Contacts of the strand formed by residues 103 - 118 (chain B) in PDB entry 5GKI


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 GLU 103 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  TYR*     2.6    36.1    +      -       +      -
     42B  ASP      3.3     5.8    -      -       -      +
     43B  GLY*     3.4     8.1    -      -       -      -
     44B  ARG*     2.9    26.3    +      -       -      +
     78B  GLN*     3.5    18.7    +      -       -      +
     79B  PRO*     4.7     0.2    -      -       -      +
     97B  ILE*     3.5     4.4    -      -       -      +
     98B  ARG*     2.5    79.1    +      -       +      +
    101B  PRO*     3.2    11.6    +      -       +      +
    102B  ARG*     1.3    80.9    -      -       -      +
    104B  THR*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  HIS      3.6     1.0    -      -       -      +
     41B  TYR*     3.3     8.0    -      -       -      -
     42B  ASP*     2.6    42.8    +      -       -      +
     78B  GLN*     4.1     1.3    -      -       -      -
     95B  VAL*     4.9     2.0    -      -       +      -
     96B  SER      3.5     2.9    -      -       -      +
     97B  ILE*     3.2    28.0    -      -       +      +
    102B  ARG*     5.3     5.7    -      -       -      +
    103B  GLU*     1.3    73.5    -      -       -      +
    105B  LEU*     1.3    72.7    +      -       -      +
    106B  GLU*     4.2    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  VAL*     3.6    27.6    -      -       +      -
     40B  HIS      3.7     1.3    -      -       -      +
     41B  TYR*     3.6    27.4    -      -       +      -
     64B  PHE*     3.7    33.5    -      -       +      -
     66B  ILE*     3.8    14.1    -      -       +      -
     76B  ASN*     4.1     8.7    -      -       +      +
     77B  TRP      3.8    22.4    -      -       -      +
     78B  GLN*     3.6    15.4    -      -       +      +
     94B  LEU      3.6     0.9    -      -       -      +
     95B  VAL*     3.3     6.1    -      -       -      +
     96B  SER*     2.8    38.7    +      -       -      +
    104B  THR*     1.3    75.2    -      -       -      +
    106B  GLU*     1.3    62.0    +      -       -      +
    107B  VAL*     4.5     3.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LYS      3.6     1.0    -      -       -      +
     39B  VAL*     3.3     5.4    -      -       -      +
     40B  HIS*     2.7    65.3    +      -       +      +
     89B  ARG*     3.1    29.5    +      -       -      -
     93B  VAL*     4.3     6.4    -      -       +      +
     94B  LEU      3.4     2.9    -      -       -      -
     95B  VAL*     3.6    19.3    -      -       +      -
    104B  THR*     4.2    16.7    -      -       +      +
    105B  LEU*     1.3    75.1    -      -       -      +
    107B  VAL*     1.3    62.8    +      -       -      +
    108B  GLU      3.8     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  CYS*     3.8    16.4    -      -       +      -
     38B  LYS      3.6     3.8    -      -       -      +
     39B  VAL*     4.3     6.1    -      -       +      +
     56B  ILE*     3.7    27.6    -      -       +      -
     64B  PHE*     3.5    24.5    -      -       +      -
     66B  ILE*     3.5    29.2    -      -       +      -
     93B  VAL*     3.4     3.0    -      -       -      -
     94B  LEU*     2.7    42.8    +      -       +      +
    105B  LEU*     4.5     3.6    -      -       +      -
    106B  GLU*     1.3    74.6    -      -       -      +
    108B  GLU*     1.3    60.3    +      -       -      +
    109B  LEU*     3.5    12.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  CYS*     3.2    21.3    -      -       -      +
     38B  LYS*     2.9    47.1    +      -       +      +
     40B  HIS*     4.1    14.8    +      -       +      +
     90B  GLU*     3.8    19.5    -      -       -      +
     91B  ASN*     3.1    35.1    +      -       +      +
     92B  PRO      3.8     3.8    -      -       -      -
     93B  VAL*     3.9    16.5    -      -       +      +
    106B  GLU      3.8     2.4    +      -       -      -
    107B  VAL*     1.3    70.5    -      -       -      +
    109B  LEU*     1.3    60.9    +      -       -      +
    110B  GLU*     3.4    10.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     4.4    12.8    -      -       +      -
     21B  VAL*     6.1     0.4    -      -       +      -
     33B  ILE*     4.3    19.3    -      -       +      -
     35B  ALA*     4.3     8.3    -      -       +      -
     36B  ARG      4.0     2.0    -      -       -      +
     37B  CYS*     4.3     4.5    -      -       +      -
     56B  ILE*     4.0    15.3    -      -       +      -
     86B  LEU*     5.0     2.2    -      -       +      -
     91B  ASN*     3.4    18.3    -      -       -      +
     92B  PRO*     2.8    34.9    +      -       +      +
     94B  LEU*     4.5    15.9    -      -       +      +
    107B  VAL*     3.7    32.1    -      -       +      +
    108B  GLU*     1.3    71.0    -      -       -      +
    110B  GLU*     1.3    64.6    +      -       -      +
    111B  GLU*     3.6     0.7    -      -       -      -
    112B  VAL*     4.0    29.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  ARG*     2.9    29.4    +      -       -      +
     37B  CYS*     3.8     2.8    -      -       -      +
     38B  LYS*     3.5    30.5    +      -       +      +
     51B  SER*     2.2    37.1    +      -       -      -
     91B  ASN*     4.0    25.3    +      -       -      +
    108B  GLU*     4.1    14.4    -      -       -      +
    109B  LEU*     1.3    74.0    -      -       -      +
    111B  GLU*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     4.6    10.0    +      -       -      -
     35B  ALA*     3.1     6.1    -      -       -      +
