Contacts of the strand formed by residues 84 - 99 (chain A) in PDB entry 5XS0


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 TRP 84 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     3.9     2.7    -      -       -      -
     72A  ILE*     4.2    13.5    -      -       +      -
     75A  ALA*     3.7    26.7    -      -       +      -
     76A  ASN*     2.7    25.5    +      -       -      +
     79A  PHE*     3.8    19.5    -      +       +      -
     80A  GLY      3.2    24.2    -      -       -      -
     81A  TYR      4.1     3.2    +      -       -      +
     82A  ASN      3.6     0.2    -      -       -      -
     83A  GLY*     1.3    80.1    -      -       -      +
     85A  ALA*     1.3    73.9    +      -       -      +
     86A  HIS*     4.2     7.2    -      -       +      -
    113A  VAL*     4.2    10.8    -      -       +      -
    114A  GLN      3.4     6.3    -      -       -      +
    115A  LEU*     4.0     8.5    -      -       +      -
    151A  LEU*     3.9    33.0    -      -       +      -
    155A  LEU*     4.0    14.1    -      -       +      -
    119B  SER*     3.5    14.9    +      -       -      -
    121B  HIS*     3.5    35.7    +      +       -      -
    157B  SER*     3.6    20.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     3.6    15.0    -      -       +      -
     84A  TRP*     1.3    79.9    -      -       -      +
     86A  HIS*     1.3    58.7    +      -       -      +
    113A  VAL*     3.2     8.3    -      -       -      +
    114A  GLN      2.8    28.4    +      -       -      +
    120B  TYR*     3.1    55.2    -      -       +      +
    121B  HIS*     3.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  TRP*     4.2     2.5    -      +       +      -
     85A  ALA*     1.3    78.6    -      -       -      +
     87A  SER*     1.3    62.3    +      -       -      +
     88A  ILE*     5.5     1.1    -      -       +      -
    111A  VAL*     3.9    15.7    -      -       +      -
    112A  ARG      3.2     6.5    -      -       -      +
    113A  VAL*     3.7    21.8    -      -       +      -
    147A  VAL*     5.3     3.8    -      -       +      +
    151A  LEU*     3.7    32.8    -      -       +      +
    120B  TYR*     3.3    13.8    +      -       -      -
    121B  HIS*     2.8    36.1    +      -       +      -
    122B  GLU      3.0    48.5    +      -       -      -
    123B  ASP*     4.4     7.2    +      -       -      -
    154B  ALA*     6.1     0.2    -      -       -      -
    157B  SER*     3.8    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  HIS*     1.3    76.6    -      -       -      +
     88A  ILE*     1.3    66.6    +      -       -      +
     89A  THR*     3.6     3.2    +      -       -      -
    111A  VAL*     3.4     7.0    -      -       -      +
    112A  ARG*     2.9    46.3    +      -       -      +
    112B  ARG*     5.0     7.0    -      -       -      -
    120B  TYR*     3.6    20.9    +      -       -      -
    122B  GLU*     3.6    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  HIS*     5.5     0.2    -      -       +      -
     87A  SER*     1.3    73.5    -      -       -      +
     89A  THR*     1.3    64.5    +      -       -      +
     90A  GLN*     4.0    24.1    -      -       -      +
     91A  GLN*     4.2     4.3    -      -       +      +
    109A  ALA*     5.0     3.1    -      -       +      -
    110A  PHE      3.7     6.1    -      -       -      +
    111A  VAL*     4.7     6.3    -      -       +      +
    147A  VAL*     3.7    34.3    -      -       +      -
     89B  THR*     5.8     1.6    -      -       -      +
    110B  PHE*     3.8    32.4    -      -       +      -
    122B  GLU*     3.0    34.4    +      -       +      +
    123B  ASP*     3.9    28.0    -      -       -      -
    124B  VAL*     3.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  SER*     3.6     3.6    +      -       -      -
     88A  ILE*     1.3    74.5    -      -       -      +
     90A  GLN*     1.3    67.7    +      -       +      +
    110A  PHE*     2.9    13.8    +      -       +      -
    112A  ARG*     3.9    20.4    -      -       -      +
    122A  GLU*     3.1    28.0    +      -       -      +
     88K  ILE      5.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ILE*     3.3     6.4    -      -       -      +
     89A  THR*     1.3    87.2    -      -       +      +
     91A  GLN*     1.3    68.3    +      -       -      +
     92A  ASN*     4.9    10.7    -      -       +      +
    109A  ALA*     3.6     0.5    -      -       -      -
    110A  PHE*     2.9    45.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ILE*     4.2     5.2    -      -       +      +
