Contacts of the strand formed by residues 7 - 24 (chain C) in PDB entry 3UGV


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 7 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  THR*     1.3    72.0    -      -       -      +
      8C  ARG*     1.3    62.0    +      -       -      +
      9C  LYS*     3.6    33.7    -      -       -      -
     10C  LEU*     3.7    13.7    -      -       +      -
     40C  ILE*     3.7    26.7    -      -       +      -
     41C  GLU      4.0     2.9    -      -       -      -
     43C  GLU*     4.8     0.9    -      -       -      +
     71C  SER*     3.7    25.8    -      -       -      -
     74C  LEU*     3.6    42.6    -      -       +      +
     75C  ALA      3.8     0.2    -      -       -      -
     76C  GLY*     2.9    30.0    +      -       -      -
     77C  GLN      2.9    20.3    +      -       -      +
     78C  PRO      4.9     0.4    -      -       -      +
     79C  LEU*     3.7    34.5    -      -       +      +
     84C  ILE*     4.8     7.0    -      -       +      -
    112C  VAL*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  THR      3.4     0.6    +      -       -      -
      7C  PHE*     1.3    75.3    -      -       -      +
      9C  LYS*     1.3    71.4    +      -       +      +
     41C  GLU*     2.8    59.0    +      -       -      +
     42C  THR      3.7    19.2    +      -       -      -
     43C  GLU*     3.5    49.3    +      -       -      +
     45C  GLY*     5.4     1.6    -      -       -      +
     75C  ALA*     3.5    25.3    -      -       -      +
     76C  GLY      4.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  PHE*     3.6     9.4    -      -       -      -
      8C  ARG*     1.3    90.5    -      -       +      +
     10C  LEU*     1.3    65.7    +      -       -      +
     11C  THR*     3.8    23.1    +      -       -      +
     39C  ASP      3.8     0.3    -      -       -      +
     40C  ILE*     3.7     1.9    -      -       -      -
     41C  GLU*     3.0    59.4    +      -       +      +
     71C  SER*     3.3    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 10 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  PHE*     3.7    14.4    -      -       +      -
      9C  LYS*     1.3    79.2    -      -       -      +
     11C  THR*     1.3    75.6    +      -       -      +
     12C  ALA*     4.3     2.7    -      -       +      +
     38C  ILE*     3.5    25.1    -      -       +      -
     39C  ASP      3.2     3.8    -      -       -      +
     40C  ILE*     3.4    24.5    -      -       +      -
     67C  LEU*     4.1    35.9    -      -       +      +
     68C  HIS*     3.4    15.0    -      -       +      -
     70C  MET*     6.4     0.2    -      -       +      -
     71C  SER*     2.7    20.9    +      -       -      +
     74C  LEU*     6.1     0.7    -      -       +      -
    108C  VAL*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 11 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  LYS*     3.8    23.9    +      -       -      +
     10C  LEU*     1.3    78.0    -      -       -      +
     12C  ALA*     1.3    63.5    +      -       -      +
     13C  ARG*     4.6    19.4    -      -       +      +
     37C  LEU      3.4     1.9    -      -       -      +
     38C  ILE*     3.3     4.5    -      -       -      -
     39C  ASP*     2.9    45.9    +      -       -      +
     41C  GLU*     4.9     3.3    +      -       -      +
     68C  HIS*     3.8     8.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 12 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  LEU*     4.5     2.7    -      -       +      -
     11C  THR*     1.3    75.3    -      -       -      +
     13C  ARG*     1.3    64.0    +      -       -      +
     14C  PRO*     3.6     9.1    -      -       -      +
     36C  ILE*     3.8     9.6    -      -       +      -
     37C  LEU      3.3     4.3    -      -       -      +
     38C  ILE*     4.6     1.6    -      -       +      +
     64C  VAL*     3.9    11.8    -      -       +      +
     67C  LEU*     3.5    39.3    -      -       +      -
     68C  HIS*     3.1    27.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 13 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  THR*     4.6    15.6    +      -       +      +
     12C  ALA*     1.3    75.3    -      -       -      +
     14C  PRO*     1.3    67.9    -      -       +      +
     15C  VAL*     3.6     9.1    +      -       +      +
     36C  ILE*     3.6     2.6    -      -       -      +
     37C  LEU*     2.8    43.8    +      -       +      +
     39C  ASP*     3.1    28.3    +      -       -      -
    356C  TRP*     3.2    14.8    -      -       -      +
    358C  GLU*     2.7    43.8    +      -       -      -
    361C  VAL*     3.7    15.2    -      -       +      +
    365C  LEU*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 14 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  ALA      3.6     8.7    -      -       -      +
     13C  ARG*     1.3    84.0    -      -       +      +
     15C  VAL*     1.3    65.2    +      -       -      +
     35C  LEU      3.6     6.7    -      -       -      +
     36C  ILE*     4.5     3.4    -      -       +      -
     60C  MET*     3.8    30.7    -      -       +      -
     64C  VAL*     4.4    13.2    -      -       +      -
    365C  LEU*     3.3    17.7    -      -       +      +
    366C  VAL*     3.5    31.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 15 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  ARG      3.8     9.0    -      -       -      +
     14C  PRO*     1.3    81.0    -      -       -      +
     16C  LEU*     1.3    64.3    +      -       -      +
     17C  LEU*     3.5    27.8    -      -       +      -
     33C  TRP      4.0     0.5    -      -       -      +
     34C  PRO*     3.4     2.4    -      -       -      +
     35C  LEU*     2.7    45.2    +      -       +      +
     37C  LEU*     4.1    13.9    -      -       +      -
