Contacts of the strand formed by residues 5 - 15 (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 HIS 5 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  ALA*     3.2     2.3    -      -       -      +
      4G  ASP*     1.3   103.2    +      -       +      +
      6G  VAL*     1.3    69.2    +      -       -      +
     26G  PHE*     4.1    15.7    -      +       +      -
     27G  ASP*     2.8    30.1    +      -       -      +
     17H  PHE*     2.8    45.7    +      -       +      -
     20H  GLY      6.0     1.6    -      -       -      -
     83H  TYR*     3.8    21.7    +      +       +      -
     91H  LEU*     3.5    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 6 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  ALA*     4.3    10.8    -      -       +      +
      5G  HIS*     1.3    82.2    -      -       -      +
      7G  GLY*     1.3    63.9    +      -       -      +
      8G  SER*     4.1     1.7    +      -       -      +
     25G  GLU      4.1     0.9    -      -       -      +
     26G  PHE*     3.5     6.2    -      -       -      -
     27G  ASP*     2.9    42.5    +      -       -      +
     28G  GLY      4.8     0.2    +      -       -      -
     14H  PHE*     4.0    21.1    -      -       +      -
     15H  CYS      3.3     5.2    -      -       -      +
     16H  TYR*     3.6    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 7 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  VAL*     1.3    74.7    -      -       -      +
      8G  SER*     1.3    60.9    +      -       -      -
      9G  TYR*     3.7    23.8    +      -       -      -
     25G  GLU      3.6     5.6    -      -       -      -
     26G  PHE*     4.2     5.6    -      -       -      -
     14H  PHE*     3.3     3.0    -      -       -      -
     15H  CYS*     2.6    49.6    +      -       -      +
     17H  PHE*     4.1     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 8 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  VAL*     4.1     2.5    +      -       -      +
      7G  GLY*     1.3    68.7    -      -       -      -
      9G  TYR*     1.3    66.9    +      -       -      +
     10G  ILE*     3.8    25.9    -      -       -      +
     23G  THR      3.9     1.6    -      -       -      +
     24G  PHE*     3.3     2.1    -      -       -      +
     25G  GLU*     2.8    43.5    +      -       -      -
    139G  VAL*     5.3     0.5    -      -       -      +
     13H  PRO*     2.8    22.6    +      -       -      -
     14H  PHE*     3.5    24.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 9 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  GLY*     3.7    16.5    +      -       -      -
      8G  SER*     1.3    72.1    -      -       -      +
      9G  GLY*     1.3    57.7    +      -       -      +
     24G  PHE*     3.4    31.4    -      +       +      -
     25G  GLU      4.6     0.7    -      -       -      -
     26G  PHE*     3.7     9.1    -      +       -      -
     31G  LEU*     4.4     7.4    -      -       +      -
     52G  ARG*     4.3     5.6    -      -       -      -
     13H  PRO*     3.7    12.2    -      -       -      +
     15H  CYS*     3.6    33.6    -      -       +      -
     17H  PHE*     4.2     6.6    -      +       -      -
     78H  VAL*     3.9    12.1    -      -       +      -
     79H  CYS*     4.5     2.2    -      -       -      -
     82H  ASN*     3.0    44.8    -      -       +      +
     86H  GLU*     2.9    42.2    +      -       -      +
      0I  GLY      3.8     2.7    -      -       -      +
      1I  ALA*     3.6     1.2    -      -       -      -
      2I  SER*     3.0    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 9 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  SER      3.2     2.4    +      -       -      -
      9G  TYR*     1.3    76.4    -      -       -      +
     10G  ILE*     1.3    67.4    +      -       -      +
     11G  VAL*     3.3     8.7    +      -       -      +
     22G  TYR*     3.6    25.0    -      -       -      -
     23G  THR      3.5     4.3    -      -       -      -
     24G  PHE*     3.2    12.9    -      -       -      -
     11H  PHE*     3.5    19.9    -      -       -      -
     13H  PRO*     3.8     5.1    -      -       -      +
      1I  ALA*     4.8     0.2    -      -       -      -
      2I  SER      4.6     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 10 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  SER*     3.8    25.8    -      -       -      +