     90A  GLN*     1.3    81.7    -      -       -      +
     92A  ASN*     1.3    64.0    +      -       -      +
     93A  VAL      4.4     0.2    +      -       -      -
    107A  VAL*     3.7    19.4    -      -       +      +
    108A  CYS      3.5     7.4    -      -       -      +
    109A  ALA*     3.9     8.1    -      -       +      +
    143A  ARG*     2.5    62.1    +      -       -      +
    146A  ALA*     4.2     0.2    -      -       -      +
    147A  VAL*     3.4    26.9    -      -       -      +
    110B  PHE*     3.7    31.9    -      -       +      -
    124B  VAL*     4.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  GLN*     4.9    12.3    -      -       +      +
     91A  GLN*     1.3    73.7    -      -       -      +
     93A  VAL*     1.3    74.7    +      -       -      +
     94A  ASP*     3.3    15.7    +      -       -      -
    107A  VAL*     4.3     1.6    -      -       -      -
    108A  CYS*     2.9    44.4    +      -       -      -
    110A  PHE*     5.6     2.7    -      -       +      -
    143K  ARG*     4.5    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ASN*     1.3    82.2    +      -       -      +
     94A  ASP*     1.3    64.5    +      -       -      +
     95A  PHE*     3.9     7.4    -      -       -      +
     96A  VAL*     3.8    28.7    -      -       +      -
    106A  GLY      4.0     0.7    -      -       -      +
    107A  VAL*     3.7    27.6    -      -       +      -
    139A  LEU*     4.5     4.3    -      -       +      -
    143A  ARG*     3.3    42.1    -      -       -      +
     92B  ASN*     6.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ASN*     3.3    19.1    +      -       -      +
     93A  VAL*     1.3    75.8    -      -       -      +
     95A  PHE*     1.3    63.1    +      -       +      +
    106A  GLY      2.6    16.7    +      -       -      +
    108A  CYS*     4.0     2.4    -      -       -      -
    126A  TYR*     2.6    36.8    +      -       -      +
     93K  VAL*     5.1     1.0    -      -       -      +
    139K  LEU*     3.7    20.4    -      -       +      +
    143K  ARG*     2.7    34.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.4     3.3    -      -       -      -
     94A  ASP*     1.3    80.6    -      -       +      +
     96A  VAL*     1.3    68.0    +      -       -      +
     97A  ASP*     3.2    28.7    -      -       -      +
    104A  TYR*     3.3    39.7    -      -       +      -
    105A  VAL*     3.2     5.5    -      -       -      +
    106A  GLY*     2.9    39.4    +      -       -      +
    135K  LYS*     3.7    23.3    -      -       +      +
    136K  ALA*     3.3    47.1    -      -       +      -
    139K  LEU*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.8     9.6    -      -       +      -
     95A  PHE*     1.3    79.3    -      -       -      +
     97A  ASP*     1.3    65.2    +      -       -      +
     98A  LEU      4.4     0.2    +      -       -      -
    103A  PHE*     4.3    10.1    -      -       +      -
    104A  TYR      3.5     4.0    -      -       -      -
    105A  VAL*     3.7    24.9    -      -       +      -
    135A  LYS*     4.0    28.3    -      -       +      -
    139A  LEU*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     3.2    19.7    -      -       -      +
     96A  VAL*     1.3    80.2    +      -       -      +
     98A  LEU*     1.3    60.6    +      -       -      +
     99A  ASN*     4.1    11.9    -      -       -      +
    102A  LYS      3.6     0.7    -      -       -      +
    103A  PHE*     3.3     9.0    -      -       -      -
    104A  TYR*     2.9    43.4    +      -       +      +
    135K  LYS*     3.1    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ASP*     1.3    73.3    -      -       -      +
     99A  ASN*     1.3    66.1    +      -       -      +
    100A  ASN      4.1     1.5    +      -       -      +
    101A  GLY*     3.7    16.2    -      -       -      +
    102A  LYS      3.4    28.3    -      -       -      +
    103A  PHE*     3.7    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ASP*     4.1    10.9    -      -       -      +
     98A  LEU*     1.3    77.8    -      -       -      +
    100A  ASN*     1.3    85.6    +      -       -      +
    101A  GLY      3.2     0.7    -      -       -      -
    102A  LYS*     2.9    27.6    +      -       -      +
    104A  TYR*     4.0    29.6    -      -       +      +
----------------------------------------------------------
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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