Contacts of the strand formed by residues 103 - 112 (chain G) in PDB entry 1U3H


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 ASN 103 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93G  PRO*     4.4     0.8    -      -       -      +
     94G  LYS*     3.7     2.9    +      -       -      +
     95G  SER*     2.9    52.9    +      -       -      -
     96G  PRO      3.3    14.8    +      -       -      -
     97G  VAL*     4.1    12.7    -      -       -      +
     98G  LEU      5.2     0.2    -      -       -      +
    101G  GLN      4.0     6.2    +      -       -      +
    102G  PRO*     1.3    75.8    -      -       -      +
    104G  THR*     1.3    87.1    +      -       -      +
    152G  THR*     3.4     5.5    -      -       -      -
    153G  PHE*     2.9    47.3    +      -       +      +
    155G  PRO*     4.5     2.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 104 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93G  PRO*     3.5     1.9    -      -       -      +
     94G  LYS*     2.8    47.6    +      -       +      +
    103G  ASN*     1.3    88.2    +      -       -      +
    105G  LEU*     1.3    72.7    +      -       -      +
    106G  ILE*     4.5     1.8    -      -       +      -
    150G  TYR*     3.7    32.1    -      -       +      -
    151G  LEU      3.5     9.9    -      -       -      +
    152G  THR*     4.3    12.5    -      -       +      +
    153G  PHE*     3.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  VAL*     3.4    26.7    -      -       +      -
     92G  PHE      3.6    18.8    -      -       -      +
     93G  PRO*     3.9     3.8    -      -       +      -
    104G  THR*     1.3    74.1    -      -       -      +
    106G  ILE*     1.3    60.1    +      -       -      +
    121G  TRP*     3.7    21.5    -      -       +      -
    150G  TYR*     3.3     5.4    -      -       -      -
    151G  LEU*     2.8    41.7    +      -       +      +
    153G  PHE*     3.7    16.0    -      -       +      -
    161G  TYR*     3.5    44.9    -      -       +      -
    178G  TRP*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90G  THR      3.7     1.0    -      -       -      +
     91G  VAL*     3.3     7.1    -      -       -      +
     92G  PHE*     2.8    78.7    +      -       +      +
     94G  LYS*     3.9    21.3    -      -       +      -
    104G  THR*     4.1     7.4    -      -       +      +
    105G  LEU*     1.3    77.0    -      -       -      +
    107G  CYS*     1.3    64.5    +      -       -      +
    108G  PHE      4.0     0.2    -      -       -      -
    121G  TRP*     3.9     2.5    -      -       -      -
    148G  LEU*     3.9    21.5    -      -       +      -
    149G  SER      3.5     4.5    -      -       -      +
    150G  TYR*     3.6    31.2    -      -       +      -
    150H  ASN*     3.8    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 107 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  ALA*     4.1     9.2    -      -       -      -
     90G  THR      3.6     1.8    -      -       -      -
     91G  VAL*     4.0     6.5    -      -       -      -
    106G  ILE*     1.3    74.5    -      -       -      +
    108G  PHE*     1.3    59.7    +      -       -      +
    109G  VAL*     3.8    19.3    +      -       -      +
    119G  ILE*     4.5     0.2    -      -       -      -
    121G  TRP*     3.5    19.2    -      -       +      -
    147G  LYS      3.8     0.9    -      -       -      +
    148G  LEU*     3.2     5.0    -      -       -      -
    149G  SER*     2.8    39.4    +      -       -      +
    163G  CYS*     2.0    49.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 108 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88G  GLN      3.5     1.2    -      -       -      +
     89G  ALA*     3.3     2.6    -      -       -      -
     90G  THR*     2.9    55.0    +      -       +      +
     92G  PHE*     3.8    20.0    -      +       +      -
    106G  ILE      4.0     0.8    -      -       -      -
    107G  CYS*     1.3    72.0    -      -       -      +
    109G  VAL*     1.3    61.5    +      -       -      +
    110G  ASP*     3.6    38.6    -      -       +      -
    146G  HIS*     3.5    31.4    -      +       +      -
    147G  LYS      3.9     2.2    -      -       -      -
    148G  LEU*     4.0    24.2    -      -       +      -
    149H  ARG      5.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 109 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87G  PRO*     3.6    30.7    -      -       +      -
     88G  GLN      3.3     8.3    -      -       -      +
     89G  ALA*     4.3     1.6    -      -       +      -
    107G  CYS*     4.0    19.7    -      -       -      +
    108G  PHE*     1.3    77.6    -      -       -      +
    110G  ASP*     1.3    59.1    +      -       -      +
    112G  ILE*     3.2    19.1    -      -       +      +
    117G  ILE*     4.0     7.9    -      -       +      -
    119G  ILE*     3.7    23.8    -      -       +      -
    146G  HIS*     2.9    26.1    -      -       -      -
    147G  LYS      3.0    17.0    +      -       -      +
    165G  VAL*     4.2    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 110 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87G  PRO*     3.3     4.2    -      -       -      +
     88G  GLN*     3.0    35.3    +      -       +      +
    108G  PHE*     3.6    32.2    -      -       +      -
    109G  VAL*     1.3    74.7    -      -       -      +
    111G  ASN*     1.3    84.7    +      -       +      +
    112G  ILE      3.2     4.1    +      -       -      -
    140G  ASN*     3.0    24.8    +      -       -      +
    146G  HIS*     3.6     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 111 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85G  GLU*     3.6    31.3    +      -       -      +
     86G  ALA      2.9    26.9    +      -       -      +
     87G  PRO*     3.6    10.9    -      -       -      +
     88G  GLN*     4.9     4.3    -      -       +      +
    110G  ASP*     1.3    90.6    +      -       +      +
    112G  ILE*     1.3    61.7    +      -       -      +
    113G  PHE      3.6     2.8    +      -       -      -
    142G  ASP*     4.3     5.7    -      -       -      +
    144G  SER*     4.0    21.0    +      -       -      -
    145G  PHE      3.4     2.1    +      -       -      -
     34H  ARG*     4.2     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 112 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87G  PRO*     4.3     5.2    -      -       +      -
    109G  VAL*     3.2    46.9    -      -       +      +
    110G  ASP      3.8     1.8    -      -       -      +
    111G  ASN*     1.3    71.1    -      -       -      +
    113G  PHE*     1.3    67.7    +      -       -      +
    114G  PRO      3.6    14.6    -      -       -      +
    115G  PRO*     4.5     0.2    -      -       +      -
    117G  ILE*     4.0    23.3    -      -       +      -
    119G  ILE*     5.3     0.2    -      -       +      -
    137G  PHE*     4.0    21.5    -      -       +      -
    145G  PHE*     2.7    51.3    +      -       +      +
    146G  HIS*     3.9     1.3    -      -       -      -
    147G  LYS*     3.7    25.8    -      -       +      +
    167G  HIS*     4.1     5.6    -      -       +      +
----------------------------------------------------------
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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