      9G  GLY*     1.3    72.9    -      -       -      +
     11G  VAL*     1.3    67.3    +      -       -      +
     12G  VAL*     4.3    11.7    -      -       +      -
     21G  GLN*     3.6     3.4    +      -       -      +
     22G  TYR*     3.3     8.0    -      -       -      -
     23G  THR*     2.8    46.6    +      -       -      +
     25G  GLU*     3.3    35.9    -      -       +      +
    137G  PHE      6.1     0.4    -      -       -      +
    139G  VAL*     3.9    32.1    -      -       +      -
     10H  GLN*     6.3     0.2    -      -       +      -
     11H  PHE      3.3    13.0    -      -       -      +
     12H  GLN*     4.5     5.8    -      -       +      -
     13H  PRO*     3.9     8.1    -      -       +      -
     14H  PHE*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 11 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  GLY      3.3    13.7    +      -       -      +
     10G  ILE*     1.3    71.6    -      -       -      +
     12G  VAL*     1.3    77.7    +      -       -      +
     13G  TYR*     4.6     1.1    -      -       +      +
     21G  GLN      3.7     2.0    -      -       -      -
     22G  TYR*     3.7    23.3    -      -       +      -
     62G  ASN*     3.8    31.6    -      -       +      +
     63G  ILE*     4.1    13.2    -      -       +      -
     66G  GLY*     4.4     7.4    -      -       -      -
      9H  VAL*     5.8     0.4    -      -       +      +
     10H  GLN*     3.4     4.0    -      -       -      +
     11H  PHE*     2.9    45.9    +      -       +      +
      4I  TYR*     3.9    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 12 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  ILE*     4.3    13.9    -      -       +      -
     11G  VAL*     1.3    83.2    -      -       -      +
     13G  TYR*     1.3    62.0    +      -       -      +
     14G  GLN*     4.5    10.1    -      -       -      +
     19G  ILE      3.7     0.3    -      -       -      +
     20G  GLY*     3.1     6.1    -      -       -      -
     21G  GLN*     3.0    52.5    +      -       +      +
     63G  ILE*     4.6     0.7    -      -       -      +
    115G  PRO*     4.3    19.5    -      -       +      -
    137G  PHE*     6.1     0.9    -      -       +      -
    145G  PHE*     3.9    25.8    -      -       +      -
      8H  VAL*     4.1    18.2    -      -       +      -
      9H  VAL      3.6     4.9    -      -       -      +
     10H  GLN*     4.6     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 13 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11G  VAL*     4.3     2.0    -      -       +      -
     12G  VAL*     1.3    73.9    -      -       -      +
     14G  GLN*     1.3    67.1    +      -       -      +
     15G  SER*     5.5     0.9    -      -       -      -
     18G  ASP*     2.8    59.1    +      -       +      +
     19G  ILE      3.6     1.3    -      -       -      -
     20G  GLY*     4.4     9.4    -      -       -      -
     63G  ILE*     3.5    40.8    -      -       +      -
     66G  GLY*     3.8    17.9    -      -       -      -
     67G  LYS*     3.3    43.3    +      -       +      +
     70G  LEU*     3.6    16.3    -      -       +      +
      8H  VAL*     3.0     2.9    -      -       -      +
      9H  VAL*     2.8    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 14 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12G  VAL*     4.5     6.6    -      -       -      +
     13G  TYR*     1.3    73.3    -      -       -      +
     15G  SER*     1.3    57.8    +      -       -      +
     16G  PRO      4.5     0.2    -      -       -      -
     18G  ASP*     3.4     6.4    +      -       -      -
     19G  ILE*     3.0    68.2    +      -       +      +
     20G  GLY*     5.8     0.6    -      -       -      -
     70G  LEU*     3.7     5.4    -      -       -      -
    115G  PRO*     3.5    43.3    +      -       -      +
    116G  VAL*     3.9     7.9    -      -       -      +
    137G  PHE*     6.0     0.2    -      -       -      -
      6H  HIS*     3.1    26.3    +      -       +      +
      7H  PHE      3.1    17.0    -      -       -      +
      8H  VAL*     3.3    20.4    -      -       +      +
----------------------------------------------------------
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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