Contacts of the strand formed by residues 7 - 24 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR*     1.3    73.4    -      -       -      +
      8B  ARG*     1.3    61.5    +      -       -      +
      9B  LYS*     3.7    27.6    -      -       -      -
     10B  LEU*     3.8    14.1    -      -       +      -
     40B  ILE*     3.9    29.4    -      -       +      -
     41B  GLU      4.2     0.9    -      -       -      -
     43B  GLU*     4.8     1.0    -      -       -      +
     71B  SER*     3.5    29.4    -      -       -      -
     74B  LEU*     3.4    42.2    -      -       +      +
     75B  ALA      3.8     0.9    -      -       -      -
     76B  GLY*     3.0    26.9    +      -       -      -
     77B  GLN*     2.8    20.5    +      -       +      +
     78B  PRO      4.8     1.1    -      -       -      +
     79B  LEU*     3.8    32.5    -      -       +      +
     84B  ILE*     4.6     9.9    -      -       +      -
    108B  VAL*     5.3     0.2    -      -       +      -
    112B  VAL*     4.9     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR      3.3     1.2    +      -       -      -
      7B  PHE*     1.3    78.6    -      -       -      +
      9B  LYS*     1.3    72.4    +      -       +      +
     41B  GLU*     2.8    42.3    +      -       -      +
     42B  THR      4.7     4.9    -      -       -      -
     43B  GLU*     3.1    49.9    +      -       -      +
     71B  SER*     4.8     0.3    +      -       -      +
     75B  ALA*     4.0    19.2    -      -       -      +
     76B  GLY      5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  PHE*     3.7     8.1    -      -       -      -
      8B  ARG*     1.3    92.0    -      -       +      +
     10B  LEU*     1.3    64.1    +      -       -      +
     11B  THR*     4.0    18.6    +      -       -      +
     39B  ASP      3.8     0.5    -      -       -      +
     40B  ILE*     3.5     3.6    -      -       -      +
     41B  GLU*     2.9    66.0    +      -       +      +
     71B  SER*     3.4    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  PHE*     3.8     9.6    -      -       +      -
      9B  LYS*     1.3    77.6    -      -       -      +
     11B  THR*     1.3    77.7    +      -       -      +
     12B  ALA*     4.2     4.5    -      -       +      +
     38B  ILE*     3.8    26.9    -      -       +      -
     39B  ASP      3.4     3.6    -      -       -      -
     40B  ILE*     3.9    20.2    -      -       +      -
     67B  LEU*     4.1    33.2    -      -       +      +
     68B  HIS*     3.5    14.1    -      -       +      -
     70B  MET*     6.1     0.2    -      -       +      -
     71B  SER*     2.7    26.1    +      -       -      +
     74B  LEU*     6.2     0.4    -      -       +      -
    108B  VAL*     3.6    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  LYS*     4.0    23.5    +      -       -      +
     10B  LEU*     1.3    78.3    +      -       -      +
     12B  ALA*     1.3    63.6    +      -       -      +
     13B  ARG*     4.1    19.7    -      -       +      +
     37B  LEU      3.5     1.6    -      -       -      +
     38B  ILE*     3.5     4.2    -      -       -      -
     39B  ASP*     2.9    45.9    +      -       -      +
     41B  GLU*     4.8     2.8    +      -       -      +
     68B  HIS*     4.0     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     4.2     3.1    -      -       +      -
     11B  THR*     1.3    74.3    -      -       -      +
     13B  ARG*     1.3    61.7    +      -       -      +
     14B  PRO*     3.7     3.5    -      -       -      +
     36B  ILE*     3.9     8.5    -      -       +      -
     37B  LEU      3.4     4.5    -      -       -      -
     38B  ILE*     4.7     1.6    -      -       +      +
     64B  VAL*     3.6    25.7    -      -       +      +
     67B  LEU*     3.6    38.4    -      -       +      -
     68B  HIS*     3.2    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  THR*     4.5    15.1    -      -       +      +
     12B  ALA*     1.3    75.2    -      -       -      +
     14B  PRO*     1.3    69.4    -      -       +      +
     15B  VAL*     3.8     7.7    +      -       +      +
     36B  ILE*     4.5     2.0    -      -       -      -
     37B  LEU*     2.9    48.2    +      -       +      +
     39B  ASP*     3.4    20.4    +      -       -      +
    356B  TRP*     3.4    24.9    -      -       -      +
    358B  GLU*     2.8    41.1    +      -       -      -
    361B  VAL*     3.4    17.2    -      -       +      +
    365B  LEU*     4.8    19.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ALA      3.7     7.9    -      -       -      +
     13B  ARG*     1.3    85.9    -      -       +      +
     15B  VAL*     1.3    64.9    +      -       -      +
     35B  LEU      3.6     6.5    -      -       -      +
     36B  ILE*     4.6     2.5    -      -       +      -
     60B  MET*     3.8    31.0    -      -       +      -
     64B  VAL*     4.2    15.7    -      -       +      -
    365B  LEU*     3.7    10.7    -      -       +      +
    366B  VAL*     3.3    39.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     3.9    12.6    -      -       +      +
     14B  PRO*     1.3    81.5    -      -       -      +
     16B  LEU*     1.3    64.9    +      -       -      +
     17B  LEU*     3.5    25.8    -      -       +      -
     34B  PRO*     3.4     4.0    -      -       -      +
     35B  LEU*     2.9    38.0    +      -       +      +
     37B  LEU*     4.2    23.3    -      -       +      -
     60B  MET*     3.7     5.3    -      -       -      +
    332B  ILE*     4.2    13.9    -      -       +      -
