -      +
    103A  LEU*     1.3    62.2    +      -       -      +
    137A  VAL      3.9     0.2    -      -       -      -
    138A  HIS*     2.8    30.5    +      -       +      +
    141A  SER*     3.2     8.3    +      -       -      -
    148A  TRP*     3.5    46.8    -      -       +      +
    153A  VAL*     3.8    34.5    -      -       +      -
    155A  PHE*     4.2     4.5    -      -       +      -
    183A  LEU*     3.9    19.7    -      -       +      -
    184A  HIS      3.3     1.8    -      -       -      -
    185A  ILE*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     3.6    23.3    -      -       +      -
    102A  LEU*     1.3    75.5    -      -       -      +
    104A  MET*     1.3    61.7    +      -       -      +
    135A  LEU*     3.7    31.0    -      -       +      -
    136A  TYR      3.2     6.5    -      -       -      +
    137A  VAL*     3.6    31.0    -      -       +      -
    155A  PHE*     4.3     2.5    -      -       -      -
    183A  LEU*     3.5     7.6    -      -       -      +
    184A  HIS*     2.8    40.6    +      -       +      +
    186A  VAL*     3.7    27.8    -      -       +      -
    201A  PHE*     5.7     2.5    -      -       +      -
    103E  LEU*     6.3     1.1    -      -       +      -
    135E  LEU*     4.7    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  MET*     4.4     7.2    -      -       -      -
     87A  TYR*     3.4    56.1    -      -       +      -
    103A  LEU*     1.3    75.2    -      -       -      +
    105A  ASP*     1.3    69.3    +      -       -      +
    106A  ILE*     4.8     5.6    -      -       +      -
    135A  LEU*     3.7     6.2    -      -       -      +
    136A  TYR*     2.8    39.2    +      -       +      +
    155A  PHE*     3.7    24.4    -      -       +      -
    158A  LEU*     3.5    29.2    -      -       +      -
    171A  ILE*     4.7     1.6    -      -       +      +
    181A  PRO*     3.8    14.6    -      -       +      -
    182A  ARG      3.4    19.5    -      -       -      +
    183A  LEU*     4.3     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  MET*     1.3    78.0    -      -       -      +
    106A  ILE*     1.3    77.2    +      -       -      +
    107A  VAL*     3.2     8.8    -      -       -      +
    134A  ARG      3.9    14.3    -      -       -      +
    135A  LEU*     4.0    14.6    -      -       +      +
    171A  ILE*     4.9     1.3    -      -       -      -
    180A  GLN      3.9     0.2    -      -       -      +
    181A  PRO*     3.4     2.6    -      -       -      +
    182A  ARG*     2.6    70.9    +      -       +      +
    184A  HIS*     3.2    25.2    +      -       +      +
    101E  ILE*     4.9     8.1    -      -       -      +
    186E  VAL*     4.2     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  MET*     5.2     5.4    -      -       +      -
    104A  MET*     4.8     4.9    -      -       +      -
    105A  ASP*     1.3    85.5    +      -       -      +
    107A  VAL*     1.3    68.4    +      -       -      +
    108A  PRO*     4.6     1.4    -      -       -      +
    134A  ARG      5.0     1.5    +      -       -      +
    158A  LEU*     4.8     5.6    -      -       +      -
    160A  LEU*     3.7    29.8    -      -       +      -
    171A  ILE*     3.7    35.1    -      -       +      +
    173A  LEU*     4.0     6.4    -      -       +      +
    179A  TYR*     3.5    38.2    -      -       +      -
    180A  GLN      3.7     8.5    -      -       -      +
    181A  PRO*     4.5     7.6    -      -       +      -
    211A  PHE*     4.4    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  ASP*     3.2    28.5    -      -       -      +
    106A  ILE*     1.3    77.8    -      -       -      +
    108A  PRO*     1.3    72.3    -      -       +      +
    179A  TYR*     4.1     4.5    -      -       -      -
    180A  GLN*     2.7    50.8    +      -       +      +
    182A  ARG*     3.5    34.3    -      -       +      +
    101E  ILE*     6.1     3.4    -      -       +      -
    187E  LYS      5.0     3.4    -      -       -      +
    188E  ALA*     5.0     8.3    -      -       +      -
    189E  ASP*     4.2    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE      4.6     1.3    -      -       -      +
    107A  VAL*     1.3    89.5    -      -       +      +
    109A  ALA*     1.3    60.1    +      -       -      +
    110A  ASP*     3.7    16.1    -      -       -      +
    130A  ALA*     6.2     3.8    -      -       +      -
    178A  LYS      3.8     7.6    -      -       -      +
    179A  TYR*     4.1    13.6    -      -       +      -
    180A  GLN*     4.9     0.2    -      -       -      +
     99E  LYS*     6.1     4.7    -      -       +      +
    188E  ALA*     5.6     5.4    -      -       +      -
    189E  ASP*     2.5    45.4    -      -       -      +
----------------------------------------------------------
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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