     36B  ARG*     2.8    63.6    +      -       +      +
    110B  GLU*     1.3    81.8    -      -       -      +
    112B  VAL*     1.3    69.9    +      -       -      +
    113B  TYR*     3.5    29.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     3.8     5.2    +      -       -      -
     12B  PRO*     3.2    36.7    -      -       +      +
     17B  LEU*     4.1    22.9    -      -       +      -
     33B  ILE*     4.2     6.3    -      -       +      -
     34B  PHE      4.1     1.8    -      -       -      +
     35B  ALA*     3.9     6.3    -      -       +      -
     92B  PRO*     5.7     1.1    -      -       +      -
    109B  LEU*     4.0    35.2    -      -       +      +
    111B  GLU*     1.3    78.4    -      -       -      +
    113B  TYR*     1.3    58.5    +      -       -      +
    114B  MET      3.4    31.2    -      -       -      +
    115B  VAL*     4.2     0.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  LYS*     3.1    40.8    +      -       +      -
      6A  VAL*     3.9    21.0    -      -       +      +
    118A  PHE*     3.8    13.9    -      +       -      -
     10B  THR*     3.2     9.5    -      -       -      +
     11B  SER*     2.8    27.9    +      -       -      +
     34B  PHE      2.8    17.6    +      -       -      +
     35B  ALA*     3.7     5.6    -      -       -      -
     36B  ARG*     3.5    35.2    +      -       +      +
     53B  ASP*     2.8    34.0    +      -       -      -
    111B  GLU*     3.5    31.9    -      -       -      -
    112B  VAL*     1.3    74.1    -      -       -      +
    114B  MET*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     4.6     3.4    -      -       +      -
      8A  VAL*     4.6     6.3    -      -       +      -
    114A  MET*     4.8     7.0    -      -       -      +
      8B  VAL*     3.7    24.7    -      -       +      -
      9B  ILE      3.4     8.3    -      -       -      +
     10B  THR*     4.2    10.1    -      -       +      -
     11B  SER      4.7     0.2    -      -       -      +
     32B  THR*     3.3    17.0    -      -       -      +
     33B  ILE*     3.3    20.1    -      -       -      +
     34B  PHE*     3.0    67.7    +      -       +      +
    112B  VAL*     3.4     5.7    -      -       -      +
    113B  TYR*     1.3    81.4    -      -       -      +
    115B  VAL*     1.3    67.5    +      -       -      +
    116B  SER*     3.2    28.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  THR      3.8     0.3    -      -       -      +
      8B  VAL*     3.6     0.5    -      -       -      -
      9B  ILE*     3.0    38.7    +      -       +      +
     12B  PRO*     3.7    24.7    -      -       +      -
     16B  GLU      5.1     0.2    -      -       -      +
     17B  LEU*     4.3    15.0    -      -       +      +
     20B  LEU*     3.6    36.2    -      -       +      +
     21B  VAL*     4.5     9.2    -      -       +      -
     31B  LEU*     4.0    20.2    -      -       +      -
     32B  THR      3.6     4.9    -      -       -      -
     33B  ILE*     4.1     9.4    -      -       +      -
    112B  VAL*     4.5     0.4    -      -       +      -
    114B  MET*     1.3    77.3    -      -       -      +
    116B  SER*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  PHE*     3.7    18.8    -      -       -      -
    114A  MET*     5.0     0.4    -      -       -      -
      6B  VAL*     5.1     0.2    -      -       -      -
      7B  THR      3.0    12.3    -      -       -      -
      8B  VAL*     4.3     7.6    -      -       -      -
     20B  LEU*     4.4     0.2    -      -       -      -
     31B  LEU*     3.4    12.1    -      -       -      +
     32B  THR*     2.9    54.5    +      -       -      -
    114B  MET*     3.2    16.7    -      -       -      +
    115B  VAL*     1.3    78.7    -      -       -      +
    117B  VAL*     1.3    64.3    +      -       -      +
    118B  PHE      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LYS      3.2     6.9    -      -       -      +
      6B  VAL*     3.2     2.0    -      -       -      +
      7B  THR*     2.9    39.3    +      -       +      -
     20B  LEU*     3.7    41.5    -      -       +      +
     23B  SER*     5.3     2.9    -      -       -      -
     24B  ALA*     4.0    20.2    -      -       +      +
     27B  GLU*     5.1     1.6    -      -       -      +
     29B  ALA*     3.9    23.8    -      -       +      -
     30B  MET      3.5     2.7    -      -       -      +
     31B  LEU*     4.6     0.4    -      -       +      -
    116B  SER*     1.3    80.1    -      -       -      +
    118B  PHE*     1.3    62.0    +      -       -      +
    119B  ARG*     4.2    23.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  PHE*     3.7    31.9    -      +       +      -
     35A  ALA      4.1     2.9    -      -       -      -
     53A  ASP*     3.8    10.1    -      -       +      -
     54A  ARG*     3.5    26.5    -      -       -      -
     55A  VAL*     3.7    20.2    -      -       +      -
    113A  TYR*     3.5    35.7    -      +       -      -
      5B  LYS*     3.2    16.2    -      -       +      -
      6B  VAL*     3.8    10.3    -      -       +      +
     29B  ALA*     4.1     0.4    -      -       -      -
     30B  MET*     2.8    44.2    +      -       +      +
     32B  THR*     5.1     0.2    -      -       -      +
    116B  SER      4.2     0.2    -      -       -      -
    117B  VAL*     1.3    74.4    -      -       -      +
    119B  ARG*     1.3    61.6    +      -       -      +
    120B  ALA*     3.2    33.5    +      -       +      -
----------------------------------------------------------
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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