Contacts of the strand formed by residues 102 - 113 (chain B) in PDB entry 5T4S


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 ILE 102 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR*     4.7     6.1    -      -       -      +
      7B  THR      5.1     0.7    -      -       -      +
      8B  SER*     3.6    25.4    -      -       -      -
     97B  ILE      3.4     1.7    -      -       -      +
     98B  THR*     3.3     5.0    -      -       -      +
     99B  VAL*     2.9    35.6    +      -       -      +
    100B  GLY      3.4     1.8    +      -       -      -
    101B  GLY*     1.3    82.9    -      -       -      +
    103B  THR*     1.3    68.8    +      -       -      +
    104B  VAL*     4.8     0.4    -      -       +      -
    147B  ILE*     4.0    30.5    -      -       +      -
    150B  GLN*     3.8    19.7    -      -       -      +
    152B  VAL*     4.6    15.9    -      -       +      -
    153B  LEU*     3.7    25.6    -      -       +      -
    178B  LEU*     5.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE*     3.7    20.2    -      -       +      -
     97B  ILE      3.4     3.8    -      -       -      -
     98B  THR*     3.9    22.4    -      -       +      +
    101B  GLY      4.4     1.1    +      -       -      +
    102B  ILE*     1.3    75.5    -      -       -      +
    104B  VAL*     1.3    54.2    +      -       -      +
    150B  GLN*     2.8    27.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE*     4.3     3.1    -      -       -      -
     97B  ILE*     2.8    44.0    +      -       +      +
     99B  VAL*     5.1     1.6    -      -       +      -
    102B  ILE*     5.1     0.7    -      -       +      -
    103B  THR*     1.3    74.9    -      -       -      +
    105B  THR*     1.3    69.9    +      -       -      +
    106B  GLN*     3.3     4.6    +      -       +      +
    143B  ILE*     3.7    32.8    -      -       +      -
    146B  ASN*     3.6    38.1    -      -       +      +
    147B  ILE*     3.9    14.8    -      -       +      +
    150B  GLN*     3.5    18.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  GLN*     3.5    34.1    -      -       +      +
     95B  ASP*     3.6     9.9    -      -       -      +
     96B  ILE*     4.0    15.2    -      -       +      +
    104B  VAL*     1.3    81.0    -      -       -      +
    106B  GLN*     1.3    59.6    +      -       -      +
    146B  ASN*     3.7    12.5    +      -       -      -
    150B  GLN*     4.8     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  VAL*     4.1    16.2    -      -       +      +
     94B  GLN*     3.4     7.7    -      -       -      +
     95B  ASP      2.9    30.8    +      -       -      +
     97B  ILE*     3.8    31.6    -      -       +      -
    104B  VAL*     3.9    10.7    -      -       +      +
    105B  THR*     1.3    74.8    -      -       -      +
    107B  MET*     1.3    84.3    +      -       -      +
    108B  PHE*     3.8     3.3    -      -       -      -
    140B  VAL*     4.5     0.8    -      -       -      +
    141B  THR      2.9    22.4    +      -       -      -
    142B  PRO*     4.0     1.2    -      -       -      +
    143B  ILE*     3.2    32.0    -      -       +      +
    146B  ASN*     2.7    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  VAL*     4.5     3.6    +      -       -      +
     75B  ASN*     5.0     5.8    -      -       +      -
     92B  LEU*     3.7    31.4    -      -       +      -
     93B  SER      3.3     9.2    -      -       -      +
     94B  GLN*     3.6    29.8    -      -       -      +
    106B  GLN*     1.3    99.9    +      -       -      +
    108B  PHE*     1.3    59.4    +      -       -      +
    140B  VAL*     3.5    32.7    -      -       +      +
    141B  THR*     5.3     2.0    -      -       -      +
    146B  ASN*     4.8     2.6    -      -       -      +
    401B  NAG      3.8    33.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ILE*     3.7    14.4    -      -       +      -
     44B  VAL*     3.3    29.4    -      -       +      +
