Contacts of the strand formed by residues 108 - 117 (chain A) in PDB entry 1XU2


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 VAL 108 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  HIS*     3.7    10.5    +      -       +      +
    107A  SER*     1.3    80.4    -      -       -      +
    109A  LEU*     1.3    64.3    +      -       -      +
    133A  LEU*     4.1    27.8    -      -       +      -
    134A  ARG*     3.3     3.8    -      -       -      +
    135A  ARG*     2.9    47.2    +      -       +      +
    139A  LEU*     5.6     2.9    -      -       -      -
    238A  PHE*     3.3    10.8    -      -       -      +
    239A  VAL*     4.2    21.3    -      -       +      -
    153D  ILE*     4.2    14.1    -      -       +      -
    207D  VAL*     4.2    15.7    -      -       +      -
    241D  LEU*     4.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     1.3    78.1    -      -       -      +
    110A  HIS*     1.3    60.1    +      -       -      +
    111A  LEU*     3.8    41.1    -      -       +      -
    131A  PRO*     4.0    10.3    -      -       +      -
    133A  LEU      3.4    15.3    -      -       -      +
    134A  ARG*     3.8    24.9    -      -       +      +
    139A  LEU*     3.7    38.1    -      -       +      -
    140A  GLU*     4.5     1.3    -      -       -      +
    141A  ALA      4.7     3.8    -      -       -      +
    146A  VAL*     4.5     5.2    -      -       +      -
    157A  TYR*     4.3     1.6    +      -       -      -
    237A  GLY*     3.1     5.2    -      -       -      -
    238A  PHE*     2.9    44.9    +      -       +      +
    207D  VAL*     6.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     1.3    73.3    -      -       -      +
    111A  LEU*     1.3    62.7    +      -       -      +
    112A  VAL*     4.5     6.2    -      -       +      +
    131A  PRO*     3.6     2.8    -      -       -      +
    132A  VAL*     3.0    44.7    +      -       +      +
    133A  LEU*     2.8    30.2    +      -       +      +
    157A  TYR*     2.6    30.5    +      +       -      +
    231A  PRO      4.9     1.6    +      -       -      -
    235A  PHE*     3.7    43.4    -      +       +      +
    236A  LEU      3.8     1.3    +      -       -      -
    184D  LEU      5.4     0.4    +      -       -      -
    207D  VAL*     3.8    15.3    +      -       +      +
    208D  PHE*     3.9    30.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     3.8    24.0    -      -       +      -
    110A  HIS*     1.3    73.8    -      -       -      +
    112A  VAL*     1.3    63.9    +      -       -      +
    129A  TRP*     3.9    20.3    -      -       +      -
    130A  GLN      3.3     6.1    -      -       -      +
    131A  PRO*     3.7    27.1    -      -       +      -
    141A  ALA*     3.8    19.7    -      -       +      -
    146A  VAL*     3.8    29.6    -      -       +      -
    235A  PHE*     3.2     9.7    -      -       -      +
    236A  LEU*     2.7    52.2    +      -       +      +
    238A  PHE*     3.9    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  HIS*     4.5     4.0    +      -       +      -
    111A  LEU*     1.3    78.0    -      -       -      +
    113A  PRO*     1.3    75.0    -      -       +      +
    129A  TRP*     3.5     8.1    -      -       -      -
    130A  GLN*     2.8    52.7    +      -       +      +
    132A  VAL*     3.6    39.3    -      -       +      -
    231A  PRO*     3.6    41.1    -      -       +      +
    234A  THR      4.3     0.4    -      -       -      -
    235A  PHE*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  VAL*     1.3    90.4    -      -       +      +
    114A  VAL*     1.3    58.9    +      -       -      +
    115A  ASN      4.4     0.2    -      -       -      +
    127A  VAL*     3.6    19.7    -      -       +      -
    128A  MET      3.4     8.1    -      -       -      +
    129A  TRP*     3.9     2.2    -      -       +      -
    130A  GLN*     3.3    15.2    +      -       -      -
    227A  LEU*     5.7     0.2    -      -       +      -
    228A  SER      4.3     0.4    -      -       -      +
    229A  LEU*     3.8    50.8    -      -       +      +
    230A  SER      4.2     0.9    -      -       -      +
    234A  THR*     3.2    40.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PRO*     1.3    76.5    -      -       -      +
    115A  ASN*     1.3    79.9    +      -       +      +
    128A  MET*     2.9    30.8    +      -       +      +
    129A  TRP      4.1    13.2    -      -       -      +
    130A  GLN*     4.1    20.0    -      -       +      +
    229A  LEU*     4.3    11.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PRO*     3.7     1.6    -      -       -      +
    114A  VAL*     1.3    97.0    +      -       +      +
    116A  ILE*     1.3    69.4    +      -       -      +
    127A  VAL*     3.5     8.7    -      -       -      +
    128A  MET*     2.9    44.8    +      -       +      +
    229A  LEU*     4.1    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ASN*     1.3    85.6    +      -       -      +
    117A  THR*     1.3    68.4    +      -       -      +
    118A  SER*     4.8     2.2    -      -       -      +
    125A  THR*     3.4    24.2    -      -       +      -
    126A  GLU      3.5     2.0    -      -       -      +
    127A  VAL*     4.0    13.5    -      -       +      -
    128A  MET*     5.0     2.3    -      -       -      +
    224A  ASN*     6.0     1.3    -      -       -      -
    225A  ALA      4.8     6.5    -      -       -      +
    227A  LEU*     3.3    46.4    -      -       +      +
    229A  LEU*     3.6    23.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     1.3    77.6    -      -       -      +
    118A  SER*     1.3    67.4    +      -       -      +
    119A  LYS*     4.7    11.8    +      -       -      +
    124A  VAL*     5.7     0.2    -      -       -      +
    125A  THR*     3.3     2.1    -      -       -      +
    126A  GLU*     2.8    55.7    +      -       +      +
    128A  MET*     4.5    18.2    -      -       +      -
    144A  ASP*     3.5    29.2    -      -       +      +
----------------------------------------------------------
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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