    361B  VAL*     4.4    21.5    -      -       +      +
    364B  ASN*     3.8    15.7    -      -       +      -
    365B  LEU*     4.5     2.2    -      -       +      -
    366B  VAL*     4.4     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  VAL*     1.3    78.9    -      -       -      +
     17B  LEU*     1.3    69.3    +      -       -      +
     18B  LYS*     5.6     0.4    -      -       +      -
     32B  ASP*     3.3    43.3    -      -       +      +
     33B  TRP      4.0     4.7    -      -       -      +
     34B  PRO*     4.6     6.3    -      -       +      -
     57B  PRO*     4.1    27.8    -      -       +      -
     60B  MET*     5.0     2.2    -      -       +      -
    364B  ASN*     3.2    30.4    +      -       -      +
    366B  VAL*     4.1    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  VAL*     3.5    23.6    -      -       +      -
     16B  LEU*     1.3    92.5    -      -       -      +
     18B  LYS*     1.3    65.7    +      -       -      +
     19B  LEU*     3.9     0.7    -      -       +      -
     32B  ASP*     3.4     2.8    -      -       -      +
     33B  TRP*     3.0    42.2    +      -       +      +
     35B  LEU*     3.7    24.0    -      -       +      -
    328B  TRP      3.7    20.0    -      -       -      +
    329B  ALA*     4.6     0.7    -      -       -      -
    331B  PRO*     3.8    33.2    -      -       +      -
    332B  ILE*     4.2     9.0    -      -       +      -
    360B  VAL*     5.2     0.4    -      -       +      -
    364B  ASN*     3.9    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  LEU*     5.6     0.2    -      -       +      -
     17B  LEU*     1.3    76.4    -      -       -      +
     19B  LEU*     1.3    70.7    +      -       -      +
     20B  GLN*     3.4     2.6    +      -       -      -
     31B  PRO*     3.8    23.2    -      -       +      +
     32B  ASP*     3.2    29.4    +      -       -      +
    331B  PRO*     6.0     2.1    -      -       -      +
    364B  ASN*     5.0     3.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     3.8     1.5    +      -       +      -
     18B  LYS*     1.3    75.7    -      -       -      +
     20B  GLN*     1.3    65.6    +      -       -      +
     21B  ARG      3.3    19.4    +      -       -      +
     22B  PRO*     4.2     8.0    -      -       +      +
     23B  VAL*     3.7    30.1    -      -       +      -
     30B  ILE      3.9    10.8    -      -       -      +
     31B  PRO*     2.8    23.9    +      -       -      +
     32B  ASP      4.5     3.1    -      -       -      +
     33B  TRP*     3.6    33.2    -      -       +      -
    328B  TRP*     3.8    45.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LYS      3.4     4.6    +      -       -      -
     19B  LEU*     1.3    74.4    -      -       -      +
     21B  ARG*     1.3    98.5    +      -       +      +
     22B  PRO*     4.0     4.9    -      -       -      +
    161B  GLU*     4.5     4.5    +      -       -      +
    327B  SER*     4.6    10.7    +      -       -      -
    328B  TRP*     6.1     1.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     3.1    14.6    -      -       -      +
     20B  GLN*     1.3   114.9    +      -       +      +
     22B  PRO*     1.3    74.8    -      -       +      +
     23B  VAL*     3.6     0.9    +      -       -      +
    141B  ASN*     4.1    37.0    -      -       -      +
    142B  GLY*     5.2     1.1    -      -       -      -
    144B  TRP*     4.6     4.6    +      -       +      -
    154B  GLU*     3.5    38.7    +      -       -      +
    157B  GLU*     3.2    27.3    +      -       -      +
    158B  LEU*     3.9    13.0    -      -       -      +
    161B  GLU*     3.2    26.1    +      -       -      +
    328B  TRP*     5.1     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     4.2    11.8    -      -       +      +
     20B  GLN      4.0     6.3    -      -       -      +
     21B  ARG*     1.3    88.0    -      -       +      +
     23B  VAL*     1.3    63.3    +      -       -      +
     24B  THR*     3.2    16.9    +      -       -      +
     29B  THR*     3.7    24.2    -      -       +      -
     30B  ILE      3.9     3.8    -      -       -      +
     31B  PRO*     4.0    16.6    -      -       +      -
    144B  TRP*     3.7     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     3.7    21.7    -      -       +      +
     21B  ARG      3.6     0.2    +      -       -      -
     22B  PRO*     1.3    67.0    -      -       -      +
     24B  THR*     1.3    61.1    +      -       -      +
     25B  ALA*     3.7    11.1    +      -       +      +
     28B  ALA      3.9     0.3    -      -       -      +
     29B  THR*     3.3     7.3    -      -       -      +
     30B  ILE*     2.8    58.5    +      -       +      +
     33B  TRP*     5.7     3.8    -      -       +      -
    144B  TRP*     3.5    47.6    -      -       +      +
    328B  TRP*     4.6     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PRO*     3.2    20.1    +      -       -      +
     23B  VAL*     1.3    70.7    -      -       -      +
     25B  ALA*     1.3    62.9    +      -       -      +
     28B  ALA      4.6     1.3    -      -       -      -
     29B  THR*     4.4    14.2    +      -       -      +
    144B  TRP*     3.4    22.4    -      -       -      +
    145B  LEU*     2.9    38.1    +      -       +      +
    146B  LYS*     4.1    28.3    -      -       +      +
----------------------------------------------------------
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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