     46B  VAL*     3.9    21.3    -      -       +      -
     64B  PHE*     3.6    27.1    -      +       -      -
     72B  TYR*     5.4     0.2    -      +       -      -
     92B  LEU*     3.5     9.7    -      -       -      +
     93B  SER*     2.7    60.0    +      -       -      +
     95B  ASP*     3.7    29.2    -      -       +      -
     97B  ILE*     4.3    13.9    -      -       +      -
    106B  GLN      3.8     9.9    -      -       -      -
    107B  MET*     1.3    75.1    -      -       -      +
    109B  GLY*     1.3    69.0    +      -       -      +
    110B  GLU*     3.7    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  VAL      2.7    16.2    +      -       -      -
     45B  TRP*     3.2     9.5    -      -       -      +
     46B  VAL      3.0    28.1    +      -       -      +
     79B  LEU*     4.2    21.8    -      -       -      +
     81B  LEU*     5.4     0.2    -      -       -      -
     91B  PHE      3.4     6.5    -      -       -      -
     92B  LEU*     4.5     0.8    -      -       -      +
    108B  PHE*     1.3    78.2    -      -       -      +
    110B  GLU*     1.3    61.9    +      -       -      -
    111B  VAL*     3.9     1.1    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     46B  VAL      3.5     3.8    -      -       -      +
     48B  SER*     2.8    31.0    +      -       -      -
     49B  SER*     4.9     1.0    +      -       -      -
     64B  PHE*     3.5    32.8    -      -       +      +
     66B  ALA*     4.0     8.1    +      -       -      +
     72B  TYR*     3.8     7.6    +      -       -      -
     90B  GLY*     3.1     2.9    -      -       -      -
     91B  PHE*     2.6    66.8    +      -       +      +
     93B  SER*     2.6    27.2    +      -       -      +
    108B  PHE*     3.7    18.5    +      -       +      -
    109B  GLY*     1.3    70.7    -      -       -      -
    111B  VAL*     1.3    61.2    -      -       -      +
    112B  THR      3.9     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TRP*     3.4    40.8    -      -       +      -
     46B  VAL      2.8    16.7    +      -       -      +
     47B  PRO*     3.6     4.8    -      -       +      +
     48B  SER*     2.8    27.9    +      -       -      +
     51B  CYS*     3.8     6.8    -      -       -      +
     79B  LEU*     6.3     0.2    -      -       +      -
     81B  LEU*     4.9     3.1    -      -       +      -
     88B  VAL*     3.6    27.1    -      -       +      -
     89B  SER      3.5    13.9    -      -       -      +
     90B  GLY*     5.0     0.4    -      -       -      -
    109B  GLY*     4.3     1.6    -      -       -      +
    110B  GLU*     1.3    74.4    -      -       -      +
    112B  THR*     1.3    63.5    +      -       -      +
    113B  GLU      3.8    19.7    -      -       -      +
    114B  MET*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  SER*     4.2     1.3    -      -       -      -
     50B  LYS*     3.4    31.0    -      -       +      +
     51B  CYS*     3.4    25.2    -      -       -      +
     52B  SER*     4.0     4.7    +      -       -      -
     55B  TYR*     3.7    11.8    -      -       -      -
     89B  SER*     3.2     8.5    +      -       -      -
     90B  GLY*     3.8     9.0    -      -       -      -
     91B  PHE*     4.1    25.7    -      -       +      -
    111B  VAL*     1.3    77.1    -      -       -      +
    113B  GLU*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  TYR*     3.4    24.9    +      -       +      +
     88B  VAL*     3.3    22.9    -      -       -      +
     89B  SER*     3.2    41.8    +      -       -      +
    111B  VAL*     4.1     0.9    -      -       -      -
    112B  THR*     1.3    81.1    +      -       -      +
    114B  MET*     1.3    59.4    +      -       -      +
    115B  PRO*     3.6     7.3    -      -       +      +
----------------------------------------------------------
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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