     60C  MET*     4.1     5.2    -      -       -      +
    332C  ILE*     4.4    10.5    -      -       +      -
    361C  VAL*     4.1    28.9    -      -       +      +
    364C  ASN*     3.6    16.8    -      -       +      +
    365C  LEU*     4.1     7.2    -      -       +      -
    366C  VAL*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 16 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  VAL*     1.3    72.0    -      -       -      +
     17C  LEU*     1.3    63.1    +      -       -      +
     32C  ASP*     3.7    37.2    -      -       +      +
     33C  TRP      4.0     0.7    -      -       -      -
     34C  PRO*     3.9    18.8    -      -       +      -
     57C  PRO*     3.7    31.9    -      -       +      -
     60C  MET*     5.1     2.5    -      -       +      -
    364C  ASN*     3.0    29.7    +      -       -      +
    365C  LEU      5.7     0.2    -      -       -      +
    366C  VAL*     4.4    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 17 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  VAL*     3.5    25.5    -      -       +      -
     16C  LEU*     1.3    75.0    -      -       -      +
     18C  LYS*     1.3    64.9    +      -       -      +
     32C  ASP*     3.3    10.2    -      -       -      +
     33C  TRP*     2.9    41.6    +      -       +      +
     35C  LEU*     3.7    22.4    -      -       +      -
    328C  TRP      3.5    23.8    -      -       -      +
    329C  ALA*     4.8     0.2    -      -       -      -
    331C  PRO*     4.0    26.7    -      -       +      -
    332C  ILE*     4.3    11.0    -      -       +      +
    360C  VAL*     4.6     1.6    -      -       +      -
    364C  ASN*     3.6    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 18 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  LEU*     1.3    78.3    -      -       -      +
     19C  LEU*     1.3    72.5    +      -       -      +
     20C  GLN      3.6     1.6    +      -       -      -
     31C  PRO*     3.6    27.2    -      -       +      +
     32C  ASP*     3.1    28.8    +      -       -      +
    331C  PRO*     5.9     2.4    -      -       -      +
    364C  ASN*     4.9     3.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 19 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  LEU      4.0     0.4    +      -       -      -
     18C  LYS*     1.3    78.6    -      -       -      +
     20C  GLN*     1.3    66.5    +      -       -      +
     21C  ARG      3.5    14.1    +      -       -      +
     22C  PRO*     4.2     7.0    -      -       +      +
     23C  VAL*     3.9    23.6    -      -       +      +
     30C  ILE*     3.4    25.8    -      -       +      +
     31C  PRO*     2.6    22.7    +      -       -      +
     32C  ASP      4.5     5.4    -      -       -      +
     33C  TRP*     3.7    28.3    -      -       +      -
    328C  TRP*     3.5    47.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  LYS      3.6     3.4    +      -       -      -
     19C  LEU*     1.3    74.0    -      -       -      +
     21C  ARG*     1.3    94.6    +      -       +      +
     22C  PRO*     3.8     6.1    -      -       -      +
    161C  GLU*     4.9     3.7    +      -       -      +
    327C  SER*     5.0     7.1    +      -       -      -
    328C  TRP*     5.9     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 21 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  LEU*     3.9    12.3    -      -       -      +
     20C  GLN*     1.3   109.3    +      -       +      +
     22C  PRO*     1.3    70.3    -      -       +      +
     23C  VAL*     3.8     1.2    +      -       -      +
    141C  ASN*     3.9    34.5    +      -       -      +
    142C  GLY*     5.1     2.2    -      -       -      -
    144C  TRP*     4.6     6.0    +      -       +      -
    154C  GLU*     3.1    37.7    +      -       -      +
    157C  GLU*     4.3    23.2    +      -       -      +
    158C  LEU*     3.7    23.8    -      -       -      +
    161C  GLU*     3.4    29.3    +      -       -      +
    327C  SER*     5.6     0.2    +      -       -      -
    328C  TRP*     5.1     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 22 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  LEU*     4.2    11.6    -      -       +      +
     20C  GLN      3.8     8.5    -      -       -      +
     21C  ARG*     1.3    87.4    -      -       +      +
     23C  VAL*     1.3    59.0    +      -       -      +
     24C  THR*     3.0    18.6    +      -       -      +
     29C  THR*     4.1    17.0    -      -       +      -
     30C  ILE      3.9     4.5    -      -       -      +
     31C  PRO*     4.0    22.2    -      -       +      -
    144C  TRP*     3.8     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 23 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  LEU*     3.9    18.8    -      -       +      +
     21C  ARG      3.8     0.2    +      -       -      -
     22C  PRO*     1.3    67.5    -      -       -      +
     24C  THR*     1.3    59.2    +      -       -      +
     25C  ALA*     3.4     9.0    +      -       +      +
     29C  THR*     3.3     6.6    -      -       -      -
     30C  ILE*     3.0    56.6    +      -       +      +
     33C  TRP*     5.9     4.3    -      -       +      -
    144C  TRP*     3.6    52.0    -      -       +      +
    328C  TRP*     4.8     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  PRO*     3.0    17.2    +      -       -      +
     23C  VAL*     1.3    68.5    -      -       -      +
     25C  ALA*     1.3    63.8    +      -       -      +
     29C  THR*     4.1    20.2    -      -       -      +
    144C  TRP*     3.4    21.8    -      -       -      +
    145C  LEU*     2.9    42.9    +      -       -      +
    146C  LYS*     4.2    20.2    -      -       +      +
----------------------------------------------------------
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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